Animals

2024

Jump to: 2023, 2022, 2021, 2020

22 pages, 2062 KiB

Open AccessReview

African Local Pig Genetic Resources in the Context of Climate Change Adaptation

by Lenox Pius, Shuntao Huang, George Wanjala, Zoltán Bagi and Szilvia Kusza

Animals 2024, 14(16), 2407; https://doi.org/10.3390/ani14162407 - 19 Aug 2024

Viewed by 814

Abstract

Africa is home to a wide diversity of locally adapted pig breeds whose genetic architecture offers important insights into livestock adaptation to climate change. However, the majority of these inherent traits have not been fully highlighted. This review presents an overview of the [...] Read more.

Africa is home to a wide diversity of locally adapted pig breeds whose genetic architecture offers important insights into livestock adaptation to climate change. However, the majority of these inherent traits have not been fully highlighted. This review presents an overview of the current state of African pig genetic resources, providing highlights on their population and production statistics, production system, population diversity indices, and genomic evidence underlying their evolutionary potential. The study results reveal an incomplete characterization of local pig genotypes across the continent. The characterized population, however, demonstrates moderate to high levels of genetic diversity, enough to support breeding and conservation programs. Owing to low genetic differentiation and limited evidence of distinct population structures, it appears that most local pig populations are strains within larger breeds. Genomic evidence has shown a higher number of selection signatures associated with various economically important traits, thus making them potential candidates for climate change adaptation. The reportedly early evidence of hybridization with wild suid groups further suggests untapped insights into disease resistance and resilience traits that need to be illuminated using higher-density markers. Nevertheless, gene introgression from commercial breeds is prevalent across Africa; thus, efforts to realize and utilize these traits must increase before they are permanently depleted. Full article

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15 pages, 4864 KiB

Open AccessArticle

Characterizing the Phan Rang Sheep: A First Look at the Y Chromosome, Mitochondrial DNA, and Morphometrics

by Nguyen Ngoc Luong, Huynh Thi Thu Ha, Nguyen Xuan Huy, Bui Van Loi, Nguyen Huu Van, Hoang Tan Quang and Nguyen Hoang Loc

Animals 2024, 14(14), 2020; https://doi.org/10.3390/ani14142020 - 9 Jul 2024

Viewed by 800

Abstract

The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country’s sheep population. These provinces are known for [...] Read more.

The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country’s sheep population. These provinces are known for their high temperatures and frequent droughts. The long-standing presence of the Phan Rang sheep in these regions suggests their potential resilience to heat stress—a trait of increasing interest in the face of global climate change. Despite the breed’s significance, a critical knowledge gap hinders conservation and breeding programs. To address this, our study employed a two-pronged approach. First, we collected body conformational data to aid in breed identification. Second, we analyzed mitochondrial DNA (D-loop) and Y chromosome markers (SRY and SRYM18) to elucidate the maternal and paternal lineages. Among the 68 Phan Rang sheep analyzed for their D-loop, 19 belonged to mitochondrial haplogroup A, while 49 belonged to haplogroup B. The haplogroups can be subdivided into 16 unique haplotypes. All 19 rams surveyed for their paternal lineages belonged to haplotypes H5 and H6. These findings strongly support the hypothesis of dual origins for the Phan Rang sheep. This study presents the first genetic data for the Phan Rang breed, providing crucial insights for future research and conservation efforts. Full article

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12 pages, 1157 KiB

Open AccessArticle

Pedigree-Based Genetic Diversity in the South African Boerboel Dog Breed

by Ripfumelo Success Mabunda, Khathutshelo Agree Nephawe, Bohani Mtileni and Mahlako Linah Makgahlela

Animals 2024, 14(6), 975; https://doi.org/10.3390/ani14060975 - 21 Mar 2024

Cited by 1 | Viewed by 1814

Abstract

The Boerboel dog breed (BBD) is indigenous to South Africa (SA) and plays an important role in safeguarding homes and farms. The Department of Agriculture, Land Reform, and Rural Development (DALRRD) classifies the BBD as a protected species, and it is valued for [...] Read more.

The Boerboel dog breed (BBD) is indigenous to South Africa (SA) and plays an important role in safeguarding homes and farms. The Department of Agriculture, Land Reform, and Rural Development (DALRRD) classifies the BBD as a protected species, and it is valued for its intelligence, boldness, and strength, as well as for continually ensuring the safety of its owners. The aim of this study was to investigate genetic diversity within the BBD population using pedigree information. The original BBD data, which contained 87,808 records, were obtained from the Integrated Registration and Genetic Information System (INTERGIS). After editing, the pedigree data included 87,755 records of animals born between 1971 and 2019. Pedigree analyses were performed using PEDIG (Fortran 77 software) to determine the completeness, inbreeding coefficients, and genetic diversity as defined by the genetic contributions of the most important ancestors of the current animals. This study identified 91.2% inbred animals in the BBD population, with an average and maximum inbreeding of 7.5% and 50% of inbred animals, respectively. The estimated inbreeding rate per year was 0.20% with an effective population size of 83.1. The most influential ancestors explained 82.63% and 80.92% of the total genetic variation for males and females in the studied populations, respectively. Only 10 important ancestors explained more than 50% of the entire population’s genetic diversity. The numbers of founders (

f

) were 348 and 356, and the effective numbers of founders (

f_{e}

) were 57.4 and 60.1, respectively, for males and females. The numbers of founders were higher than the effective numbers of founders, implying a loss of genetic diversity due to unequal founder contributions. The BBD population was not critically endangered based on the inbreeding rates and effective population size; however, the population experienced a significant loss of genetic variability, unequal genetic contributions by founders, and a genetic bottleneck. Future breeding strategies could benefit from using equal proportions of parent stock and including new genetically distant breeds. Full article

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11 pages, 1524 KiB

Open AccessArticle

Analysis of Genetic Diversity in Romanian Carpatina Goats Using SNP Genotyping Data

by Bogdan Alin Vlaic, Augustin Vlaic, Isa-Rita Russo, Licia Colli, Michael William Bruford, Antonia Odagiu, Pablo Orozco-terWengel and CLIMGEN Consortium

Animals 2024, 14(4), 560; https://doi.org/10.3390/ani14040560 - 7 Feb 2024

Cited by 2 | Viewed by 1499

Abstract

Animal husbandry is one of man’s oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. [...] Read more.

