Animals

2024

Jump to: 2023, 2022, 2020, 2019

14 pages, 3839 KiB

Open AccessArticle

Genomic Prediction of Growth Traits in Yorkshire Pigs of Different Reference Group Sizes Using Different Estimated Breeding Value Models

by Chang Yin, Haoran Shi, Peng Zhou, Yuwei Wang, Xuzhe Tao, Zongjun Yin, Xiaodong Zhang and Yang Liu

Animals 2024, 14(7), 1098; https://doi.org/10.3390/ani14071098 - 4 Apr 2024

Viewed by 1299

Abstract

The need for sufficient reference population data poses a significant challenge in breeding programs aimed at improving pig farming on a small to medium scale. To overcome this hurdle, investigating the advantages of combing reference populations of varying sizes is crucial for enhancing [...] Read more.

The need for sufficient reference population data poses a significant challenge in breeding programs aimed at improving pig farming on a small to medium scale. To overcome this hurdle, investigating the advantages of combing reference populations of varying sizes is crucial for enhancing the accuracy of the genomic estimated breeding value (GEBV). Genomic selection (GS) in populations with limited reference data can be optimized by combining populations of the same breed or related breeds. This study focused on understanding the effect of combing different reference group sizes on the accuracy of GS for determining the growth effectiveness and percentage of lean meat in Yorkshire pigs. Specifically, our study investigated two important traits: the age at 100 kg live weight (AGE100) and the backfat thickness at 100 kg live weight (BF100). This research assessed the efficiency of genomic prediction (GP) using different GEBV models across three Yorkshire populations with varying genetic backgrounds. The GeneSeek 50K GGP porcine high-density array was used for genotyping. A total of 2295 Yorkshire pigs were included, representing three Yorkshire pig populations with different genetic backgrounds—295 from Danish (small) lines from Huaibei City, Anhui Province, 500 from Canadian (medium) lines from Lixin County, Anhui Province, and 1500 from American (large) lines from Shanghai. To evaluate the impact of different population combination scenarios on the GS accuracy, three approaches were explored: (1) combining all three populations for prediction, (2) combining two populations to predict the third, and (3) predicting each population independently. Five GEBV models, including three Bayesian models (BayesA, BayesB, and BayesC), the genomic best linear unbiased prediction (GBLUP) model, and single-step GBLUP (ssGBLUP) were implemented through 20 repetitions of five-fold cross-validation (CV). The results indicate that predicting one target population using the other two populations yielded the highest accuracy, providing a novel approach for improving the genomic selection accuracy in Yorkshire pigs. In this study, it was found that using different populations of the same breed to predict small- and medium-sized herds might be effective in improving the GEBV. This investigation highlights the significance of incorporating population combinations in genetic models for predicting the breeding value, particularly for pig farmers confronted with resource limitations. Full article

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12 pages, 288 KiB

Open AccessArticle

Risk Factor Analysis and Genetic Parameter Estimation for Pre-Weaning Mortality Traits in Boer, Spanish, and Crossbred Goat Kids

by Liuhong Chen, William Foxworth, Scott Horner, Mustafa Hitit, Negusse Kidane and Erdogan Memili

Animals 2024, 14(7), 1085; https://doi.org/10.3390/ani14071085 - 3 Apr 2024

Viewed by 1102

Abstract

The objectives of this study were to evaluate fixed risk factors associated with PWM and to estimate genetic parameters for PWM. A total of 927 birth records from a mixed population of purebred and crossbred Boer and Spanish goats born between 2016 and [...] Read more.

The objectives of this study were to evaluate fixed risk factors associated with PWM and to estimate genetic parameters for PWM. A total of 927 birth records from a mixed population of purebred and crossbred Boer and Spanish goats born between 2016 and 2023 at the International Goat Research Center (IGRC) were used for this study. Four binary traits were studied: D0–3 (death within 3 days after birth), D4–60 (death between 4 and 60 days), D61–90 (death between 61 and 90 days), and D0–90 (death within 90 days). Logistic regression models were used to evaluate the risk factors associated with PWM traits. Bayesian threshold models and Gibbs sampling were used to estimate the genetic parameters. Birth weight, season, litter size, sex, dam age, breed, and heterosis were found to be significantly associated with at least one of the PWM traits. Heritability estimates were 0.263, 0.124, 0.080, and 0.207, for D0–3, D4–60, D61–90, and D0–90, respectively. The genetic correlations between the studied traits ranged from 0.892 (D0–3 and D0–90) to 0.999 (D0–3 and D61–90). These results suggest that PWM in goats is influenced by both non-genetic and genetic factors and can be reduced by management, genetic selection, and crossbreeding approaches. Full article

2023

Jump to: 2024, 2022, 2020, 2019

10 pages, 298 KiB

Open AccessArticle

Estimation of (Co) Variance Components and Genetic Parameters for Pre- and Post-Weaning Growth Traits in Dağlıç Sheep

by Serdar Koçak, Samet Çinkaya, Mustafa Tekerli, Mustafa Demirtaş, Zehra Bozkurt, Koray Çelikeloğlu, Özlem Hacan and Metin Erdoğan

Animals 2024, 14(1), 108; https://doi.org/10.3390/ani14010108 - 27 Dec 2023

Cited by 2 | Viewed by 1497

Abstract

The goal of this study was to estimate (co) variance components and genetic parameters for pre- and post-weaning growth traits in Dağlıç sheep, considering the direct additive genetic, maternal genetic, and maternal permanent environmental effects, with different statistical models. The information of 21,735 [...] Read more.

The goal of this study was to estimate (co) variance components and genetic parameters for pre- and post-weaning growth traits in Dağlıç sheep, considering the direct additive genetic, maternal genetic, and maternal permanent environmental effects, with different statistical models. The information of 21,735 native Dağlıç lambs born between 2011 and 2021 was used to estimate (co) variance components by the Average Information-Restricted Maximum Likelihood algorithm. The results showed that the most suitable model was Model 3 for birth weight (BW), average daily gain (ADG), and weaning weight (WW). Model 4 was the most appropriate for weight at three (W3), weight at six (W6), and weight at twelve months of age (W12). The direct heritabilities for BW, W3, ADG, WW, W6, and W12 were 0.35 ± 0.02, 0.36 ± 0.03, 0.27 ± 0.02, 0.22 ± 0.02, 0.47 ± 0.05, and 0.47 ± 0.05, respectively. Genetic and phenotypic correlations amongst the traits were in the range of 0.103 ± 0.008 to 0.995 ± 0.002. These results can be used for the improvement of growth traits in the Dağlıç breed of sheep through selection. Full article

19 pages, 1767 KiB

Open AccessArticle

Genome-Wide Association Study of Maternal Genetic Effects on Intramuscular Fat and Fatty Acid Composition in Rabbits

by Ayman G. EL Nagar, Imen Heddi, Bolívar Samuel Sosa-Madrid, Agustín Blasco, Pilar Hernández and Noelia Ibáñez-Escriche

Animals 2023, 13(19), 3071; https://doi.org/10.3390/ani13193071 - 30 Sep 2023

Cited by 3 | Viewed by 1466

Abstract

Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on [...] Read more.

Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from −0.53 to −0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits. Full article

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26 pages, 1084 KiB

Open AccessReview

Perspectives in Genome-Editing Techniques for Livestock

by Julia Popova, Victoria Bets and Elena Kozhevnikova

Animals 2023, 13(16), 2580; https://doi.org/10.3390/ani13162580 - 10 Aug 2023

Cited by 3 | Viewed by 6177

Abstract

Genome editing of farm animals has undeniable practical applications. It helps to improve production traits, enhances the economic value of livestock, and increases disease resistance. Gene-modified animals are also used for biomedical research and drug production and demonstrate the potential to be used [...] Read more.

Genome editing of farm animals has undeniable practical applications. It helps to improve production traits, enhances the economic value of livestock, and increases disease resistance. Gene-modified animals are also used for biomedical research and drug production and demonstrate the potential to be used as xenograft donors for humans. The recent discovery of site-specific nucleases that allow precision genome editing of a single-cell embryo (or embryonic stem cells) and the development of new embryological delivery manipulations have revolutionized the transgenesis field. These relatively new approaches have already proven to be efficient and reliable for genome engineering and have wide potential for use in agriculture. A number of advanced methodologies have been tested in laboratory models and might be considered for application in livestock animals. At the same time, these methods must meet the requirements of safety, efficiency and availability of their application for a wide range of farm animals. This review aims at covering a brief history of livestock animal genome engineering and outlines possible future directions to design optimal and cost-effective tools for transgenesis in farm species. Full article

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9 pages, 1989 KiB

Open AccessCommunication

A Bayesian Multivariate Gametic Model in a Reciprocal Cross with Genomic Information: An Example with Two Iberian Varieties

by Houssemeddine Srihi, David López-Carbonell, Noelia Ibáñez-Escriche, Joaquim Casellas, Pilar Hernández, Sara Negro and Luis Varona

Animals 2023, 13(10), 1648; https://doi.org/10.3390/ani13101648 - 16 May 2023

Cited by 1 | Viewed by 1329

Abstract

INGA FOOD, S.A. initiated a crossbreeding program between two Iberian pig varieties, Retinto (R) and Entrepelado (E), with the goal of producing a hybrid sow (F1). Several studies have been conducted to evaluate its productive performance, and these studies have revealed differences in [...] Read more.

INGA FOOD, S.A. initiated a crossbreeding program between two Iberian pig varieties, Retinto (R) and Entrepelado (E), with the goal of producing a hybrid sow (F1). Several studies have been conducted to evaluate its productive performance, and these studies have revealed differences in litter size between the two reciprocal crosses, suggesting the presence of genomic imprinting effects. To further investigate these effects, this study introduces a multivariate gametic model designed to estimate gametic correlations between paternal and maternal effects originating from both genetic backgrounds involved in the reciprocal crosses. The dataset consisted of 1258 records (the total number born—TNB and the number born alive—NBA) from 203 crossbred dams for the Entrepelado (sire) × Retinto (dam) cross and 700 records from 125 crossbred dams for the Retinto (sire) × Entrepelado (dam) cross. All animals were genotyped using the GeneSeek^® GPP Porcine 70 K HDchip (Illumina Inc., San Diego, CA, USA). The results indicated that the posterior distribution of the gametic correlation between paternal and maternal effects was distinctly different between the two populations. Specifically, in the Retinto population, the gametic correlation showed a positive skew with posterior probabilities of 0.78 for the TNB and 0.80 for the NBA. On the other hand, the Entrepelado population showed a posterior probability of a positive gametic correlation between paternal and maternal effects of approximately 0.50. The differences in the shape of the posterior distribution of the gametic correlations between paternal and maternal effects observed in the two varieties may account for the distinct performance outcomes observed in the reciprocal crosses. Full article

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13 pages, 729 KiB

Open AccessArticle

Genetic Analysis of Methane Emission Traits in Holstein Dairy Cattle

by Stephanie Kamalanathan, Kerry Houlahan, Filippo Miglior, Tatiane C. S. Chud, Dave J. Seymour, Dagnachew Hailemariam, Graham Plastow, Hinayah R. de Oliveira, Christine F. Baes and Flavio S. Schenkel

Animals 2023, 13(8), 1308; https://doi.org/10.3390/ani13081308 - 11 Apr 2023

Cited by 7 | Viewed by 4710

Abstract

Genetic selection can be a feasible method to help mitigate enteric methane emissions from dairy cattle, as methane emission-related traits are heritable and genetic gains are persistent and cumulative over time. The objective of this study was to estimate heritability of methane emission [...] Read more.