Animal husbandry is one of man’s oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country’s goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (H_E), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The N_e has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the N_e trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed. Full article

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2023

Jump to: 2024, 2022, 2021, 2020

14 pages, 2344 KiB

Open AccessArticle

Variations in Casein Genes Are Associated with Milk Protein and Fat Contents in Sarda Goats (Capra hircus), with an Important Role of CSN1S2 for Milk Yield

by Maria Luisa Dettori, Michele Pazzola, Antonia Noce, Vincenzo Landi and Giuseppe Massimo Vacca

Animals 2024, 14(1), 56; https://doi.org/10.3390/ani14010056 - 22 Dec 2023

Cited by 2 | Viewed by 1466

Abstract

This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, [...] Read more.

This work aimed to assess the variability of casein genes in a population of 153 bucks and 825 lactating does of the Sarda breed, and to perform association analysis between polymorphic sites and milk yield and composition traits. To genotype the casein genes, we chose an SNP panel including 44 SNPs mapping to the four casein genes CSN1S1, CSN2, CSN1S2, and CSN3. Genotyping (made by KASP™ genotyping assay, based on competitive allele-specific PCR) revealed the high variability of the Sarda goat, and haplotype analysis revealed linkage disequilibrium (LD) between CSN1S1 and CSN2 genes, in addition to two LD blocks within the CSN1S2 and two LD blocks within the CSN3 gene, in bucks and does. Association analysis revealed that variability at all four casein genes was associated with milk protein content, total solids, and milk energy. The three Ca-sensitive casein genes were associated with lipid content, and CSN1S2 showed a unique pattern, with intron variants associated with milk yield, in addition to milk pH, NaCl, and SCS (Somatic Cell Score). This information might prove useful in selection schemes and in future investigations aiming to better understand the biology of lactation, and the direct link between genotype and phenotype. Full article

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12 pages, 267 KiB

Open AccessArticle

Investigating How Genetic Merit and Country of Origin Impact the Profitability of Grass-Based Sheep Production Systems

by Nicola Fetherstone, Fiona M. McGovern, Noirin McHugh, Tommy M. Boland and Alan Bohan

Animals 2023, 13(18), 2908; https://doi.org/10.3390/ani13182908 - 13 Sep 2023

Viewed by 1184

Abstract

The objective of this study was to simulate and assess the profitability of sheep production systems that varied in maternal genetic merit (high or low) and country of origin (New Zealand (NZ) or Ireland), using the Teagasc Lamb Production Model (TLPM). A production [...] Read more.

The objective of this study was to simulate and assess the profitability of sheep production systems that varied in maternal genetic merit (high or low) and country of origin (New Zealand (NZ) or Ireland), using the Teagasc Lamb Production Model (TLPM). A production system study performed at Teagasc Athenry, Co. Galway, Ireland, from 2016 to 2019, inclusive, provided key animal performance input parameters, which were compared across three scenarios: high maternal genetic merit NZ (NZ), high maternal genetic merit Irish (High Irish) and low maternal genetic merit Irish (Low Irish). Prior to the beginning of the study ewes and rams were imported from New Zealand to Ireland in order to compare animals within the same management system. Ewes were selected based on the respective national maternal genetic indexes; i.e., either the New Zealand Maternal Worth (NZ group) or the €uro-star Replacement index (Irish groups). The TLPM was designed to simulate the impact of changes in physical and technical outputs (such as number of lambs, drafting rates and replacement rates) on a range of economic parameters including variable costs, fixed costs, gross margin and net profit. Results showed that total farm costs (variable and fixed) were similar across the three scenarios, driven by the similar number of ewes in each scenario. The number of lambs produced and the cost of production per lamb was 14.05 lambs per hectare for the NZ scenario at a cost of EUR 82.35 per lamb, 11.40 lambs per hectare for the High Irish scenario at a cost of EUR 101.42 per lamb and 11.00 lambs per hectare for the Low Irish scenario at a cost of EUR 105.72 per lamb. The net profit of the three scenarios was EUR 514, EUR 299, and EUR 258 per hectare, for the NZ, High Irish and Low Irish scenarios, respectively. Overall, the NZ scenario had a lower cost of production in comparison to either Irish group, while the High Irish scenario had a 14% greater net profit than the Low Irish scenario, equating to an additional EUR 41 per hectare net profit. Output from this simulation model reiterates the importance, for overall farm profitability, of maximising the number of lambs weaned per hectare, particularly through maximising income and diluting the total farm costs. To conclude, the use of high-maternal-genetic-merit animals, regardless of their country of origin impacts farm profitability. Full article

11 pages, 272 KiB

Open AccessArticle

Porcine Reproductive and Respiratory Syndrome (PRRS) and CD163 Resistance Polymorphic Markers: What Is the Scenario in Naturally Infected Pig Livestock in Central Italy?

by Martina Torricelli, Anna Fratto, Marcella Ciullo, Carla Sebastiani, Chiara Arcangeli, Andrea Felici, Samira Giovannini, Francesca Maria Sarti, Marco Sensi and Massimo Biagetti

Animals 2023, 13(15), 2477; https://doi.org/10.3390/ani13152477 - 31 Jul 2023

Cited by 3 | Viewed by 1622

Abstract

Porcine Reproductive and Respiratory Syndrome (PRRS) caused by the PRRS virus affects farmed pigs worldwide, causing direct and indirect losses. The most severe manifestations of PRRS infection are observed in piglets and pregnant sows. The clinical outcome of the infection depends on the [...] Read more.

Porcine Reproductive and Respiratory Syndrome (PRRS) caused by the PRRS virus affects farmed pigs worldwide, causing direct and indirect losses. The most severe manifestations of PRRS infection are observed in piglets and pregnant sows. The clinical outcome of the infection depends on the PRRSV strain’s virulence, the pregnancy state of the female, environmental factors, the presence of protective antibodies due to previous infections, and the host’s genetic susceptibility. The latter aspect was investigated in this study, in particular, evaluating the most significant polymorphisms (SNPs) of the CD163 gene in slaughtered pigs reared in Central Italy. Total RNAs were extracted from 377 swine samples and subjected to RT-PCR targeted to the CD163 gene, followed by sequencing analysis. Contextually, the viral RNA was detected by RT-qPCR in order to phenotypically categorize animals into infected and not infected. In particular, 36 haplotypes were found, and their frequencies ranged from 0.13% to 35.15%. There were 62 resulting genotypes, three of which were associated with a putative resistance to the disease. Both the haplotypes and genotypes were inferred by PHASE v.2.1 software. To the best of our knowledge, this type of investigation was conducted for the first time on pig livestock distributed in different regions of Central Italy. Thus, the obtained findings may be considered very important since they add useful information about swine genetic background in relation to PRRS infection, from the perspective of adopting Marker-Assisted Selection (MAS) as a possible and alternative strategy to control this still widespread disease. Full article

14 pages, 2180 KiB

Open AccessArticle

Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses

by Mohamed Machmoum, Bouabid Badaoui, Daniel Petit, Agnès Germot, Moulay Abdelaziz El Alaoui, Ismaïl Boujenane and Mohammed Piro

Animals 2023, 13(12), 2021; https://doi.org/10.3390/ani13122021 - 17 Jun 2023

Cited by 1 | Viewed by 2066

Abstract

Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a [...] Read more.

Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin culture. To that end, we collected 211 hair samples from stud farms renowned for breeding Arabian show horses from Nejd KSA, Bahrain, Egypt, Qatar, Morocco, UAE, and Poland. The phylogenetic and network analyses of the whole mitochondrial DNA D-loop sequence highlighted a great genetic diversity among the Arabian horse populations, in which about 75% of variance was assigned to populations and 25% to strains. The discriminant analysis of principal components illustrated a relative distinction between those populations. A clear subdivision between traditional strains was found in PL, in contrast to the situation of DB and EG populations. However, several Polish horse individuals could not be traced back to the Bedouin tribes by historical documentation and were shown to differ genetically from other studied Bedouin strains, hence motivating extended investigations. Full article

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11 pages, 1577 KiB

Open AccessArticle

An Analysis of DNA Sequence Polymorphism in the Swamp Buffalo Toll-like Receptor (TLR2) Gene

by Wootichai Kenchaiwong, Pongphol Pongthaisong, Srinuan Kananit, Monchai Duangjinda and Wuttigrai Boonkum

Animals 2023, 13(12), 2012; https://doi.org/10.3390/ani13122012 - 16 Jun 2023

Viewed by 1694

Abstract

Toll-like receptors (TLRs) are transmembrane proteins important for directing immune responses. Their primary role is to recognize pathogens based on single-nucleotide polymorphism (SNP) characteristics. TLR2 is categorized as a pattern recognition receptor (PRR) that is important for the recognition of pathogens. Nucleotide variation [...] Read more.

Toll-like receptors (TLRs) are transmembrane proteins important for directing immune responses. Their primary role is to recognize pathogens based on single-nucleotide polymorphism (SNP) characteristics. TLR2 is categorized as a pattern recognition receptor (PRR) that is important for the recognition of pathogens. Nucleotide variation in the coding region determines the conformation of the TLR protein, affecting its protein domain efficiency. This study aimed to identify SNPs in the coding region of TLR2 to enhance available genetic tools for improving health and production in swamp buffalo. A total of 50 buffaloes were randomly sampled from the northeastern part of Thailand for genomic DNA extraction and sequencing. Nucleotide sequences were aligned and compared with cattle and river buffalo based on the database. The results showed, there were 29 SNP locations in swamp buffalo and 14 different locations in both cattle and buffaloes. Haplotype analysis revealed that 27 haplotypes occurred. Swamp buffalo were identified from 13 SNPs based on biallelic analysis, which found eight synonymous and five nonsynonymous SNPs. Nucleotide diversity (π) was 0.16, indicating genetic diversity. Genetic diversity (haplotype diversity; HD) was high at 0.99 ± 0.04. This indicates a high probability that the two sample haplotypes are different. The π and HD values are important indicators of the genetic diversity of the swamp buffalo population. In summary, the Thai swamp buffalo population detected a polymorphism of the coding region of the TRL2 gene. Therefore, further, in-depth study of the relationship between these genes in the immune system and disease resistance should be recommended. Full article

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14 pages, 3059 KiB

Open AccessArticle

Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations

by Ziqi Zhong, Ziyi Wang, Xinfeng Xie, Shuaishuai Tian, Feifan Wang, Qishan Wang, Shiheng Ni, Yuchun Pan and Qian Xiao

Animals 2023, 13(12), 2010; https://doi.org/10.3390/ani13122010 - 16 Jun 2023

Cited by 9 | Viewed by 2116

Abstract

Indigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, [...] Read more.

Indigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, the number of these pig populations has decreased sharply, largely due to a decrease in growth rate and poor lean meat percentage. For effective conservation of these genetic resources (such as heat tolerance, meat quality and disease resistance), the whole-genome sequencing data of 78 individuals from 3 native Chinese pig populations, including Wuzhishan (WZS), Tunchang (TC) and Dingan (DA), were obtained using a 150 bp paired-end platform, and 25 individuals from two foreign breeds, including Landrace (LR) and Large White (LW), were downloaded from a public database. A total of 28,384,282 SNPs were identified, of which 27,134,233 SNPs were identified in native Chinese pig populations. Both genetic diversity statistics and linkage disequilibrium (LD) analysis indicated that indigenous pig populations displayed high genetic diversity. The result of population structure implied the uniqueness of each native Chinese pig population. The selection signatures were detected between indigenous pig populations and foreign breeds by using the population differentiation index (F_ST) method. A total of 359 candidate genes were identified, and some genes may affect characteristics such as immunity (IL-2, IL-21 and ZFYVE16), adaptability (APBA1), reproduction (FGF2, RNF17, ADAD1 and HIPK4), meat quality (ABCA1, ADIG, TLE4 and IRX5), and heat tolerance (VPS13A, HSPA4). Overall, the findings of this study will provide some valuable insights for the future breeding, conservation and utilization of these three Chinese indigenous pig populations. Full article