Genetic selection can be a feasible method to help mitigate enteric methane emissions from dairy cattle, as methane emission-related traits are heritable and genetic gains are persistent and cumulative over time. The objective of this study was to estimate heritability of methane emission phenotypes and the genetic and phenotypic correlations between them in Holstein cattle. We used 1765 individual records of methane emission obtained from 330 Holstein cattle from two Canadian herds. Methane emissions were measured using the GreenFeed system, and three methane traits were analyzed: the amount of daily methane produced (g/d), methane yield (g methane/kg dry matter intake), and methane intensity (g methane/kg milk). Genetic parameters were estimated using univariate and bivariate repeatability animal models. Heritability estimates (±SE) of 0.16 (±0.10), 0.27 (±0.12), and 0.21 (±0.14) were obtained for daily methane production, methane yield, and methane intensity, respectively. A high genetic correlation (rg = 0.94 ± 0.23) between daily methane production and methane intensity indicates that selecting for daily methane production would result in lower methane per unit of milk produced. This study provides preliminary estimates of genetic parameters for methane emission traits, suggesting that there is potential to mitigate methane emission in Holstein cattle through genetic selection. Full article

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2022

Jump to: 2024, 2023, 2020, 2019

12 pages, 843 KiB

Open AccessArticle

Estimation of Genetic Parameters for Conformation Traits and Milk Production Traits in Chinese Holsteins

by Xiaoshu Xue, Honghong Hu, Junxing Zhang, Yanfen Ma, Liyun Han, Feng Hao, Yu Jiang and Yun Ma

Animals 2023, 13(1), 100; https://doi.org/10.3390/ani13010100 - 27 Dec 2022

Cited by 14 | Viewed by 2402

Abstract

The objective of this study was to explore the genetic parameters of conformation traits and milk production traits in Chinese Holstein cattle and to provide a reference for dairy cattle breeding. We collected the phenotypic data of 23 conformation traits and five milk [...] Read more.

The objective of this study was to explore the genetic parameters of conformation traits and milk production traits in Chinese Holstein cattle and to provide a reference for dairy cattle breeding. We collected the phenotypic data of 23 conformation traits and five milk production traits of Chinese Holsteins and used animal models to estimate the genetic parameters of conformation traits and milk production traits. The estimated heritability of conformation traits ranged from 0.11 (angularity) to 0.37 (heel depth) and the genetic correlation between conformation traits ranged from −0.73 (bone quality and rear leg-rear view) to 0.76 (chest width and loin strength). The heritability of milk production traits ranged from 0.23 (somatic cell score) to 0.50 (305-d milk yield). The estimated values of genetic correlation between conformation traits and milk production traits ranged from −0.56 (heel depth and 305-d milk yield) to 0.57 (udder texture and milk fat percentage). There was a positive genetic correlation between most conformation traits and milk fat percentage, but a weak negative genetic correlation with milk yield. Strengthening the moderately and highly heritable milk production and conformation traits, especially the selection of rear udder traits and body shape total score, will be beneficial in improving the performance of dairy cows. Full article

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13 pages, 1609 KiB

Open AccessArticle

Association between Synonymous SNPs of SOX10 and Plumage Color and Reproductive Traits of Ducks

by Teysar Adi Sarjana and Gongyan Zhang

Animals 2022, 12(23), 3345; https://doi.org/10.3390/ani12233345 - 29 Nov 2022

Viewed by 1493

Abstract

Mutations in the SOX10 gene affect the plumage color of chickens and pigeons. The mutation also causes abnormal pigmentation of the skin and hair color, as well as postnatal growth retardation and reproduction problems in humans and mice. In this study, we investigated [...] Read more.

Mutations in the SOX10 gene affect the plumage color of chickens and pigeons. The mutation also causes abnormal pigmentation of the skin and hair color, as well as postnatal growth retardation and reproduction problems in humans and mice. In this study, we investigated the association between the SOX10 gene and plumage color and reproductive traits of ducks using SNPs. We found six novel SNPs from 11 identified SNP sites using direct sequencing for PCR products from three different mixed DNA pools. We found two coding SNPs to be associated with the plumage color of ducks (ZJU1.0 Chr1. g.54065419C>T and g.54070844C>T), and found three coding SNPs associated with the reproductive traits of ducks (g.54065419C>T, g.54070844C>T, and g.54070904C>T), which were age at sexual maturity, body weight at sexual maturity, and the Haugh unit for egg quality traits and egg production in different productive periods. These results also indicated that the T alleles of the three SNPs of the coding region of SOX10 contribute to lower reproductive traits. Full article

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11 pages, 726 KiB

Open AccessArticle

Direct–Maternal Genetic Parameters for Litter Size and Body Weight of Piglets of a New Black Breed for the Taiwan Black Hog Market

by Hsiu-Lan Lee, Mu-Yao Lin, Han-Sheng Wang, Chin-Bin Hsu, Cheng-Yung Lin, Shen-Chang Chang, Perng-Chih Shen and Hsiu-Luan Chang

Animals 2022, 12(23), 3295; https://doi.org/10.3390/ani12233295 - 25 Nov 2022

Cited by 2 | Viewed by 1614

Abstract

The objective of this study was to estimate the genetic parameters of litter size and piglet weight from farrowing to weaning in KHAPS Black sows. The genetic parameters investigated were the direct (h²_d), maternal (h²_m), realized (h [...] Read more.

The objective of this study was to estimate the genetic parameters of litter size and piglet weight from farrowing to weaning in KHAPS Black sows. The genetic parameters investigated were the direct (h²_d), maternal (h²_m), realized (h²_r), and total (h²_T) heritability, as well as correlations (r_d, r_m, and r_dm) within and between traits. The analyses were performed using single- and three-trait animal models with and without maternal genetic effects. In the three-trait model with maternal genetic effect, all estimates of h²_d and h²_m were significantly different from zero except the h²_d of mean birth weight. Positive values of r_d and r_m between traits were observed as expected in the range of 0.322–1.000. Negative values of r_dm were found within and between traits and were less associated with mean piglet weight traits than litter size traits. Estimates of h²_T were consistently larger than those of h²_r in both the single- and three-trait model analyses. In addition, the three-trait model can take into account the association between the traits, so the estimates are more accurate with smaller SEs. In conclusion, maternal genetic effects were not negligible in this study, and thus, a multiple-trait animal model with maternal genetic effects and full pedigree is recommended to assist future pig breeding decisions in this new breed. Full article

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17 pages, 494 KiB

Open AccessSystematic Review

Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits

by Frances Margaret Titterington, Rachel Knox, Steven James Morrison and Masoud Shirali

Animals 2022, 12(19), 2602; https://doi.org/10.3390/ani12192602 - 28 Sep 2022

Cited by 6 | Viewed by 2877

Abstract

People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a [...] Read more.

People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required. Full article

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11 pages, 312 KiB

Open AccessArticle

Estimation of Genetic Parameters for Heifer and Cow Fertility Traits Derived from On-Farm AI Service Records of South African Holstein Cattle

by Ramadimetje Delight Kgari, Carel Muller, Kennedy Dzama and Mahlako Linah Makgahlela

Animals 2022, 12(16), 2023; https://doi.org/10.3390/ani12162023 - 10 Aug 2022

Cited by 2 | Viewed by 1472

Abstract

This study aimed to derive additional fertility traits from service data and estimate their genetic parameters for their possible inclusion in the South African Holstein cattle breeding programs. Service records (n = 64,464) were collected from 18 South African Holstein herds using [...] Read more.

This study aimed to derive additional fertility traits from service data and estimate their genetic parameters for their possible inclusion in the South African Holstein cattle breeding programs. Service records (n = 64,464) were collected from 18 South African Holstein herds using on-farm automated milk recording systems. Using a multivariate model, the data were used to estimate heritabilities and correlations among several fertility traits. The pedigree data consisted of information on 18,592 animals born between 1981 and 2013. Heritability estimates observed were low to moderate (0.02 ± 0.00 to 0.24 ± 0.00), indicating that there is some genetic basis for the explored fertility traits to warrant selection. The genetic correlations observed between fertility traits were generally favorable, with some high correlations between age at first service (AFS) and services per conception for heifers (SPCh) (0.73 ± 0.00) and between days from calving to first service (CFS) and services per conception for cows (SPC) (0.90 ± 0.01). Positive genetic correlations indicate that improvement in one trait is coupled with a correlated genetic increase in another trait. The studied fertility traits could be used in addition to AFC and CI to serve as a basis for the selection of reproduction in dairy cattle to minimize selection bias. Full article

9 pages, 520 KiB

Open AccessArticle

Effective Selection for Lower Mortality in Organic Pigs through Selection for Total Number Born and Number of Dead Piglets

by Roos M. Zaalberg, Trine M. Villumsen, Just Jensen and Thinh T. Chu

Animals 2022, 12(14), 1796; https://doi.org/10.3390/ani12141796 - 13 Jul 2022

Cited by 4 | Viewed by 1742

Abstract

Selection for the number of living pigs on day 11 (L11) aims to reduce piglet mortality and increase litter size simultaneously. This approach could be sub-optimal, especially for organic pig breeding. This study evaluated the effect of selecting for a trait by separating [...] Read more.

Selection for the number of living pigs on day 11 (L11) aims to reduce piglet mortality and increase litter size simultaneously. This approach could be sub-optimal, especially for organic pig breeding. This study evaluated the effect of selecting for a trait by separating it into two traits. Genetic parameters for L11, the total number born (TNB), and the number of dead piglets at day 11 (D11) were estimated using data obtained from an organic pig population in Denmark. Based on these estimates, two alternative breeding schemes were simulated. Specifically, selection was made using: (1) a breeding goal with L11 only versus (2) a breeding goal with TNB and D11. Different weightings for TNB and D11 were tested. The simulations showed that selection using the first breeding scheme (L11) produced lower annual genetic gain (0.201) compared to the second (TNB and D11; 0.207). A sensitivity analysis showed that the second scheme performed better because it exploited differences in heritability, and accounted for genetic correlations between the two traits. When the second breeding scheme placed more emphasis on D11, D11 declined, whereas genetic gain for L11 remained high (0.190). In conclusion, selection for L11 could be optimized by separating it into two correlated traits with different heritability, reducing piglet mortality and enhancing L11. Full article

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11 pages, 1369 KiB

Open AccessArticle

Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats

by Bowen Gu, Ruifan Sun, Xingqiang Fang, Jipan Zhang, Zhongquan Zhao, Deli Huang, Yuanping Zhao and Yongju Zhao

Animals 2022, 12(5), 548; https://doi.org/10.3390/ani12050548 - 23 Feb 2022

Cited by 18 | Viewed by 3355

Abstract

Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats [...] Read more.

Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats. Full article

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13 pages, 1358 KiB

Open AccessArticle

Genetic Evaluation of Body Weights and Egg Production Traits Using a Multi-Trait Animal Model and Selection Index in Thai Native Synthetic Chickens (Kaimook e-san2)

by Kitsadee Chomchuen, Veeraya Tuntiyasawasdikul, Vibuntita Chankitisakul and Wuttigrai Boonkum

Animals 2022, 12(3), 335; https://doi.org/10.3390/ani12030335 - 29 Jan 2022

Cited by 26 | Viewed by 7741

Abstract

To improve the genetics of both growth and egg production, which are limitations in purebred native chickens, new genetic lines can be developed using an appropriate genetic approach. The data used in this study included 2713 body weight (BW0, BW4, BW6, BW8, and [...] Read more.

To improve the genetics of both growth and egg production, which are limitations in purebred native chickens, new genetic lines can be developed using an appropriate genetic approach. The data used in this study included 2713 body weight (BW0, BW4, BW6, BW8, and BW10), breast circumference (BrC6), chicken age at first egg (AFE), and egg production (240EP, 270EP, 300EP, and 365EP) records covering the period 2015 to 2020. A multi-trait animal model with the average information-restricted maximum likelihood (AI-REML) and a selection index was used to estimate the variance components, genetic parameters, and breeding values. The results showed that males had significantly higher weights than females (p < 0.05) from 4 to 10 weeks of age and that this difference increased over the generations. The differences between BW0 and BrC6 by sex and generation were not significant (p > 0.05). The estimated heritability of body weight ranged from 0.642 (BW0) to 0.280 (BW10); meanwhile, the estimated heritability of BrC6 was moderate (0.284). For egg production traits, the estimated heritability of 240EP, 270EP, 300EP, and 365EP was 0.427, 0.403, 0.404, and 0.426, respectively, while the estimated heritability of AFE was 0.269. The genetic and phenotypic correlations among the growth traits (BW0 to BW10) were low to highly positive. The genetic and phenotypic correlations between growth (BW0 to BW10) and BrC6 traits were positive, and the genetic correlations between BW6 (0.80), BW8 (0.84), BW10 (0.93), and BrC6 were strongly positive. Genetic correlations among the egg production traits (240EP, 270EP, 300EP, and 365EP) were low to highly positive and ranged from 0.04 to 0.86. The genetic correlations between AFE and all egg production traits were low to moderately negative and ranged from −0.14 to −0.29. The positive genetic correlations between body weight (BW6, BW8, and BW10) and egg production traits were found only in 240EP. The average genetic progress of body weight traits ranged from −0.38 to 30.12 g per generation for BW0 to BW10 (p < 0.05); the genetic progress was 0.28 cm per generation for BrC6 (p > 0.05). The average genetic progress of cumulative egg production traits ranged from 4.25 to 12.42 eggs per generation for 240EP to 365EP (p < 0.05), while the average genetic progress of AFE was −7.12 days per generation (p < 0.05). In conclusion, our study suggests that the body weight at six weeks of age (BW6), breast circumference at six weeks of age (BrC6), cumulative egg production at 240 days of age (240EP), and age at first egg (AFE) are the traits that should be used as selection criteria, as they have a positive effect on the development of growth and egg production. Full article

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2020

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11 pages, 976 KiB

Open AccessArticle

Accuracies of Genomic Prediction for Growth Traits at Weaning and Yearling Ages in Yak

by Fei Ge, Congjun Jia, Pengjia Bao, Xiaoyun Wu, Chunnian Liang and Ping Yan

Animals 2020, 10(10), 1793; https://doi.org/10.3390/ani10101793 - 2 Oct 2020

Cited by 5 | Viewed by 2500

Abstract

Genomic selection is a promising breeding strategy that has been used in considerable numbers of breeding projects due to its highly accurate results. Yak are rare mammals that are remarkable because of their ability to survive in the extreme and harsh conditions predominantly [...] Read more.