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10 pages, 2824 KiB

Open AccessArticle

Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas (Vicugna pacos) in Southern Peru

by Deyanira Figueroa, Flor-Anita Corredor, Ruben H. Mamani-Cato, Roberto F. Gallegos-Acero, Nicoll Condori-Rojas, Richard Estrada, Lizeth Heredia, Wilian Salazar, Carlos Quilcate and Carlos I. Arbizu

Animals 2023, 13(9), 1552; https://doi.org/10.3390/ani13091552 - 5 May 2023

Viewed by 2737

Abstract

The alpaca population mostly consists of the Huacaya phenotype and is widely distributed in Southern Peru. This study aimed to estimate the genetic diversity and population structure of two Huacaya alpaca populations (Ajoyani and Quimsachata) using fourteen and twelve microsatellite markers for each [...] Read more.

The alpaca population mostly consists of the Huacaya phenotype and is widely distributed in Southern Peru. This study aimed to estimate the genetic diversity and population structure of two Huacaya alpaca populations (Ajoyani and Quimsachata) using fourteen and twelve microsatellite markers for each population, respectively. A total of 168 alpaca biological samples were outsourced to Peruvian laboratories for DNA extraction and genotyping. For genetic diversity, observed heterozygosity (H_o), expected heterozygosity (H_e), polymorphism information content (PIC), and fixation indices values were estimated. An admixture analysis was performed for the population structure analysis. Different programs were used for these estimations. In total, 133 (Ajoyani) and 129 (Quimsachata) alleles were found, with a range of 4 to 17 by locus. The mean H_O, H_E, and PIC per marker for Ajoyani were 0.764 ± 0.112, 0.771 ± 0.1, and 0.736; for Quimsachata, they were 0.783 ± 0.087, 0.773 ± 0.095, and 0.738, respectively. The population structure showed no structure with K = 2. This study provides useful indicators for the creation of appropriate alpaca conservation programs. Full article

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19 pages, 2908 KiB

Open AccessArticle

Genetic Diversity and Trends of Ancestral and New Inbreeding in German Sheep Breeds by Pedigree Data

by Cathrin Justinski, Jens Wilkens and Ottmar Distl

Animals 2023, 13(4), 623; https://doi.org/10.3390/ani13040623 - 10 Feb 2023

Cited by 8 | Viewed by 2303

Abstract

In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of [...] Read more.

In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of rams may risk losing genetic diversity and increasing rates of inbreeding. On the other hand, breeds with a low number of founder animals and only regional popularity may not leave their endangered status, as the number of breeders interested in the breed is limited. The objective of the present study was to determine demographic measures of genetic diversity and recent as well as ancestral trends of inbreeding in all autochthonous German sheep breeds and sheep of all breeding directions, including wool, meat, and milk. We used pedigree data from 1,435,562 sheep of 35 different breeds and a reference population of 981,093 sheep, born from 2010 to 2020. The mean number of equivalent generations, founders, effective founders, effective ancestors, and effective founder genomes were 5.77, 1669, 123.2, 63.5, and 33.0, respectively. Genetic drift accounted for 69% of the loss of genetic diversity, while loss due to unequal founder contributions was 31%. The mean inbreeding coefficient, individual rate of inbreeding (∆F_i), and realized effective population size across breeds were 0.031, 0.0074, and 91.4, respectively, with a significantly decreasing trend in ∆F_i in 11/35 breeds. New inbreeding, according to Kalinowski, contributed to 71.8% of individual inbreeding, but ancestral inbreeding coefficients showed an increasing trend in all breeds. In conclusion, in our study, all but one of the mountain-stone sheep breeds and the country sheep breed Wald were the most vulnerable populations, with N_e < 50. The next most endangered breeds are exotic, country, and heath breeds, with average N_e of 66, 83, and 89, respectively. The wool, meat, and milk breeds showed the highest genetic diversity, with average N_e of 158, 120, and 111, respectively. The results of our study should help strengthen conservation program efforts for the most endangered sheep breeds and maintain a high genetic diversity in all sheep breeds. Full article

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2022

Jump to: 2024, 2023, 2021, 2020

11 pages, 551 KiB

Open AccessArticle

Characterization of the Sarcidano Horse Coat Color Genes

by Giovanni Cosso, Vincenzo Carcangiu, Sebastiano Luridiana, Stefania Fiori, Nicolò Columbano, Gerolamo Masala, Giovanni Mario Careddu, Eraldo Sanna Passino and Maria Consuelo Mura

Animals 2022, 12(19), 2677; https://doi.org/10.3390/ani12192677 - 5 Oct 2022

Cited by 3 | Viewed by 1893

Abstract

The goal of this study was to contribute to the general knowledge of the Sarcidano Horse, both by the identification of the genetic basis of the coat color and by updating the exact locations of the genotyping sites, based on the current EquCab3.0 [...] Read more.

The goal of this study was to contribute to the general knowledge of the Sarcidano Horse, both by the identification of the genetic basis of the coat color and by updating the exact locations of the genotyping sites, based on the current EquCab3.0 genome assembly version. One-hundred Sarcidano Horses, living in semi-feral condition, have been captured to perform health and biometric checks. From that total number, 70 individual samples of whole blood were used for DNA extraction, aimed to characterize the genetic basis of the coat color. By genotyping and sequencing analyses of the MC1R Exon 1 and ASIP Exon 3, a real image of the coat color distribution in the studied population has been obtained. Chestnut and Black resulted in the most representative coat colors both from a phenotypic and genotypic point of view, that is suggestive of no human domestication or crossbreeding with domestic breed. Due to its ancient origin and genetic isolation, an active regional plan for the conservation of this breed would be desirable, focused on maintenance of resident genotypes and genetic resources. Collection and management of DNA, sperm, embryos, with the involvement of research centers and Universities, could be a valid enhancing strategy. Full article

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14 pages, 6252 KiB

Open AccessArticle

Genome-Wide Population Structure and Selection Signatures of Yunling Goat Based on RAD-seq

by Yuming Chen, Rong Li, Jianshu Sun, Chunqing Li, Heng Xiao and Shanyuan Chen

Animals 2022, 12(18), 2401; https://doi.org/10.3390/ani12182401 - 13 Sep 2022

Cited by 5 | Viewed by 2438

Abstract

Animal diseases impose a huge burden on the countries where diseases are endemic. Conventional control strategies of vaccines and veterinary drugs are to control diseases from a pharmaceutical perspective. Another alternative approach is using pre-existing genetic disease resistance or tolerance. We know that [...] Read more.

Animal diseases impose a huge burden on the countries where diseases are endemic. Conventional control strategies of vaccines and veterinary drugs are to control diseases from a pharmaceutical perspective. Another alternative approach is using pre-existing genetic disease resistance or tolerance. We know that the Yunling goat is an excellent local breed from Yunnan, southwestern China, which has characteristics of strong disease resistance and remarkable adaptability. However, genetic information about the selection signatures of Yunling goats is limited. We reasoned that the genes underlying the observed difference in disease resistance might be identified by investigating selection signatures between two different goat breeds. Herein, we selected the Nubian goat as the reference group to perform the population structure and selection signature analysis by using RAD-seq technology. The results showed that two goat breeds were divided into two clusters, but there also existed gene flow. We used Fst (F-statistics) and π (pi/θπ) methods to carry out selection signature analysis. Eight selected regions and 91 candidate genes were identified, in which some genes such as DOK2, TIMM17A, MAVS, and DOCK8 related to disease and immunity and some genes such as SPEFI, CDC25B, and MIR103 were associated with reproduction. Four GO (Gene Ontology) terms (GO:0010591, GO:001601, GO:0038023, and GO:0017166) were associated with cell migration, signal transduction, and immune responses. The KEGG (Kyoto Encyclopedia of Genes and Genomes) signaling pathways were mainly associated with immune responses, inflammatory responses, and stress reactions. This study preliminarily revealed the genetic basis of strong disease resistance and adaptability of Yunling goats. It provides a theoretical basis for the subsequent genetic breeding of disease resistance of goats. Full article

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10 pages, 1072 KiB

Open AccessCommunication

Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages

by Ying Yuan, Weiyi Zhang, Chengli Liu, Yongmeng He, Haoyuan Zhang, Lu Xu, Baigao Yang, Yongju Zhao, Yuehui Ma, Mingxing Chu, Zhongquan Zhao, Yongfu Huang, Yanguo Han, Yan Zeng, Hangxing Ren, Gaofu Wang and Guangxin E

Animals 2022, 12(11), 1356; https://doi.org/10.3390/ani12111356 - 26 May 2022

Cited by 5 | Viewed by 2249

Abstract

Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection [...] Read more.

Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, F_ST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats. Full article

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10 pages, 3217 KiB

Open AccessArticle

The Transcription Regulator YgeK Affects Biofilm Formation and Environmental Stress Resistance in Avian Pathogenic Escherichia coli

by Mei Xue, Dandan Fu, Jiangang Hu, Ying Shao, Jian Tu, Xiangjun Song and Kezong Qi

Animals 2022, 12(9), 1160; https://doi.org/10.3390/ani12091160 - 30 Apr 2022

Cited by 5 | Viewed by 1971

Abstract

Avian pathogenic Escherichia coli (APEC) is one of the most common pathogens in poultry and a potential gene source of human extraintestinal pathogenic E. coli (ExPEC), leading to serious economic losses in the poultry industry and public health concerns. Exploring the pathogenic mechanisms [...] Read more.

Avian pathogenic Escherichia coli (APEC) is one of the most common pathogens in poultry and a potential gene source of human extraintestinal pathogenic E. coli (ExPEC), leading to serious economic losses in the poultry industry and public health concerns. Exploring the pathogenic mechanisms underpinning APEC and the identification of new targets for disease prevention and treatment are warranted. YgeK is a transcriptional regulator in APEC and is localized to the type III secretion system 2 of E. coli. In our previous work, the transcription factor ygeK significantly affected APEC flagella formation, bacterial motility, serum sensitivity, adhesion, and virulence. To further explore ygeK functions, we evaluated its influence on APEC biofilm formation and resistance to environmental stress. Our results showed that ygeK inactivation decreased biofilm formation and reduced bacterial resistance to environmental stresses, including acid and oxidative stress. In addition, the multi-level regulation of ygeK in APEC was analyzed using proteomics, and associations between differentially expressed proteins and the key targets of ygeK were investigated. Overall, we identified ygeK’s new function in APEC. These have led us to better understand the transcriptional regulatory ygeK and provide new clues about the pathogenicity of APEC. Full article

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11 pages, 1724 KiB

Open AccessArticle

Genetic Variability Trend of Lusitano Horse Breed Reared in Italy

by Maria Cristina Cozzi, Paolo Valiati, Maria Longeri, Carlos Ferreira and Sofia Abreu Ferreira

Animals 2022, 12(1), 98; https://doi.org/10.3390/ani12010098 - 1 Jan 2022

Cited by 4 | Viewed by 2841

Abstract

The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using [...] Read more.