Genomic selection is a promising breeding strategy that has been used in considerable numbers of breeding projects due to its highly accurate results. Yak are rare mammals that are remarkable because of their ability to survive in the extreme and harsh conditions predominantly at the so-called “roof of the world”—the Qinghai–Tibetan Plateau. In the current study, we conducted an exploration of the feasibility of genomic evaluation and compared the predictive accuracy of early growth traits with five different approaches. In total, four growth traits were measured in 354 yaks, including body weight, withers height, body length, and chest girth in two early stages of development (weaning and yearling). Genotyping was implemented using the Illumina BovineHD BeadChip. The predictive accuracy was calculated through five-fold cross-validation in five classical statistical methods including genomic best linear unbiased prediction (GBLUP) and four Bayesian methods. Body weights at 30 months in the same yak population were also measured to evaluate the prediction at 6 months. The results indicated that the predictive accuracy for the early growth traits of yak ranged from 0.147 to 0.391. Similar performance was found for the GBLUP and Bayesian methods for most growth traits. Among the Bayesian methods, Bayes B outperformed Bayes A in the majority of traits. The average correlation coefficient between the prediction at 6 months using different methods and observations at 30 months was 0.4. These results indicate that genomic prediction is feasible for early growth traits in yak. Considering that genomic selection is necessary in yak breeding projects, the present study provides promising reference for future applications. Full article

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17 pages, 2759 KiB

Open AccessCommunication

Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages

by Guofang Wu, Lin Ma, Lei Wang, Jiping Zhou, Yuhong Ma and Chen Yang

Animals 2020, 10(7), 1198; https://doi.org/10.3390/ani10071198 - 15 Jul 2020

Cited by 5 | Viewed by 2973

Abstract

The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. [...] Read more.

The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding. Full article

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11 pages, 1407 KiB

Open AccessArticle

Heat-Shock Proteins Gene Expression in Peripheral Blood Mononuclear Cells as an Indicator of Heat Stress in Beef Calves

by Won-Seob Kim, Jalil Ghassemi Nejad, Sang-Gun Roh and Hong-Gu Lee

Animals 2020, 10(5), 895; https://doi.org/10.3390/ani10050895 - 21 May 2020

Cited by 56 | Viewed by 5341

Abstract

This study was conducted to investigate the effect of HS on HSPs gene expression in bovine PBMCs of beef calves in in vitro and in vivo models. In the in vitro experiment, blood samples were collected from the jugular vein of five beef [...] Read more.

This study was conducted to investigate the effect of HS on HSPs gene expression in bovine PBMCs of beef calves in in vitro and in vivo models. In the in vitro experiment, blood samples were collected from the jugular vein of five beef calves (age: 174.2 ± 5.20 days, BW: 145.2 ± 5.21 kg). In the in vivo experiment, sixteen Korean native male beef calves (age: 169.6 ± 4.60 days, BW: 136.9 ± 6.23 kg) were exposed to ambient temperature for seven days (22 to 24 °C, relative humidity 60%; temperature–humidity index (THI) = 68 to 70) and subsequently to the temperature and humidity corresponding to the target THI level for 21 days (HS). For PBMC isolation, blood samples were collected every three days. In the in vitro model, the cell viability was significantly decreased in HS groups compared with the control group (p = 0.015). The expression of HSP70 (p = 0.022), HSP90 (p = 0.003) and HSPB1 (p = 0.026) genes was increased in the HS group in in vitro model. In the in vivo experiment, the HSP70 gene expression was increased after sudden exposure to HS conditions (severe THI levels; THI = 88 to 90), whereas HSP90 and HSPB1 showed no differences among the THI groups (p > 0.05). However, in the severe THI group, the HSP70 gene expression returned to normal range after six days of continuous HS. In conclusion, the HSP70 gene plays a pivotal role in protecting cells from damage and is sensitive to HS in immune cells compared with other HSP genes in in vitro and in vivo models. In addition, the in vivo models suggest that calves exhibit active physiological mechanisms of adaptation to HS after six days of continuous exposure by regulating the HSP70 gene expression. Full article

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8 pages, 1661 KiB

Open AccessArticle

Use of the HRM Method in Quick Identification of FecX^O Mutation in Highly Prolific Olkuska Sheep

by Grzegorz Smołucha, Katarzyna Piórkowska, Katarzyna Ropka-Molik and Jacek Sikora

Animals 2020, 10(5), 844; https://doi.org/10.3390/ani10050844 - 14 May 2020

Cited by 6 | Viewed by 2790

Abstract

Olkuska is a highly prolific sheep breed in Poland. Thanks to earlier identification of the genetic basis of its prolificacy, a mutation in the BMP-15 gene, we can use molecular biology tools to identify this causative mutation affecting prolificacy. In our research, we [...] Read more.

Olkuska is a highly prolific sheep breed in Poland. Thanks to earlier identification of the genetic basis of its prolificacy, a mutation in the BMP-15 gene, we can use molecular biology tools to identify this causative mutation affecting prolificacy. In our research, we used the High-Resolution Melting (HRM) and Sanger sequencing methods to identify the genotypes of the studied animals. The result obtained by the HRM method is identical to those obtained by the sequencing method, which confirms the effectiveness of the HRM method and the possibility of quick and cheap identification of individuals with a FecX^O mutation. Full article

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13 pages, 1409 KiB

Open AccessArticle

Validation of Suitable Reference Genes for Gene Expression Studies on Yak Testis Development

by Xuelan Zhou, Xiaoyun Wu, Min Chu, Chunnian Liang, Xuezhi Ding, Jie Pei, Lin Xiong, Pengjia Bao, Xian Guo and Ping Yan

Animals 2020, 10(2), 182; https://doi.org/10.3390/ani10020182 - 21 Jan 2020

Cited by 8 | Viewed by 2719

Abstract

Testis has an important function in male reproduction. Its development is regulated by a large number of genes. The real-time reserve transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a useful tool to evaluate the gene expression levels. However, unsuitable reference genes (RGs) can cause [...] Read more.

Testis has an important function in male reproduction. Its development is regulated by a large number of genes. The real-time reserve transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a useful tool to evaluate the gene expression levels. However, unsuitable reference genes (RGs) can cause the misinterpretation of gene expression levels. Unfortunately, the ideal RGs for yak testis development are yet to be studied. In this study, 13 commonly used RGs were selected to identify the most stable RGs in yak testis at four different developmental stages, including two immature stages (6 months and 18 months) and two mature stages (30 months and 6 years). This study used GeNorm, NormFinder, BestKeeper, ∆Ct, and RefFinder programs to evaluate the stability of 13 candidate genes. The results of RefFinder showed that the stabilities of TATA box-binding protein (TBP) and ubiquitously expressed transcript protein (UXT) were ranked the top two across all developmental stages. TBP and hydroxymethylbilane synthase (HMBS) were stably expressed in immature stages, while mitochondrial ribosomal protein L39 (MRPL39) and TBP had higher stability than other candidate genes in mature stages. This study provided valuable information for gene expression studies to assist further investigation on the molecular mechanisms in underlying yak testis development. Full article

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16 pages, 650 KiB

Open AccessArticle

Evaluation of SCD, ACACA and FASN Mutations: Effects on Pork Quality and Other Production Traits in Pigs Selected Based on RNA-Seq Results

by Katarzyna Piórkowska, Martyna Małopolska, Katarzyna Ropka-Molik, Magdalena Szyndler-Nędza, Angelika Wiechniak, Kacper Żukowski, Barry Lambert and Mirosław Tyra

Animals 2020, 10(1), 123; https://doi.org/10.3390/ani10010123 - 12 Jan 2020

Cited by 29 | Viewed by 4131

Abstract

In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In [...] Read more.

In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In this study, three mutations within candidate genes for fat content (SCD, ACACA, and FASN) were selected, based on RNA-seq results and the relationship between polymorphisms in genes related to lipid metabolism, fattening and slaughter characteristics, as well as pork quality, including IMF level, were evaluated to identify selection markers. Moreover, their impact on gene expression was also examined. The PCR–RFLP (polymerase cha- in reaction – restriction fragments length) method was used to establish genotypes and effect sizes of potential genetic markers were estimated using a GLM model. It was identified that a FASN missense variant was positively associated with the expression level of this gene, which suggested its linkage with a mutation having a regulatory function. The association study indicated that the FASN missense variant may play a role in the determination of feed conversion and meat colour. In turn, a mutation in the ACACA gene showed a relationship with IMF content in the Puławska breed where the differences reached as much as 20%. We suggest considering all three mutations in further studies based on different pig populations due to the crucial role of SCD, ACACA, and FASN genes in lipid metabolism. Full article

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2019

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12 pages, 277 KiB

Open AccessReview

Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep (Ovies aries)

by Gebremedhin Gebreselassie, Haile Berihulay, Lin Jiang and Yuehui Ma

Animals 2020, 10(1), 33; https://doi.org/10.3390/ani10010033 - 23 Dec 2019

Cited by 71 | Viewed by 7687

Abstract

Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these [...] Read more.

Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in sheep. Full article

11 pages, 1755 KiB

Open AccessArticle

Polymorphism of the Myostatin (MSTN) Gene in Landes and Kielecka Geese Breeds

by Grzegorz Smołucha, Anna Kozubska-Sobocińska, Anna Koseniuk, Kacper Żukowski, Mirosław Lisowski and Bartosz Grajewski

Animals 2020, 10(1), 10; https://doi.org/10.3390/ani10010010 - 19 Dec 2019

Cited by 7 | Viewed by 3961

Abstract

Myostatin, also known as growth differentiation factor 8 (GDF8), belongs to the TGF-

β

superfamily of proteins. MSTN is a highly conserved protein that acts as a negative regulator of skeletal muscle growth. Loss of myostatin functionality causes the phenotype to appear in [...] Read more.

Myostatin, also known as growth differentiation factor 8 (GDF8), belongs to the TGF-

β

superfamily of proteins. MSTN is a highly conserved protein that acts as a negative regulator of skeletal muscle growth. Loss of myostatin functionality causes the phenotype to appear in the form of ‘double musculature’, among others in cattle, sheep, and house mice. The presented results of the research were carried out on two geese breeds—Landes and Kielecka. The aim of the study was to identify mutations in the MSTN gene and study their impact on body weight in both geese breeds in different periods of life. Analysis of the obtained results showed the existence of polymorphism in exon 3 (c.1231C>T) and suggested a possible association (p < 0.05) between BW and genotype in 12 weeks of life in male Kielecka geese breed. The identified polymorphism may be one of the factors important for improving body weight in the studied Kielecka breed, therefore, it is necessary to conduct further research on a larger population of geese breeds in order to more accurately estimate the effect of the identified SNP c.1231C>T on BW in geese. Full article

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11 pages, 283 KiB

Open AccessArticle

Estimation of the Genetic Parameters for Semen Traits in Spanish Dairy Sheep

by Rocío Pelayo, Manuel Ramón, Itsasne Granado-Tajada, Eva Ugarte, Malena Serrano, Beatriz Gutiérrez-Gil and Juan-José Arranz

Animals 2019, 9(12), 1147; https://doi.org/10.3390/ani9121147 - 13 Dec 2019

Cited by 9 | Viewed by 3419

Abstract

This work aimed to estimate genetic parameters for traits related to semen production and quality in Spanish dairy sheep breeds. For that, ejaculates of rams from Assaf, Churra, Latxa Cara Negra, Latxa Cara Rubia, and Manchega breeds were analyzed to measure volume, semen [...] Read more.