The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975–1990, 1991–2000, 2001–2010, 2010–2019). Standard genetic diversity parameters, including observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE; P-Val), allelic richness, and inbreeding coefficient (F_is) were estimated. In the whole period, the total population showed Ho as high as 0.69, low F_is (0.057), and imbalance for HWE. When considering the unrelated horses, Ho was seen to increase over time (from 0.594 in 1975–1990 to 0.68 in 2010–2019) and frequencies were in HWE, again having low and decreasing values of Fis (from 0.208 in 1975–1990 to 0.019 in 2010–2019). Bottleneck analysis excluded a recent population decline. Principal Coordinate Analysis at the individual level defined two clusters, the major cluster including all the most recent horses. An increasing number of dams (156% more from 2001–2010 to 2011–2019) supports the good variability recorded in the population so far. However, the high number of foals (77.2%) sired by only four stallions in recent years suggests caution in the choice of the sires for the future. Full article

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2021

Jump to: 2024, 2023, 2022, 2020

13 pages, 2439 KiB

Open AccessArticle

Investigating Genetic and Phenotypic Variability of Queen Bees: Morphological and Reproductive Traits

by Elena Facchini, Maria Grazia De Iorio, Federica Turri, Flavia Pizzi, Daniela Laurino, Marco Porporato, Rita Rizzi and Giulio Pagnacco

Animals 2021, 11(11), 3054; https://doi.org/10.3390/ani11113054 - 26 Oct 2021

Cited by 10 | Viewed by 3193

Abstract

The quality of the honeybee queen has an important effect on a colony’s development, productivity, and survival. Queen failure or loss is considered a leading cause for colonies’ mortality worldwide. The queen’s quality, resulting from her genetic background, developmental conditions, mating success, and [...] Read more.

The quality of the honeybee queen has an important effect on a colony’s development, productivity, and survival. Queen failure or loss is considered a leading cause for colonies’ mortality worldwide. The queen’s quality, resulting from her genetic background, developmental conditions, mating success, and environment, can be assessed by some morphological measures. The study aims to investigate variability for traits that could assess the quality of the queen. Related animals were enrolled in this study. Variance components were estimated fitting a mixed animal model to collected data. Heritabilities of body and tagmata weights ranged from 0.46 to 0.54, whereas lower estimates were found for the tagmata width and wing length. Heritabilities estimated for the spermatheca diameter and volume, number of ovarioles, and number of sperms were 0.17, 0.88, 0.70, and 0.57, respectively. Many phenotypic correlations related to size were high and positive, while weak correlations were found between morphology and reproductive traits. Introducing a queen’s traits in a selection program could improve colonies’ survivability. Further research should focus on better defining the correlations between the individual qualities of a queen and her colony’s performance. Full article

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12 pages, 285 KiB

Open AccessFeature PaperArticle

Polymorphisms at Myostatin Gene (MSTN) and the Associations with Sport Performances in Anglo-Arabian Racehorses

by Emanuela Pira, Giuseppe Massimo Vacca, Maria Luisa Dettori, Gianpiera Piras, Massimiliano Moro, Pietro Paschino and Michele Pazzola

Animals 2021, 11(4), 964; https://doi.org/10.3390/ani11040964 - 30 Mar 2021

Cited by 10 | Viewed by 3076

Abstract

One hundred and eighty Anglo-Arabian horses running 1239 races were sampled for the present study. DNA was extracted from the blood and myostatin gene, MSTN, was genotyped. Moreover, prizes won and places were achieved for the 1239 races to perform association analyses [...] Read more.

One hundred and eighty Anglo-Arabian horses running 1239 races were sampled for the present study. DNA was extracted from the blood and myostatin gene, MSTN, was genotyped. Moreover, prizes won and places were achieved for the 1239 races to perform association analyses between the different genotypes and sport traits. Two SNPs already reported in previous studies regarding the Thoroughbred breed, rs69472472 and rs397152648, were revealed as polymorphic. The linkage disequilibrium analysis investigating the haplotype structure of MSTN did not evidence any association block. Polymorphism at SNP rs397152648, previously known as g.66493737 T>C, significantly influenced sport traits, with heterozygous horses TC showing better results than homozygotes TT. The portion of variance due to the random effect of the individual animal, and the other phenotypic effects of sex, percentage of Arabian blood and race distance, computed together with the genotype at MSTN in the statistical models, exerted a significant influence. Hence, this information is useful to improve knowledge of the genetic profile of Anglo-Arabian horses and a possible selection for better sport performance. Full article

11 pages, 1710 KiB

Open AccessCommunication

Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies

by Yang Li, Lei Pu, Liangyu Shi, Hongding Gao, Pengfei Zhang, Lixian Wang and Fuping Zhao

Animals 2021, 11(3), 806; https://doi.org/10.3390/ani11030806 - 13 Mar 2021

Cited by 17 | Viewed by 3028

Abstract

The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic [...] Read more.

The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10—98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs. Full article

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21 pages, 1823 KiB

Open AccessReview

Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

by Miguel A. Gutierrez-Reinoso, Pedro M. Aponte and Manuel Garcia-Herreros

Animals 2021, 11(3), 599; https://doi.org/10.3390/ani11030599 - 25 Feb 2021

Cited by 38 | Viewed by 9032

Abstract

Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The [...] Read more.

Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future. Full article

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8 pages, 262 KiB

Open AccessArticle

The Polymorphism in Various Milk Protein Genes in Polish Holstein-Friesian Dairy Cattle

by Magdalena Kolenda and Beata Sitkowska

Animals 2021, 11(2), 389; https://doi.org/10.3390/ani11020389 - 3 Feb 2021

Cited by 10 | Viewed by 2662

Abstract

The aim of the present study was to evaluate the genotype and allele frequencies of 24 polymorphisms in casein alpha S1 (CSN1S1), casein alpha S2 (CSN1S2), beta-casein (CSN2), kappa-casein (CSN3), and progestagen-associated endometrial protein (PAEP) genes. The study included 1900 Polish Black and [...] Read more.