This work aimed to estimate genetic parameters for traits related to semen production and quality in Spanish dairy sheep breeds. For that, ejaculates of rams from Assaf, Churra, Latxa Cara Negra, Latxa Cara Rubia, and Manchega breeds were analyzed to measure volume, semen concentration, and motility. Estimates of variance components were obtained with multiple-trait animal models using the average information REML method in the BLUPF90 family of programs. Repeatability estimates for all the traits were also calculated, with values ranging from 0.077 to 0.304 for the motility and the semen concentration traits, respectively. Heritability estimates were of low to moderate magnitude, ranging from 0.014 (motility in Latxa Cara Rubia) to 0.198 (volume in Churra), although the estimates differed among the breeds. The estimated genetic correlations among the three semen traits showed adequate precision only in the MAN breed. The heritability estimates for the semen traits reported in the present paper suggest an adequate response to selection. The practical extension of these results to the other breeds studied here will be secondary to the estimation of more reliable genetic correlations in these breeds. Full article

9 pages, 1905 KiB

Open AccessArticle

RNA-Seq Analysis Identifies Differentially Expressed Genes in Subcutaneous Adipose Tissue in Qaidaford Cattle, Cattle-Yak, and Angus Cattle

by Chengchuang Song, Yongzhen Huang, Zhaoxin Yang, Yulin Ma, Buren Chaogetu, Zhaxi Zhuoma and Hong Chen

Animals 2019, 9(12), 1077; https://doi.org/10.3390/ani9121077 - 3 Dec 2019

Cited by 27 | Viewed by 3774

Abstract

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different [...] Read more.

In the beef industry, fat tissue is closely related to meat quality. In this study, high-throughput RNA sequencing was utilized for adipose tissue transcriptome analysis between cattle-yak, Qaidamford cattle, and Angus cattle. The screening and identification of differentially expressed genes (DEGs) between different breeds of cattle would facilitate cattle breeding. Compared to Angus cattle adipose tissue, a total of 4167 DEGs were identified in cattle-yak adipose tissue and 3269 DEGs were identified in Qaidamford cattle adipose tissue. Considering cattle-yak as a control group, 154 DEGs were identified in Qaidamford cattle adipose tissue. GO analysis indicated the significant enrichment of some DEGs related to lipid metabolism. The KEGG pathway database was also used to map DEGs and revealed that most annotated genes were involved in ECM-receptor interaction and the PI3K-Akt signal pathway, which are closely related to cell metabolism. Eight selected DEGs related to adipose tissue development or metabolism were verified by RT-qPCR, indicating the reliability of the RNA-seq data. The results of this comparative transcriptome analysis of adipose tissue and screening DEGs suggest several candidates for further investigations of meat quality in different cattle breeds. Full article

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11 pages, 809 KiB

Open AccessArticle

Differential Expression of ACTL8 Gene and Association Study of Its Variations with Growth Traits in Chinese Cattle

by Cuicui Cai, Jiawei Xu, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Xueyao Yang, Jianliang Xie, Yuhua Li and Hong Chen

Animals 2019, 9(12), 1068; https://doi.org/10.3390/ani9121068 - 2 Dec 2019

Cited by 2 | Viewed by 2570

Abstract

Mutations are heritable changes at the base level of genomic DNA. Furthermore, mutations lead to genetic polymorphisms and may alter animal growth phenotypes. Our previous study found that mutations in the bovine Actin-like protein 8 (ACTL8) gene may be involved in [...] Read more.

Mutations are heritable changes at the base level of genomic DNA. Furthermore, mutations lead to genetic polymorphisms and may alter animal growth phenotypes. Our previous study found that mutations in the bovine Actin-like protein 8 (ACTL8) gene may be involved in muscle growth and development. This study explored several mutations of the ACTL8 gene and their influence on body size in Chinese beef cattle, as well as tested the tissue expression profile of the ACTL8 gene in Qinchuan cattle at different ages. Five single nucleotide polymorphisms (SNPs) (including one synonymous mutation (c.2135552895G > A)) and two insertion/deletion polymorphisms (indels) were identified in the ACTL8 gene from 1138 cattle by DNA-seq, RFLP and other methods. Then, the expression profile of the ACTL8 gene in Qinchuan cattle showed that it was expressed in heart, spleen, lung, liver, muscle, and fat tissues. Moreover, the expression level of ACTL8 was increased with cattle growth (p < 0.01). The ACTL8 mRNA expression level in kidney and muscle tissues was the highest in the calves, while lowest in the fetal stage. Overall, we showed that the mutations could act as markers in beef molecular breeding and selection of the growth traits of cattle. Full article

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10 pages, 776 KiB

Open AccessArticle

Estimation of Genetic Parameters by Single-Trait and Multi-Trait Models for Carcass Traits in Hanwoo Cattle

by Swati Srivastava, Bryan Irvine Lopez, Sara de las Heras-Saldana, Jong-Eun Park, Dong-Hyun Shin, Han-Ha Chai, Woncheol Park, Seung-Hwan Lee and Dajeong Lim

Animals 2019, 9(12), 1061; https://doi.org/10.3390/ani9121061 - 2 Dec 2019

Cited by 14 | Viewed by 3593

Abstract

Hanwoo breed is preferred in South Korea because of the high standards in marbling and the palatability of its meat. Numerous studies have been conducted and are ongoing to increase the meat production and quality in this beef population. The aim of this [...] Read more.

Hanwoo breed is preferred in South Korea because of the high standards in marbling and the palatability of its meat. Numerous studies have been conducted and are ongoing to increase the meat production and quality in this beef population. The aim of this study was to estimate and compare genetic parameters for carcass traits using BLUPF90 software. Four models were constructed, single trait pedigree model (STPM), single-trait genomic model (STGM), multi-trait pedigree model (MTPM), and multi-trait genomic model (MTGM), using the pedigree, phenotype, and genomic information of 7991 Hanwoo cattle. Four carcass traits were evaluated: Back fat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Heritability estimates of 0.40 and 0.41 for BFT, 0.33 and 0.34 for CWT, 0.36 and 0.37 for EMA, and 0.35 and 0.38 for MS were obtained for the single-trait pedigree model and the multi-trait pedigree model, respectively, in Hanwoo. Further, the genomic model showed more improved results compared to the pedigree model, with heritability of 0.39 (CWT), 0.39 (EMA), and 0.46 (MS), except for 0.39 (BFT), which may be due to random events. Utilization of genomic information in the form of single nucleotide polymorphisms (SNPs) has allowed more capturing of the variance from the traits improving the variance components. Full article

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24 pages, 3067 KiB

Open AccessArticle

A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types

by Tomasz Szmatoła, Artur Gurgul, Igor Jasielczuk, Tomasz Ząbek, Katarzyna Ropka-Molik, Zygmunt Litwińczuk and Monika Bugno-Poniewierska

Animals 2019, 9(12), 1024; https://doi.org/10.3390/ani9121024 - 25 Nov 2019

Cited by 43 | Viewed by 4365

Abstract

In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed [...] Read more.

In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (F_ROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the F_ROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds. Full article

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10 pages, 1732 KiB

Open AccessArticle

Four Novel SNPs of MYO1A Gene Associated with Heat-Tolerance in Chinese Cattle

by Peng Jia, Cuicui Cai, Kaixing Qu, Ningbo Chen, Yutang Jia, Quratulain Hanif, Jianyong Liu, Jicai Zhang, Hong Chen, Bizhi Huang and Chuzhao Lei

Animals 2019, 9(11), 964; https://doi.org/10.3390/ani9110964 - 13 Nov 2019

Cited by 21 | Viewed by 3470

Abstract

Based on the previous GWAS research related to bovine heat tolerance trait, this study aimed to explore the effect of myosin-1a (MYO1A) gene on bovine heat tolerance trait, and find the molecular markers related to the heat tolerance of Chinese cattle. [...] Read more.

Based on the previous GWAS research related to bovine heat tolerance trait, this study aimed to explore the effect of myosin-1a (MYO1A) gene on bovine heat tolerance trait, and find the molecular markers related to the heat tolerance of Chinese cattle. In our study, four novel candidate SNPs highly conserved in B. indicus breeds but barely existed in B. taurus were identified in MYO1A gene according to Bovine Genome Variation Database and Selective Signatures (BGVD). PCR and DNA sequencing were used to genotype 1072 individuals including 34 Chinese indigenous cattle breeds as well as Angus and Indian zebu. Two synonymous mutations (rs208210464 and rs110123931), one missense mutation (rs209999142; Phe172Ser), and one intron mutation (rs135771836) were detected. The frequencies of mutant alleles of the four SNPs gradually increased from northern groups to southern groups of Chinese cattle, which was consistent with the distribution of various climatic conditions of China. Additionally, four SNPs were significantly associated with four climatic conditions including annual mean temperature (T), relative humidity (H), temperature-humidity index (THI), and average annual sunshine hours (100-cloudiness) (SR). Among these, rs209999142 and Hap 1/1 had better performance than others. Our results suggested that rs209999142 was associated with heat-tolerance trait and rs208210464, rs110123931, and rs135771836 showed high phenotypic effect on heat-tolerance trait because of the strong linkage with rs209999142. These SNPs could be used as candidates for marker-assisted selection (MAS) in cattle breeding. Full article

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18 pages, 284 KiB

Open AccessReview

Genetic Selection for Thermotolerance in Ruminants

by Richard Osei-Amponsah, Surinder S. Chauhan, Brian J. Leury, Long Cheng, Brendan Cullen, Iain J. Clarke and Frank R. Dunshea

Animals 2019, 9(11), 948; https://doi.org/10.3390/ani9110948 - 11 Nov 2019

Cited by 57 | Viewed by 7815

Abstract

Variations in climatic variables (temperature, humidity and solar radiation) negatively impact livestock growth, reproduction, and production. Heat stress, for instance, is a source of huge financial loss to livestock production globally. There have been significant advances in physical modifications of animal environment and [...] Read more.

Variations in climatic variables (temperature, humidity and solar radiation) negatively impact livestock growth, reproduction, and production. Heat stress, for instance, is a source of huge financial loss to livestock production globally. There have been significant advances in physical modifications of animal environment and nutritional interventions as tools of heat stress mitigation. Unfortunately, these are short-term solutions and may be unsustainable, costly, and not applicable to all production systems. Accordingly, there is a need for innovative, practical, and sustainable approaches to overcome the challenges posed by global warming and climate change-induced heat stress. This review highlights attempts to genetically select and breed ruminants for thermotolerance and thereby sustain production in the face of changing climates. One effective way is to incorporate sustainable heat abatement strategies in ruminant production. Improved knowledge of the physiology of ruminant acclimation to harsh environments, the opportunities and tools available for selecting and breeding thermotolerant ruminants, and the matching of animals to appropriate environments should help to minimise the effect of heat stress on sustainable animal genetic resource growth, production, and reproduction to ensure protein food security. Full article

12 pages, 823 KiB

Open AccessArticle

The Selection of Reference Genes for Quantitative Real-Time PCR in the Ashidan Yak Mammary Gland During Lactation and Dry Period

by Xiaoyun Wu, Xuelan Zhou, Xuezhi Ding, Min Chu, Chunnian Liang, Jie Pei, Lin Xiong, Pengjia Bao, Xian Guo and Ping Yan

Animals 2019, 9(11), 943; https://doi.org/10.3390/ani9110943 - 10 Nov 2019

Cited by 10 | Viewed by 2753

Abstract

Investigating the critical genes related to milk synthesis is essential for the improvement of the milk yield of the yak. Real-time quantitative polymerase chain reaction (RT-qPCR) is a reliable and widely used method to measure and evaluate gene expression levels. Selection of suitable [...] Read more.