The aim of the present study was to evaluate the genotype and allele frequencies of 24 polymorphisms in casein alpha S1 (CSN1S1), casein alpha S2 (CSN1S2), beta-casein (CSN2), kappa-casein (CSN3), and progestagen-associated endometrial protein (PAEP) genes. The study included 1900 Polish Black and White Holstein-Friesian dairy cows that were subjected to genotyping via microarrays. A total of 24 SNPs (Single Nucleotide Polymorphisms) within tested genes were investigated. Two CSN1S1 SNPs were monomorphic, while allele CSN1S1_3*G in CSN1S1_3 SNP dominated with a frequency of 99.39%. Out of seven CSN2 SNPs, four were polymorphic; however, only for CSN2_3 all three genotypes were detected. Only three out of nine SNPs within CSN3 were monomorphic. Three PAEP SNPs were also found to be polymorphic with heterozygotes being most frequent. Hardy–Weinberg equilibrium (HWE) was observed for eight variants. It was shown that only CSN3_6 was not in HWE. The fact that many of investigated SNPs were monomorphic may suggest that in the past the reproduction program favored one of these genotypes. SNPs that are included in commercially available microarrays should be monitored in relation to changes in their frequencies. If a SNP has turned monomorphic, maybe it should be considered for removal from the microarray. Full article

27 pages, 1909 KiB

Open AccessArticle

Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses

by Carmen Marín Navas, Juan Vicente Delgado Bermejo, Amy Katherine McLean, José Manuel León Jurado, Antonio Rodriguez de la Borbolla y Ruiberriz de Torres and Francisco Javier Navas González

Animals 2021, 11(2), 269; https://doi.org/10.3390/ani11020269 - 21 Jan 2021

Cited by 25 | Viewed by 4199

Abstract

Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of [...] Read more.

Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei’s distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright’s fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders’ gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively). Full article

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2020

Jump to: 2024, 2023, 2022, 2021

11 pages, 2990 KiB

Open AccessArticle

Transcriptome Sequencing and Comparative Analysis of Amphoteric ESCs and PGCs in Chicken (Gallus gallus)

by Kai Jin, Jing Zhou, Qisheng Zuo, Jiuzhou Song, Yani Zhang, Guobing Chang, Guohong Chen and Bichun Li

Animals 2020, 10(12), 2228; https://doi.org/10.3390/ani10122228 - 27 Nov 2020

Cited by 4 | Viewed by 2718

Abstract

Chicken (Gallus gallus) pluripotent embryonic stem cells (ESCs) and primordial germ cells (PGCs) can be broadly applied in the research of developmental and embryonic biology, but the difference between amphoteric ESCs and PGCs is still elusive. This study determined the sex [...] Read more.

Chicken (Gallus gallus) pluripotent embryonic stem cells (ESCs) and primordial germ cells (PGCs) can be broadly applied in the research of developmental and embryonic biology, but the difference between amphoteric ESCs and PGCs is still elusive. This study determined the sex of collected samples by identifying specific sex markers via polymerase chain reaction (PCR) and fluorescence activated cell sorter (FACS). RNA-seq was utilized to investigate the transcriptomic profile of amphoteric ESCs and PGCs in chicken. The results showed no significant differentially expressed genes (DEGs) in amphoteric ESCs and 227 DEGs exhibited in amphoteric PGCs. Moreover, those 227 DEGs were mainly enriched in 17 gene ontology (GO) terms and 27 pathways according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Furthermore, qRT-PCR was performed to verify RNA-seq results, and the results demonstrated that Notch1 was highly expressed in male PGCs. In summary, our results provided a knowledge base of chicken amphoteric ESCs and PGCs, which is helpful for future research in relevant biological processes. Full article

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13 pages, 1312 KiB

Open AccessArticle

Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers

by Maria Luisa Dettori, Elena Petretto, Michele Pazzola, Oriol Vidal, Marcel Amills and Giuseppe Massimo Vacca

Animals 2020, 10(12), 2194; https://doi.org/10.3390/ani10122194 - 24 Nov 2020

Viewed by 2240

Abstract

A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on [...] Read more.

A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The F_ST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations. Full article

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17 pages, 3056 KiB

Open AccessArticle

The Mediation of miR-34a/miR-449c for Immune Cytokines in Acute Cold/Heat-Stressed Broiler Chicken

by Tao Li, Yiping Song, Xiuyu Bao and Jianqin Zhang

Animals 2020, 10(11), 2168; https://doi.org/10.3390/ani10112168 - 20 Nov 2020

Cited by 7 | Viewed by 2365

Abstract

An increasing amount of evidence has revealed that microRNAs (miRNAs) participated in immune regulation and reaction to acute cold and heat stresses. As a new type of post-transcriptional regulatory factor, miRNA has received widespread attention; However, the specific mechanism used for this regulation [...] Read more.

An increasing amount of evidence has revealed that microRNAs (miRNAs) participated in immune regulation and reaction to acute cold and heat stresses. As a new type of post-transcriptional regulatory factor, miRNA has received widespread attention; However, the specific mechanism used for this regulation still needs to be determined. In this study, thirty broilers at the same growth period were divided into three groups and treated with different temperature and humidity of CS (10–15 °C and 90% Relative Humidity (RH)), HS (39 °C and 90% RH), and NS (26 °C and 50–60% RH) respectively. After 6 h, splenic tissues were collected from all study groups. miRNA sequencing was performed to identify the differentially expressed miRNAs (DEMs) between HS, CS, and NS. We found 33, 37, and 7 DEMs in the HS-NS, HS-CS, CS-NS group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEMs were significantly enriched in cytokine–cytokine receptor interaction and functioned as the cellular responders to stress. We chose two miRNA, miR-34a and miR-449c, from the same family and differential expressed in HS-CS and HS-NS group, as the research objects to predict and verify the target genes. The dual-luciferase reporter assay and quantitative real-time PCR (qRT-PCR) confirmed that two cytokines, IL-2 and IL-12α, were the direct target genes of miR-34a and miR-449c. To further understand the mediation mechanism of miRNAs in acute cold/heat-stressed broiler chicken, a splenic cytokines profile was constructed. The results showed that IL-1β was strongly related to acute heat stress in broiler chicken, and from this we predicted that the increased expression of IL-1β might promote the expression of miR-34a, inducing the upregulation of interferon-γ (INF-γ) and IL-17. Our finds have laid a theoretical foundation for the breeding of poultry resistance and alleviation of the adverse effects of stress. Full article

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20 pages, 4732 KiB

Open AccessArticle

Genomic Characterization of the Istrian Shorthaired Hound

by Ivona Djurkin Kušec, Ivica Bošković, Minja Zorc, Kristina Gvozdanović, Dubravko Škorput, Peter Dovč and Goran Kušec

Animals 2020, 10(11), 2013; https://doi.org/10.3390/ani10112013 - 1 Nov 2020

Cited by 2 | Viewed by 3871

Abstract

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there [...] Read more.