Investigating the critical genes related to milk synthesis is essential for the improvement of the milk yield of the yak. Real-time quantitative polymerase chain reaction (RT-qPCR) is a reliable and widely used method to measure and evaluate gene expression levels. Selection of suitable reference genes is mandatory to acquire accurate normalization of gene expression results from RT-qPCR. To select the most stable reference genes for reliable normalization of mRNA expression by RT-qPCR in the mammary gland of the Ashidan yak, we selected 16 candidate reference genes and analyzed their expression stability at different physiological stages (lactation and dry period). The expression stability of the candidate reference genes was assessed using geNorm, NormFinder, BestKeeper, Delta Ct, and RefFinder methods. The results showed that the hydroxymethylbilane synthase gene (HMBS) and the tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide gene (YWHAZ) were the most stable genes across all treatment samples. The reliability of selected reference genes was validated by normalizing relative expression of the lactation-related 60S ribosomal protein L35 gene (RPL35). The relative expression of RPL35 varied considerably according to the different reference genes. This work provides valuable information to further promote research in the molecular mechanisms involved in lactation and mammary gland development and provides a foundation for the improvement of the milk yield and quality of the Ashidan yak. Full article

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10 pages, 670 KiB

Open AccessArticle

A Study of Genomic Prediction of 12 Important Traits in the Domesticated Yak (Bos grunniens)

by Donghai Fu, Xiaoming Ma, Congjun Jia, Min Chu, Qinhui Lei, Zhiping Wen, Xiaoyun Wu, Jie Pei, Pengjia Bao, Xuezhi Ding, Xian Guo, Ping Yan and Chunnian Liang

Animals 2019, 9(11), 927; https://doi.org/10.3390/ani9110927 - 7 Nov 2019

Cited by 3 | Viewed by 2963

Abstract

The aim of this study was to explore the possibility of applying GP to important economic traits in the domesticated yak, thus providing theoretical support for its molecular breeding. A reference population was constructed consisting of 354 polled yaks, measuring four growth traits [...] Read more.

The aim of this study was to explore the possibility of applying GP to important economic traits in the domesticated yak, thus providing theoretical support for its molecular breeding. A reference population was constructed consisting of 354 polled yaks, measuring four growth traits and eight hematological traits related to resistance to disease (involved in immune response and phagocytosis). The Illumina bovine HD 770k chip was used to obtain SNP information of all the individuals. With these genotypes and phenotypes, GBLUP, Bayes B and Bayes Cπ methods were used to predict genomic estimated breeding values (GEBV) and assess prediction capability. The correlation coefficient of the association of GEBV with estimated breeding value (EBV) was used as PA for each trait. The prediction accuracy varied from 0.043 to 0.281 for different traits. Each trait displayed similar PAs when using the three methods. Lymphocyte counts (LYM) exhibited the highest predictive accuracy (0.319) during all GP, while chest girth (CG) provided the lowest predictive accuracy (0.043). Our results showed moderate PA in most traits such as body length (0.212) and hematocrit (0.23). Those traits with lower PA could be improved by using SNP chips designed specifically for yak, a better optimized reference group structure, and more efficient statistical algorithms and tools. Full article

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12 pages, 965 KiB

Open AccessArticle

Tracing Worldwide Turkey Genetic Diversity Using D-loop Sequence Mitochondrial DNA Analysis

by Amado Manuel Canales Vergara, Vincenzo Landi, Juan Vicente Delgado Bermejo, Amparo Martínez, Patricia Cervantes Acosta, Águeda Pons Barro, Daniele Bigi, Phillip Sponenberg, Mostafa Helal, Mohammad Hossein Banabazi and María Esperanza Camacho Vallejo

Animals 2019, 9(11), 897; https://doi.org/10.3390/ani9110897 - 1 Nov 2019

Cited by 17 | Viewed by 4267

Abstract

According to recent archeological evidence, turkey (Meleagris gallopavo gallopavo) domestication may have occurred in Mexico around 2000 years ago. However, little is known about the phylogenetic and genealogical background underlying domestic turkey populations. This study aimed to further understand the domestication process and [...] Read more.

According to recent archeological evidence, turkey (Meleagris gallopavo gallopavo) domestication may have occurred in Mexico around 2000 years ago. However, little is known about the phylogenetic and genealogical background underlying domestic turkey populations. This study aimed to further understand the domestication process and identify inter- or intraspecific connections between turkey populations to determine their origins, trace their global expansion, and define the species’ genetic value. Ninety-three domestic turkeys (local breeds) were sampled from populations in Brazil, Mexico, USA, Spain, Italy, Iran, and Egypt. Publicly available sequences from previous studies were also included. Standard mitochondrial DNA, genetic diversity, and haplotype network analyses were performed. Seventy-six polymorphic sites were identified. Turkeys from Mexico showed the greatest number of polymorphic sites (40), while turkeys from Italy and Brazil reported only one site each. Nucleotide diversity was also highest in Mexico and the USA (π = 0.0175 and 0.0102, respectively) and lowest in Brazil and Italy. Of the six major haplogroups defined, the Mexican and USA populations appeared to have remained more stable and diverse than the other populations. This may be due to conservative husbandry policies in the rural areas of other populations, which have prevented the introduction of commercial turkey lines. Full article

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15 pages, 1155 KiB

Open AccessArticle

Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies

by Maria Chiara Fabbri, Marcos Paulo Gonçalves de Rezende, Christos Dadousis, Stefano Biffani, Riccardo Negrini, Paulo Luiz Souza Carneiro and Riccardo Bozzi

Animals 2019, 9(11), 880; https://doi.org/10.3390/ani9110880 - 29 Oct 2019

Cited by 18 | Viewed by 3893

Abstract

The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and [...] Read more.

The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were <1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent–offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds. Full article

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15 pages, 2023 KiB

Open AccessArticle

Bta-miR-24-3p Controls the Myogenic Differentiation and Proliferation of Fetal Bovine Skeletal Muscle-Derived Progenitor Cells by Targeting ACVR1B

by Xin Hu, Yishen Xing, Ling Ren, Yahui Wang, Qian Li, Xing Fu, Qiyuan Yang, Lingyang Xu, Luc Willems, Junya Li and Lupei Zhang

Animals 2019, 9(11), 859; https://doi.org/10.3390/ani9110859 - 24 Oct 2019

Cited by 14 | Viewed by 4695

Abstract

MicroRNAs modulate a variety of cellular events, including skeletal muscle development, but the molecular basis of their functions in fetal bovine skeletal muscle development is poorly understood. In this study, we report that bta-miR-24-3p promotes the myogenic differentiation of fetal bovine PDGFRα^- [...] Read more.

MicroRNAs modulate a variety of cellular events, including skeletal muscle development, but the molecular basis of their functions in fetal bovine skeletal muscle development is poorly understood. In this study, we report that bta-miR-24-3p promotes the myogenic differentiation of fetal bovine PDGFRα^- progenitor cells. The expression of bta-miR-24-3p increased during myogenic differentiation. Overexpression of bta-miR-24-3p significantly promoted myogenic differentiation, but inhibited proliferation. A dual-luciferase assay identified ACVR1B as a direct target of bta-miR-24-3p. Similarly, knocking down ACVR1B by RNA interference also significantly inhibited proliferation and promoted the differentiation of bovine PDGFRα^- progenitor cells. Thus, our study provides a mechanism in which bta-miR-24-3p regulates myogenesis by inhibiting ACVR1B expression. Full article

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12 pages, 1066 KiB

Open AccessArticle

Association of Twelve Candidate Gene Polymorphisms with the Intramuscular Fat Content and Average Backfat Thickness of Chinese Suhuai Pigs

by Binbin Wang, Pinghua Li, Wuduo Zhou, Chen Gao, Hang Liu, Huixia Li, Peipei Niu, Zongping Zhang, Qiang Li, Juan Zhou and Ruihua Huang

Animals 2019, 9(11), 858; https://doi.org/10.3390/ani9110858 - 23 Oct 2019

Cited by 25 | Viewed by 5033

Abstract

The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations [...] Read more.

The present study aimed to identify the molecular markers for genes that influence intramuscular fat content (IFC), but not average backfat thickness (ABT). A total of 330 Suhuai pigs were slaughtered, and measurements of IFC and ABT were obtained. Phenotypic and genetic correlations between IFC and ABT were calculated. Thirteen single nucleotide polymorphisms (SNPs) among 12 candidate genes for IFC were analyzed, including FABP3, LIPE, IGF1, IGF2, LEP, LEPR, MC4R, PHKG1, RETN, RYR1, SCD, and UBE3C. Associations of the evaluated SNPs with IFCIFC and ABT were performed. Our results showed that the means of IFC and ABT were 1.99 ± 0.03 % and 26.68 ± 0.28 mm, respectively. The coefficients of variation (CVs) of IFC and ABT were 31.21% and 19.36%, respectively. The phenotypic and genetic correlations between IFC and ABT were moderate. Only the FABP3 (rs1110770079) was associated with IFC (p < 0.05) but not with ABT. Besides, there was a tendency for associations of RYR1 (rs344435545) and SCD (rs80912566) with IFC (p < 0.1). Our results indicated that the FABP3 (rs1110770079) SNP could be used as a marker to improve IFC without changing ABT in the Suhuai pig breeding system. Full article

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15 pages, 1755 KiB

Open AccessArticle

Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome

by Donghyeok Seol, Byung June Ko, Bongsang Kim, Han-Ha Chai, Dajeong Lim and Heebal Kim

Animals 2019, 9(10), 809; https://doi.org/10.3390/ani9100809 - 15 Oct 2019

Cited by 14 | Viewed by 5693

Abstract

Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection [...] Read more.

Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens. Full article

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14 pages, 2048 KiB

Open AccessArticle

Theoretical Evaluation of Multi-Breed Genomic Prediction in Chinese Indigenous Cattle

by Lei Xu, Zezhao Wang, Bo Zhu, Ying Liu, Hongwei Li, Farhad Bordbar, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, Shengli Zhang, Lingyang Xu and Junya Li

Animals 2019, 9(10), 789; https://doi.org/10.3390/ani9100789 - 11 Oct 2019

Cited by 5 | Viewed by 3160

Abstract

Genomic selection (GS) has been widely considered as a valuable strategy for enhancing the rate of genetic gain in farm animals. However, the construction of a large reference population is a big challenge for small populations like indigenous cattle. In order to evaluate [...] Read more.

Genomic selection (GS) has been widely considered as a valuable strategy for enhancing the rate of genetic gain in farm animals. However, the construction of a large reference population is a big challenge for small populations like indigenous cattle. In order to evaluate the potential application of GS for Chinese indigenous cattle, we assessed the influence of combining multiple populations on the reliability of genomic predictions for 10 indigenous breeds of Chinese cattle using simulated data. Also, we examined the effect of different genetic architecture on prediction accuracy. In this study, we simulated a set of genotype data by a resampling approach which can reflect the realistic linkage disequilibrium pattern for multiple populations. We found within-breed evaluations yielded the highest accuracies ranged from 0.64 to 0.68 for four different simulated genetic architectures. For scenarios using multiple breeds as reference, the predictive accuracies were higher when the reference was comprised of breeds with a close relationship, while the accuracies were low when prediction were carried out among breeds. In addition, the accuracy increased in all scenarios with the heritability increased. Our results suggested that using meta-population as reference can increase accuracy of genomic predictions for small populations. Moreover, multi-breed genomic selection was feasible for Chinese indigenous populations with genetic relationships. Full article

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15 pages, 2450 KiB

Open AccessArticle

Comprehensive Analysis of Porcine Prox1 Gene and Its Relationship with Meat Quality Traits

by Chao Dong, Xiying Zhang, Kaiqing Liu, Bojiang Li, Zhe Chao, Aiwen Jiang, Rongyang Li, Pinghua Li, Honglin Liu and Wangjun Wu

Animals 2019, 9(10), 744; https://doi.org/10.3390/ani9100744 - 29 Sep 2019

Cited by 11 | Viewed by 2911

Abstract

Prox1 is involved in muscle fiber conversion, adult-onset obesity, and type 2 diabetes. However, information regarding porcine Prox1 and its relationship with meat quality traits is still unknown. In this study, we characterized the full-length cDNA and proximal promoter of two transcript variants [...] Read more.

Prox1 is involved in muscle fiber conversion, adult-onset obesity, and type 2 diabetes. However, information regarding porcine Prox1 and its relationship with meat quality traits is still unknown. In this study, we characterized the full-length cDNA and proximal promoter of two transcript variants of porcine Prox1. Moreover, Prox1 was expressed abundantly in the skeletal muscle and its expression was higher in the soleus muscle than that in the biceps femoris muscle. Its expression pattern in the high and low meat color (redness) value a* groups was similar to that of myoglobin and MyHC I, but opposed to that of MyHC IIB. Importantly, there was a significant positive correlation between Prox1 expression and meat color (redness) value a* (r = 0.3845, p = 0.0394), and a significant negative correlation between Prox1 expression and drip loss (r = −0.4204, p = 0.0232), as well as the ratio of MyHC IIB to MyHC I expression (r = −0.3871, p = 0.0380). In addition, we found that the polymorphisms of three closely linked SNPs in Prox1 promoter 1 were significantly associated with pH_24h in a pig population. Taken together, our data provide valuable insights into the characteristics of porcine Prox1 and indicate that Prox1 is a promising candidate gene affecting meat quality traits. Full article

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10 pages, 736 KiB

Open AccessArticle

Genome-Wide Association Study for Reproductive Traits in a Duroc Pig Population

by Zhe Zhang, Zitao Chen, Shaopan Ye, Yingting He, Shuwen Huang, Xiaolong Yuan, Zanmou Chen, Hao Zhang and Jiaqi Li

Animals 2019, 9(10), 732; https://doi.org/10.3390/ani9100732 - 26 Sep 2019

Cited by 34 | Viewed by 5978

Abstract

In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) [...] Read more.

In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) chips, and four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. The results showed that 20 potential SNPs reached the level of suggestive significance and were associated with these traits of interest. Several important candidate genes, including TXN2, KCNA1, ENSSSCG00000003546, ZDHHC18, MAP2K6, BICC1, FAM135B, EPHB2, SEMA4D, ST3GAL1, KCTD3, FAM110A, TMEM132D, TBX3, and FAM110A, were identified and might compose the underlying genetic architecture of porcine reproductive traits. These findings help to understand the genetic basis of porcine reproductive traits and provide important information for molecular breeding in pigs. Full article

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9 pages, 256 KiB

Open AccessArticle

Associations between Bovine β-Defensin 4 Genotypes and Production Traits of Polish Holstein-Friesian Dairy Cattle

by Paulina Brodowska, Lech Zwierzchowski, Sylwester Marczak, Wiesław Jarmuż and Emilia Bagnicka

Animals 2019, 9(10), 723; https://doi.org/10.3390/ani9100723 - 25 Sep 2019

Cited by 4 | Viewed by 2814

Abstract

This study analyzed the associations between two single-nucleotide polymorphisms (C2239T and A1674C), used together as a genotype located in BNBD4, and milk traits and breeding values of productivity traits of Polish Holstein-Friesian dairy cows. The research was carried out on 322 cows, with [...] Read more.

This study analyzed the associations between two single-nucleotide polymorphisms (C2239T and A1674C), used together as a genotype located in BNBD4, and milk traits and breeding values of productivity traits of Polish Holstein-Friesian dairy cows. The research was carried out on 322 cows, with 7070 milk parameter and somatic cell count records in daily milking, as well as 897 records covering data on whole lactations, and 2209 breeding value records for productivity traits. The DMU statistical package with a one-trait repeatability test-day animal model was used to estimate the associations. The differences between the genotype effects were analyzed using Duncan’s post-hoc tests. The CC/AA and CT/AC genotypes had the highest frequencies (0.62 and 0.23, respectively). For use in marker-assisted selection, the CC/AC genotype is the most promising as an indicator of high-yielding cows potentially resistant to mastitis, because it was associated with the lowest somatic cell count (SCC), highest milk, fat, and protein yields in daily milking, as well as with milk yield in the whole lactation. The studied genotypes were also related to the breeding values of all the investigated production traits. However, some simulation studies have indicated a high rate of false-positives in GWAS based on classically calculated EBVs. Full article

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7 pages, 223 KiB

Open AccessArticle

Estimation of Genetic Parameters for Reproductive Traits in Hanwoo (Korean Cattle)

by Bryan Irvine Lopez, Ju-Hwan Son, Kangseok Seo and Dajeong Lim

Animals 2019, 9(10), 715; https://doi.org/10.3390/ani9100715 - 24 Sep 2019

Cited by 18 | Viewed by 4147

Abstract

Genetic parameters for the reproductive traits of Hanwoo cattle were estimated using data obtained from 15,355 cows in 92 herds across South Korea, which were inseminated from May 1997 to July 2016. An “average information” restricted maximum likelihood (REML) procedure that fit in [...] Read more.

Genetic parameters for the reproductive traits of Hanwoo cattle were estimated using data obtained from 15,355 cows in 92 herds across South Korea, which were inseminated from May 1997 to July 2016. An “average information” restricted maximum likelihood (REML) procedure that fit in single-trait and multi-trait animal models was used to estimate the variance components of age at first calving (AFC), calving interval (CI), days open (DO), and gestation length (GL). Results showed the low estimates of heritability for all reproductive traits from both single-trait and multi-trait models. Estimates of heritability for AFC were 0.08 and 0.10 with single-trait and multi-trait models, respectively, while the estimates of heritability using the same animal models ranged from 0.01 to 0.07, 0.01 to 0.09, and 0.10 to 0.16 for CI, DO, and GL, accordingly. While AFC showed positive genetic correlations of 0.52 and 0.46 with CI and DO, respectively, the estimates of genetic and phenotypic correlations of GL with AFC were close to zero. Moreover, phenotypic correlations of GL with CI and DO were also close to zero; however, the corresponding genetic correlations were 0.13 and –0.38 for CI and DO, respectively. These estimated variance components and genetic correlations for reproductive traits can be utilized for genetic improvement programs of Hanwoo cattle. Full article

9 pages, 755 KiB

Open AccessArticle

Genetic Parameter Estimation and Genomic Prediction of Duroc Boars’ Sperm Morphology Abnormalities

by Yunxiang Zhao, Ning Gao, Jian Cheng, Saeed El-Ashram, Lin Zhu, Conglin Zhang and Zhili Li

Animals 2019, 9(10), 710; https://doi.org/10.3390/ani9100710 - 23 Sep 2019

Cited by 5 | Viewed by 3204

Abstract

Artificial insemination (AI) has been used globally as a routine technology in the swine production industry. However, genetic parameters and genomic prediction accuracy of semen traits have seldom been reported. In this study, we estimated genetic parameters and conducted genomic prediction for five [...] Read more.

Artificial insemination (AI) has been used globally as a routine technology in the swine production industry. However, genetic parameters and genomic prediction accuracy of semen traits have seldom been reported. In this study, we estimated genetic parameters and conducted genomic prediction for five types of sperm morphology abnormalities in a large Duroc boar population. The estimated heritability of the studied traits ranged from 0.029 to 0.295. In the random cross-validation scenario, the predictive ability ranged from 0.212 to 0.417 for genomic best linear unbiased prediction (GBLUP) and from 0.249 to 0.565 for single-step GBLUP (ssGBLUP). In the forward prediction scenario, the predictive ability ranged from 0.069 to 0.389 for GBLUP and from 0.085 to 0.483 for ssGBLUP. In conclusion, the studied sperm morphology abnormalities showed moderate to low heritability. Both GBLUP and ssGBLUP showed comparative predictive abilities of breeding values, and ssGBLUP outperformed GBLUP under many circumstances in respect to predictive ability. To our knowledge, this is the first time that the genetic parameters and genomic predictive ability of these traits were reported in such a large Duroc boar population. Full article

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7 pages, 423 KiB

Open AccessCommunication

A Missense Mutation of the HSPB7 Gene Associated with Heat Tolerance in Chinese Indicine Cattle

by Lulan Zeng, Yanhong Cao, Zhuyue Wu, Mingguang Huang, Guoliang Zhang, Chuzhao Lei and Yumin Zhao

Animals 2019, 9(8), 554; https://doi.org/10.3390/ani9080554 - 14 Aug 2019

Cited by 13 | Viewed by 3215

Abstract

The small heat shock proteins (HSPB) are expressed in response to heat stress, and the heat shock protein family B (small) member 7 (HSPB7) gene has been reported to play an important role in heat tolerance pathways. Only a missense mutation [...] Read more.

The small heat shock proteins (HSPB) are expressed in response to heat stress, and the heat shock protein family B (small) member 7 (HSPB7) gene has been reported to play an important role in heat tolerance pathways. Only a missense mutation (NC_037329.1: g.136054902 C > G: p.Ala69Gly) was identified in the HSPB7 gene in indicine cattle, which might be a candidate mutation associated with the heat tolerance. Here, we explore the allele frequency of this mutation in 774 individuals belonging to 32 Chinese indigenous cattle breeds using polymerase chain reaction (PCR) and DNA sequencing methods. The distribution of alleles of NC_037329.1: g.136054902 C > G displays significant geographical difference across native Chinese cattle breeds that the allele C was dominant in northern cattle groups, while allele G was dominant in southern indicine cattle groups. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH), and temperature humidity index (THI) (p < 0.01), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. Our results demonstrate that the mutation of the HSPB7 gene in Chinese indicine cattle might be a candidate gene associated with the heat tolerance. Full article

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14 pages, 2935 KiB

Open AccessArticle

Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes in Three Pig Breeds

by Rui Xie, Liangyu Shi, Jiaxin Liu, Tianyu Deng, Lixian Wang, Yang Liu and Fuping Zhao

Animals 2019, 9(8), 518; https://doi.org/10.3390/ani9080518 - 1 Aug 2019

Cited by 41 | Viewed by 5275

Abstract

Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the [...] Read more.

Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH (F_ROH) and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (F_HOM). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 Mb in the three breeds. The F_ROH results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between F_ROH and F_HOM was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (GATM, SPATA46, HSD17B7, VANGL2, DAXX, CPEB1), meat quality traits (NR1I3, APOA2, USF1) and energy conversion (NDUFS2) were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection. Full article

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9 pages, 1608 KiB

Open AccessArticle

Identification of the Ovine Keratin-Associated Protein 21-1 Gene and Its Association with Variation in Wool Traits

by Shaobin Li, Huitong Zhou, Hua Gong, Fangfang Zhao, Jiqing Wang, Xiu Liu, Jiang Hu, Yuzhu Luo and Jon G.H. Hickford

Animals 2019, 9(7), 450; https://doi.org/10.3390/ani9070450 - 16 Jul 2019

Cited by 8 | Viewed by 3837

Abstract

Keratin-associated proteins (KAPs) are key constituents of wool and hair fibers. In this study, an ovine KAP gene encoding a HGT-KAP protein was identified. The gene was different from all of the HGT-KAP genes identified in sheep, but was closely related to the [...] Read more.

Keratin-associated proteins (KAPs) are key constituents of wool and hair fibers. In this study, an ovine KAP gene encoding a HGT-KAP protein was identified. The gene was different from all of the HGT-KAP genes identified in sheep, but was closely related to the human KAP21-1 gene, suggesting that it represented the unidentified ovine KRTAP21-1. Four variants (named A to D) of ovine KRTAP21-1 were found in 360 Merino × Southdown-cross lambs from four sire lines. Three sequence variations were detected among these variants. Two of the sequence variations were located upstream of the coding region and the remaining one was a synonymous variation in the coding sequence. Six genotypes were found in the Merino-cross lambs, with only two of the genotypes (AA and AC) occurring at a frequency of over 5%. Wool from sheep of genotype AA had a higher yield than that from AC sheep (p = 0.014), but tended to have a lower greasy fleece weight (GFW) than that of genotype AC (P = 0.078). This suggests that variation in KRTAP21-1 affects wool yield and the gene may have potential for use as a genetic maker for improving wool yield. Full article

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15 pages, 999 KiB

Open AccessArticle

Single Nucleotide Polymorphisms in SLC5A1, CCNA1, and ABCC1 and the Association with Litter Size in Small-Tail Han Sheep

by Yongfu La, Qiuyue Liu, Liping Zhang and Mingxing Chu

Animals 2019, 9(7), 432; https://doi.org/10.3390/ani9070432 - 9 Jul 2019

Cited by 11 | Viewed by 3194

Abstract

SLC5A1, CCNA1, and ABCC1 have been extensively studied as candidate genes because of their great influence on the reproductive traits of animals. However, little is known about the association between polymorphisms of the SLC5A1, CCNA1, and ABCC1 genes and [...] Read more.

SLC5A1, CCNA1, and ABCC1 have been extensively studied as candidate genes because of their great influence on the reproductive traits of animals. However, little is known about the association between polymorphisms of the SLC5A1, CCNA1, and ABCC1 genes and litter size in Small-Tail Han sheep. In this study, the expression levels of SLC5A1, CCNA1, and ABCC1 in HPG (hypothalamic–pituitary–gonadal) axis tissues of polytocous and monotocous Small-Tail Han sheep were analyzed by qPCR. To better understand the effects of four single nucleotide polymorphisms (SNPs) comprising of g.70067210 T > C in SLC5A1, g.25350431 C > T and g.25360220 T > C in CCNA1, and g.14413132 C > T in ABCC1, a population genetic analysis was conducted using data obtained from genotyping in 728 sheep from seven breeds. The results indicated that all genes included in this study were differentially expressed in the pituitary and uterus of polytocous and monotocous Small-Tail Han sheep (p < 0.05). The associations of these four SNPs and the FecB mutation with litter size in 384 Small-Tail Han sheep were analyzed, therefore, and it was found that both g.70067210T > C and the FecB mutation were significantly associated with litter size (p < 0.05). The linear regression analysis of the association of multiple markers (FecB and g.70067210 T > C in SCL5A1) with litter size indicated that homozygous ewes carrying the BB/TT genotype had larger litter size than any ewes with any other genotype. In conclusion, the SLC5A1 SNPs significantly affect litter size in sheep and are useful as genetic marker for litter size. Full article

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6 pages, 800 KiB

Open AccessArticle

Characterization of a Novel Porcine CSN2 Polymorphism and Its Distribution in Five European Breeds

by Mihai Șuteu, Augustin Vlaic and Stelian Vasile Dărăban

Animals 2019, 9(7), 419; https://doi.org/10.3390/ani9070419 - 4 Jul 2019

Viewed by 2947

Abstract

Here, we describe a novel porcine β-casein (CNS2) polymorphism, initially identified using the isoelectric focusing (IEF) technique, and provide its distribution in five European breeds. Porcine CSN2 cDNA samples, from sows identified using IEF as carriers of polymorphic variants, were sequenced, [...] Read more.

Here, we describe a novel porcine β-casein (CNS2) polymorphism, initially identified using the isoelectric focusing (IEF) technique, and provide its distribution in five European breeds. Porcine CSN2 cDNA samples, from sows identified using IEF as carriers of polymorphic variants, were sequenced, and based on the sequence alignments, a genotyping assay was developed. The distribution of the polymorphism was investigated by genotyping 167 sows. Population genetic indexes were computed using POPGENE32 version 1.32. Sequence alignments revealed that the mutation which caused the different β-casein IEF migration profiles was c.647G>A, a substitution located in exon 7, which modifies the amino acid from position 201 of the mature protein from arginine to glutamine. The frequency of the G allele was 0.965 in the investigated Landrace population (number of individuals genotyped n = 67), one in the Pietrain population (n = 40), 0.705 in the Large White population (n = 36), 0.885 in the Bazna population (n = 13), and 0.555 in the Mangalita population (n = 11). For all breeds, except Pietrain (monomorphic), the genotype distribution was in accordance with the Hardy–Weinberg equilibrium. Given that β-casein is the most important protein in sows’ milk, a polymorphism like the one described here may prove interesting for marker-assisted selection. Full article

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13 pages, 289 KiB

Open AccessArticle

Estimation of Genetic Parameters for Peak Yield, Yield and Persistency Traits in Murciano-Granadina Goats Using Multi-Traits Models

by Judith C. Miranda, José M. León, Camillo Pieramati, Mayra M. Gómez, Jesús Valdés and Cecilio Barba

Animals 2019, 9(7), 411; https://doi.org/10.3390/ani9070411 - 1 Jul 2019

Cited by 2 | Viewed by 3507

Abstract

This paper studies parameters of a lactation curve such as peak yield (PY) and persistency (P), which do not conform to the usual selection criteria in the Murciano-Granadina (MG) breed, but are considered to be an alternative to benefit animal welfare without reducing [...] Read more.

This paper studies parameters of a lactation curve such as peak yield (PY) and persistency (P), which do not conform to the usual selection criteria in the Murciano-Granadina (MG) breed, but are considered to be an alternative to benefit animal welfare without reducing production. Using 315,663 production records (of 122,883 animals) over a period of 24 years (1990–2014), genetic parameters were estimated with uni-, bi- and multivariate analysis using multiple trait derivative free restricted maximum likelihood (MTDFREML). The heritability (h²)/repeatability (r_e) of PY, yield (Y) and P was estimated as 0.13/0.19, 0.16/0.25 and 0.08/0.09 with the uni-trait and h² of bi- and multi-traits analysis ranging from 0.16 to 0.17 of Y, while that of PY and Y remained constant. Genetic correlations were high between PY–Y (0.94 ± 0.011) but low between PY–P (–0.16 ± 0.054 to –0.17 ± 0.054) and between Y–P (–0.06 ± 0.058 to –0.05 ± 0.058). Estimates of h²/r_e were low to intermediate. The selection for Y–PY or both can be implemented given the genetic correlation between these traits. PY–P and Y–P showed low to negligible correlation values indicating that if these traits are implemented in the early stages of evaluation, they would not be to the detriment of PY–Y. The combination of estimated breeding values (EBVs) for all traits would be a good criterion for selection. Full article

10 pages, 267 KiB

Open AccessArticle

Association of Ghrelin Gene Polymorphisms with Fattening Traits and Feed Intake in Pig: A Preliminary Study

by Mirosław Tyra, Katarzyna Ropka-Molik, Katarzyna Piórkowska, Maria Oczkowicz, Magdalena Szyndler-Nędza and Martyna Małopolska

Animals 2019, 9(7), 410; https://doi.org/10.3390/ani9070410 - 1 Jul 2019

Cited by 7 | Viewed by 3174

Abstract

Numerous studies have been conducted to explain the biological functions and mechanism of ghrelin (GHRL) action in animals. However, the exact role of ghrelin in the regulation of growth and development in pigs is still unclear. The ghrelin gene is considered to be [...] Read more.

Numerous studies have been conducted to explain the biological functions and mechanism of ghrelin (GHRL) action in animals. However, the exact role of ghrelin in the regulation of growth and development in pigs is still unclear. The ghrelin gene is considered to be a good candidate marker for the identification of economically important traits in pig production such as feed intake, growth or carcass quality. The objectives of the present study were to investigate the regulatory regions and coding sequence of the porcine GHRL gene and determine the effect of polymorphisms at the ghrelin gene locus on selected fattening traits. Data were obtained from 346 gilts (pure breeds: Landrace, 188; Duroc, 74; Pietrain, 84). The PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) method was used to detect polymorphisms within GHRL. Three polymorphisms were found, one in the promoter region (c.-93A>G) and two in the 3’UTR sequence (g.4428T>C; g.4486C>T). A significant (p ≤ 0.01) additive effect on daily gain (negative) and age at slaughter (positive) was obtained at the locus c.-93A>G. However, the most promising mutation was at the locus g.4486C > T, which is associated with total feed intake. Overall, the described GHRL polymorphisms may be useful as molecular markers in pig selection but future studies are required. Full article

12 pages, 4316 KiB

Open AccessArticle

Characterization of Circular RNAs in Chinese Buffalo (Bubalus bubalis) Adipose Tissue: A Focus on Circular RNAs Involved in Fat Deposition

by Jieping Huang, Jinhui Zhao, Qiuzhi Zheng, Shuzhe Wang, Xuefeng Wei, Fen Li, Jianghua Shang, Chuzhao Lei and Yun Ma

Animals 2019, 9(7), 403; https://doi.org/10.3390/ani9070403 - 1 Jul 2019

Cited by 25 | Viewed by 3319

Abstract

Circular RNAs (circRNAs) have been identified as a novel type of regulators involved in multiple biological processes. However, circRNAs with a potential function in fat deposition in buffalo are poorly understood. In this study, six RNA libraries of adipose tissue were constructed for [...] Read more.

Circular RNAs (circRNAs) have been identified as a novel type of regulators involved in multiple biological processes. However, circRNAs with a potential function in fat deposition in buffalo are poorly understood. In this study, six RNA libraries of adipose tissue were constructed for three young and three adult Chinese buffaloes with paired-ends RNA sequencing using the Illumina HiSeq 3000 platform. A total of 5141 circRNAs were computationally identified. Among them, 252 circRNAs were differentially expressed (DE) between the young and adult buffaloes. Of these, 54 were upregulated and 198 were downregulated in the adult group. Eight DE circRNAs were further identified by quantitative real-time-PCR (qRT-PCR) and Sanger sequencing. Co-expression analysis revealed that 34 circRNAs demonstrated a strong correlation with fat deposition-associated genes (|r| > 0.980). Among these, expressional correlation between two circRNAs (19:45387150|45389986 and 21:6969877|69753491) and PR/SET domain 16 was further verified using qRT-PCR, and a strong correlation was revealed (1 > |r| > 0.8). These results strongly suggest that circRNAs 19:45387150|45389986 and 21:6969877|69753491 are potential regulators of buffalo fat deposition. In summary, this study characterized the circRNA profiles of adipose tissues at different stages for the first time and revealed two circRNAs strongly correlated with fat deposition-associated genes, which provided new candidate regulators for fat deposition in buffalo. Full article

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14 pages, 1174 KiB

Open AccessArticle

Two Insertion/Deletion Variants within SPAG17 Gene Are Associated with Goat Body Measurement Traits

by Sihuan Zhang, Enhui Jiang, Ke Wang, Yu Zhang, Hailong Yan, Lei Qu, Hong Chen, Xianyong Lan and Chuanying Pan

Animals 2019, 9(6), 379; https://doi.org/10.3390/ani9060379 - 21 Jun 2019

Cited by 36 | Viewed by 4249

Abstract

Sperm-associated antigen 17 (SPAG17) gene encodes a multifunctional cytoplasmic protein, which influences not only reproduction but also skeletal development related body measurement traits, especially body height. Thus, this study aimed to identify crucial insertion-deletion (indel) variations, which influence the body measurement [...] Read more.

Sperm-associated antigen 17 (SPAG17) gene encodes a multifunctional cytoplasmic protein, which influences not only reproduction but also skeletal development related body measurement traits, especially body height. Thus, this study aimed to identify crucial insertion-deletion (indel) variations, which influence the body measurement traits of goats in large goat populations (n = 1725). As a result, two intronic indels (14 bp and 17 bp indel) were identified by sequencing. For the two indel loci, the distributions of genotypes and alleles were significantly different between the Shaanbei white cashmere goat (SBWC) and the Hainan black goat (HNBG). In SBWC goats, the different genotypes of the 14 bp indel were markedly associated with goat body height, chest width, body length and chest depth. The genotypes of the 17 bp indel were significantly related to body height and chest width. At the two loci, for all seven analyzed traits of SBWC goat, the growth data of DD homozygotes were the worst, which means that the 14 bp insertion and the 17 bp deletion were beneficial and detrimental variations, respectively. Moreover, the combined genotypes were significantly related to body height and chest width of SBWC goats and ten traits of HNBG. These results suggested that the 14 and 17 bp indels within SPAG17 can be used in goat growth related traits marker-assisted selection breeding, especially body height. Full article

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17 pages, 1969 KiB

Open AccessArticle

Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

by Shuqi Diao, Shuwen Huang, Zhiting Xu, Shaopan Ye, Xiaolong Yuan, Zanmou Chen, Hao Zhang, Zhe Zhang and Jiaqi Li

Animals 2019, 9(6), 361; https://doi.org/10.3390/ani9060361 - 16 Jun 2019

Cited by 22 | Viewed by 4789

Abstract

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. [...] Read more.

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs. Full article

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13 pages, 1911 KiB

Open AccessArticle

Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

by Haile Berihulay, Rabiul Islam, Lin Jiang and Yuehui Ma

Animals 2019, 9(6), 350; https://doi.org/10.3390/ani9060350 - 13 Jun 2019

Cited by 16 | Viewed by 4458

Abstract

Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the [...] Read more.

Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r² and D’ values, respectively. The average r² between all the populations varied little and ranged from 0.055 r² for the Jining Grey to 0.128 r² for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations. Full article

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13 pages, 2837 KiB

Open AccessArticle

Genomic Analysis Reveals Specific Patterns of Homozygosity and Heterozygosity in Inbred Pigs

by Ligang Wang, Yulian Mu, Linyang Xu, Kui Li, Jianlin Han, Tianwen Wu, Lan Liu, Qian Gao, Ying Xia, Guanyu Hou, Shulin Yang, Xiaohong He, George E. Liu and Shutang Feng

Animals 2019, 9(6), 314; https://doi.org/10.3390/ani9060314 - 1 Jun 2019

Cited by 8 | Viewed by 4595

Abstract

The inbred strain of miniature pig is an ideal model for biomedical research due to its high level of homozygosity. In this study, we investigated genetic diversity, relatedness, homozygosity, and heterozygosity using the Porcine SNP60K BeadChip in both inbred and non-inbred Wuzhishan pigs [...] Read more.

The inbred strain of miniature pig is an ideal model for biomedical research due to its high level of homozygosity. In this study, we investigated genetic diversity, relatedness, homozygosity, and heterozygosity using the Porcine SNP60K BeadChip in both inbred and non-inbred Wuzhishan pigs (WZSPs). Our results from multidimensional scaling, admixture, and phylogenetic analyses indicated that the inbred WZSP, with its unique genetic properties, can be utilized as a novel genetic resource for pig genome studies. Inbreeding depression and run of homozygosity (ROH) analyses revealed an average of 61 and 12 ROH regions in the inbred and non-inbred genomes of WZSPs, respectively. By investigating ROH number, length, and distribution across generations, we further briefly studied the impacts of recombination and demography on ROH in these WZSPs. Finally, we explored the SNPs with higher heterozygosity across generations and their potential functional implications in the inbred WZSP. We detected 56 SNPs showing constant heterozygosity with He = 1 across six generations in inbred pigs, while only one was found in the non-inbred population. Among these SNPs, we observed nine SNPs located in swine RefSeq genes, which were found to be involved in signaling and immune processes. Together, our findings indicate that the inbred-specific pattern of homozygosity and heterozygosity in inbred pigs can offer valuable insights for elucidating the mechanisms of inbreeding in farm animals. Full article

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13 pages, 1282 KiB

Open AccessArticle

A Fast and Powerful Empirical Bayes Method for Genome-Wide Association Studies

by Tianpeng Chang, Julong Wei, Mang Liang, Bingxing An, Xiaoqiao Wang, Bo Zhu, Lingyang Xu, Lupei Zhang, Xue Gao, Yan Chen, Junya Li and Huijiang Gao

Animals 2019, 9(6), 305; https://doi.org/10.3390/ani9060305 - 31 May 2019

Cited by 2 | Viewed by 3578

Abstract

Linear mixed model (LMM) is an efficient method for GWAS. There are numerous forms of LMM-based GWAS methods. However, improving statistical power and computing efficiency have always been the research hotspots of the LMM-based GWAS methods. Here, we proposed a fast empirical Bayes [...] Read more.

Linear mixed model (LMM) is an efficient method for GWAS. There are numerous forms of LMM-based GWAS methods. However, improving statistical power and computing efficiency have always been the research hotspots of the LMM-based GWAS methods. Here, we proposed a fast empirical Bayes method, which is based on linear mixed models. We call it Fast-EB-LMM in short. The novelty of this method is that it uses a modified kinship matrix accounting for individual relatedness to avoid competition between the locus of interest and its counterpart in the polygene. This property has increased statistical power. We adopted two special algorithms to ease the computational burden: Eigenvalue decomposition and Woodbury matrix identity. Simulation studies showed that Fast-EB-LMM has significantly increased statistical power of marker detection and improved computational efficiency compared with two widely used GWAS methods, EMMA and EB. Real data analyses for two carcass traits in a Chinese Simmental beef cattle population showed that the significant single-nucleotide polymorphisms (SNPs) and candidate genes identified by Fast-EB-LMM are highly consistent with results of previous studies. We therefore believe that the Fast-EB-LMM method is a reliable and efficient method for GWAS. Full article

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12 pages, 870 KiB

Open AccessArticle

Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array

by Zezhao Wang, Haoran Ma, Lei Xu, Bo Zhu, Ying Liu, Farhad Bordbar, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, Shengli Zhang, Lingyang Xu and Junya Li

Animals 2019, 9(6), 296; https://doi.org/10.3390/ani9060296 - 30 May 2019

Cited by 19 | Viewed by 4963

Abstract

Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of [...] Read more.

Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of genome selection signatures in Chinese Wagyu cattle. In total, we obtained 478,903 SNPs and 24,820 no-overlap regions for |iHS| (integrated haplotype score) estimations. Under the threshold of the top 1%, 239 regions were finally identified as candidate selected regions and 162 candidate genes were found based on the UMD3.1 genome assembly. These genes were reported to be associated with fatty acids, such as Bos taurus nitric oxide synthase 1 adaptor protein (NOS1AP), Bos taurus hydroxysteroid 17-beta dehydrogenase 7 (HSD17B7), Bos taurus WD repeat domain 7 (WDR7), Bos taurus ELOVL fatty acid elongase 2 (ELOVL2), Bos taurus calpain 1 (CAPN1), Bos taurus parkin RBR E3 ubiquitin protein ligase (PRKN, also known as PARK2), Bos taurus mitogen-activated protein kinase kinase 6 (MAP2K6), meat quality, including Bos taurus ADAM metallopeptidase domain 12 (ADAM12), Bos taurus 5′-aminolevulinate synthase 1 (ALAS1), Bos taurus small integral membrane protein 13 (SMIM13) and Bos taurus potassium two pore domain channel subfamily K member 2 (KCNK2), growth, and developmental traits, such as Bos taurus insulin like growth factor 2 receptor (IGF2R), Bos taurus RAR related orphan receptor A (RORA), Bos taurus fibroblast growth factor 14 (FGF14), Bos taurus paired box 6 (PAX6) and Bos taurus LIM homeobox 6 (LHX6). In addition, we identified several genes that are associated with body size and weight, including Bos taurus sorting nexin 29 (SNX29), Bos taurus zinc finger imprinted 2 (ZIM2), Bos taurus family with sequence similarity 110 member A (FAM110A), immune system, including Bos taurus toll like receptor 9 (TLR9), Bos taurus TAFA chemokine like family member 1 (TAFA1), Bos taurus glutathione peroxidase 8 (putative) (GPX8), Bos taurus interleukin 5 (IL5), Bos taurus PR domain containing 9 (PRDM9), Bos taurus glutamate ionotropic receptor kainate type subunit 2 (GRIK2) and feed intake efficiency, Bos taurus sodium voltage-gated channel alpha subunit 9 (SCN9A), Bos taurus relaxin family peptide/INSL5 receptor 4 (RXFP4), Bos taurus RNA polymerase II associated protein 3 (RPAP3). Moreover, four GO terms of biological regulation (GO:0009987, GO:0008152) and metabolic process (GO:0003824, GO:0005488) were found based on these genes. In addition, we found that 232 candidate regions (~18 Mb) overlapped with the Quantitative trait loci (QTL)regions extracted from cattle QTLdb. Our findings imply that many genes were selected for important traits in Chinese Wagyu cattle. Moreover, these results can contribute to the understanding of the genetic basis of the studied traits during the formation of this population. Full article

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13 pages, 1647 KiB

Open AccessArticle

Differential Expression of KCNJ12 Gene and Association Analysis of Its Missense Mutation with Growth Traits in Chinese Cattle

by Jie Cheng, Wenwen Peng, Xiukai Cao, Yongzhen Huang, Xianyong Lan, Chuzhao Lei and Hong Chen

Animals 2019, 9(5), 273; https://doi.org/10.3390/ani9050273 - 24 May 2019

Cited by 9 | Viewed by 3583

Abstract

The potassium inwardly rectifying channel, subfamily J, member 12 (KCNJ12) gene is a promising candidate for economic traits because of its crucial roles in myoblast development. Here, a missense mutation (Cys > Arg) was first detected to be located in exon [...] Read more.

The potassium inwardly rectifying channel, subfamily J, member 12 (KCNJ12) gene is a promising candidate for economic traits because of its crucial roles in myoblast development. Here, a missense mutation (Cys > Arg) was first detected to be located in exon 3 of KCNJ12 from three Chinese cattle breeds by DNA-pool sequencing. Then, we performed an association analysis of this single-nucleotide polymorphism (SNP) with stature in three Chinese cattle populations (n = 820). A significantly positive correlation was revealed by a reduced animal general linear model and the CC genotype was the most favorable in three breeds. Further, we measured the expression profile of the KCNJ12 gene in various cattle tissues and primary bovine skeletal muscle cells. Ubiquitous expression with high abundance in muscle was observed. Further, in primary bovine skeletal muscle cells, the KCNJ12 mRNA expression was gradually up-regulated in differentiation medium (DM) compared with that in growth medium (GM), suggesting that the KCNJ12 gene is involved in bovine myocyte differentiation. Conclusively, the KCNJ12 gene is a functional candidate gene which can be used as a molecular marker for cattle breeding. Full article

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10 pages, 614 KiB

Open AccessArticle

Genetic Mutation Analysis of High and Low IgY Chickens by Capture Sequencing

by Qiao Wang, Fei Wang, Lu Liu, Qinghe Li, Ranran Liu, Maiqing Zheng, Huanxian Cui, Jie Wen and Guiping Zhao

Animals 2019, 9(5), 272; https://doi.org/10.3390/ani9050272 - 23 May 2019

Cited by 39 | Viewed by 3671

Abstract

Based on the results of our previous genome-wide association study (GWAS), a comprehensive analysis on single nucleotide polymorphisms (SNPs) was performed on White Leghorn and Beijing-You chickens with high and low IgY levels in defined genomic regions using the capture-sequencing approach. High and [...] Read more.

Based on the results of our previous genome-wide association study (GWAS), a comprehensive analysis on single nucleotide polymorphisms (SNPs) was performed on White Leghorn and Beijing-You chickens with high and low IgY levels in defined genomic regions using the capture-sequencing approach. High and low IgY chickens showed substantial genetic variations. In total, more than 30,000 SNPs were found in all four chicken groups, among which 1045 were non-synonymous mutations resulting in amino acids alterations. In total, 23,309 Indels were identified. Among the 1169 Indels that were found only in Beijing-You chickens, 702 were shared between high and low IgY chickens compared with the reference genome. There were 1016 Indels specific to the White Leghorn chickens, among which 188 were high IgY-specific, 134 were low IgY-specific and 694 were shared between the high and low IgY chicken lines. Many genetic mutations were located in the regulatory regions of important immunomodulatory genes, including TAP1, TAP2 and BF1. Our findings provide an in-depth understanding of genetic mutations in chicken microchromosomes. Full article

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24 pages, 2469 KiB

Open AccessArticle

Selection Decisions and Trait Preferences for Local and Imported Cattle and Sheep Breeds in Peri-/Urban Livestock Production Systems in Ouagadougou, Burkina Faso

by Regina Roessler

Animals 2019, 9(5), 207; https://doi.org/10.3390/ani9050207 - 30 Apr 2019

Cited by 11 | Viewed by 4078

Abstract

Background: Participatory approaches of designing livestock breeding programs for tropical production systems have been extensively applied for rural livestock, whereas the peri-/urban livestock production sector tends to be widely neglected. In order to ensure the viability of the commercial cattle and sheep production [...] Read more.

Background: Participatory approaches of designing livestock breeding programs for tropical production systems have been extensively applied for rural livestock, whereas the peri-/urban livestock production sector tends to be widely neglected. In order to ensure the viability of the commercial cattle and sheep production sector in Ouagadougou, Burkina Faso, structured breed improvement programs are needed. The study aims to better understand selection decisions of cattle and sheep breeders and their trait preferences for local and imported breeds. Methods: 49 cattle and 31 sheep breeders in peri-/urban areas of the city were approached in personal interviews. Data were analyzed in R version 3.5.1. Results: The main motivation for keeping cattle and sheep was to generate regular cash income through the selling of milk (cattle only) and surplus animals. Some (modern) breeders used imported breeds because of higher production performances. For imported cattle breeds, improved breeding technologies and management were applied to further enhance production outputs. Nevertheless, local livestock breeds were predominantly used due to their good adaptation. Conclusions: Selection decisions and trait preferences for local and imported cattle and sheep breeds were strongly based on performance traits. Especially sheep breeders, but also traditional cattle breeders, did not record performance traits and did not take conscious breeding decisions. Full article

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