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed. Full article

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22 pages, 2498 KiB

Open AccessArticle

Does Functionality Condition the Population Structure and Genetic Diversity of Endangered Dog Breeds under Island Territorial Isolation?

by José Manuel Alanzor Puente, Águeda Laura Pons Barro, Manuel Rafael de la Haba Giraldo, Juan Vicente Delgado Bermejo and Francisco Javier Navas González

Animals 2020, 10(10), 1893; https://doi.org/10.3390/ani10101893 - 16 Oct 2020

Cited by 8 | Viewed by 2773

Abstract

Despite the undefinition of the origins of Ca de Rater (CR) and Ca de Bestiar (CB) dogs, references to these endangered autochthonous breeds highlighted their ratting/pet and shepherding/guard skills for centuries. Genealogical historical records were traced back to founders. Founder number in the [...] Read more.

Despite the undefinition of the origins of Ca de Rater (CR) and Ca de Bestiar (CB) dogs, references to these endangered autochthonous breeds highlighted their ratting/pet and shepherding/guard skills for centuries. Genealogical historical records were traced back to founders. Founder number in the reference population (146 and 53 for CR and CB, respectively), historical and reference maximum generations traced (eight and seven for CR and CB, respectively), and historical average number of complete generations (1.04 for both breeds) were determined. Structure assessment revealed the existence of subpopulations regarding criteria such as breeders (75 and 17), breeder location (32 and eight), owners (368 and 198), and owner location (73 and 51) for CR and CB, respectively. Average inbreeding (F) within breed subpopulations ranged from 0.27–1.20% for CB breeders and the rest of subpopulation criteria for both breeds, respectively, except for CB owners and owner location. F ranged from 0.27–1.41% for CB historical population and CR current population, respectively. The study of genetic diversity revealed a relatively similar genetic background between subpopulations. Average coancestry between and within breeds suggested a similar evolutionary process. However, Mann–Whitney U test determined significant differences for diversity parameters (F, ΔR, coancestry, nonrandom mating degree, maximum, complete, and equivalent generations, ΔF, and genetic conservation index) between breeds and their functionalities. Conclusively, functionality in dog breeds may determine the genetic diversity evolution of endangered breeds, even when these share the same geographic isolation conditions. Full article

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18 pages, 2196 KiB

Open AccessArticle

Genomic Evaluation of Primiparous High-Producing Dairy Cows: Inbreeding Effects on Genotypic and Phenotypic Production–Reproductive Traits

by Miguel A. Gutiérrez-Reinoso, Pedro Manuel Aponte, Joel Cabezas, Lleretny Rodriguez-Alvarez and Manuel Garcia-Herreros

Animals 2020, 10(9), 1704; https://doi.org/10.3390/ani10091704 - 21 Sep 2020

Cited by 12 | Viewed by 4189

Abstract

The main objective of this study was to analyze the effects of the inbreeding degree in high-producing primiparous dairy cows genotypically and phenotypically evaluated and its impacts on production and reproductive parameters. Eighty Holstein–Friesian primiparous cows (age: ~26 months; ~450 kg body weight) [...] Read more.

The main objective of this study was to analyze the effects of the inbreeding degree in high-producing primiparous dairy cows genotypically and phenotypically evaluated and its impacts on production and reproductive parameters. Eighty Holstein–Friesian primiparous cows (age: ~26 months; ~450 kg body weight) were previously genomically analyzed to determine the Inbreeding Index (II) and were divided into two groups: low inbreeding group (LI: <2.5; n = 40) and high inbreeding group (HI: ≥2.5 and ≤5.0; n = 40). Genomic determinations of production and reproductive parameters (14 in total), together with analyses of production (12) and reproductive (11) phenotypic parameters (23 in total) were carried out. Statistically significant differences were obtained between groups concerning the genomic parameters of Milk Production at 305 d and Protein Production at 305 d and the reproductive parameter Daughter Calving Ease, the first two being higher in cows of the HI group and the third lower in the LI group (p < 0.05). For the production phenotypic parameters, statistically significant differences were observed between both groups in the Total Fat, Total Protein, and Urea parameters, the first two being higher in the LI group (p < 0.05). Also, significant differences were observed in several reproductive phenotypic parameters, such as Number of Services per Conception, Calving to Conception Interval, Days Open Post Service, and Current Inter-Partum Period, all of which negatively influenced the HI group (p < 0.05). In addition, correlation analyses were performed between production and reproductive genomic parameters separately and in each consanguinity group. The results showed multiple positive and negative correlations between the production and reproductive parameters independently of the group analyzed, being these correlations more remarkable for the reproductive parameters in the LI group and the production parameters in the HI group (p < 0.05). In conclusion, the degree of inbreeding significantly influenced the results, affecting different genomic and phenotypic production and reproductive parameters in high-producing primiparous cows. The determination of the II in first-calf heifers is crucial to evaluate the negative effects associated with homozygosity avoiding an increase in inbreeding depression on production and reproductive traits. Full article

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13 pages, 2376 KiB

Open AccessArticle

Transcriptional Regulator YqeI, Locating at ETT2 Locus, Affects the Pathogenicity of Avian Pathogenic Escherichia coli

by Mei Xue, Yating Xiao, Dandan Fu, Muhammad Akmal Raheem, Ying Shao, Xiangjun Song, Jian Tu, Ting Xue and Kezong Qi

Animals 2020, 10(9), 1658; https://doi.org/10.3390/ani10091658 - 16 Sep 2020

Cited by 14 | Viewed by 2674

Abstract

Avian pathogenic Escherichia coli (APEC) is the leading cause of systemic infections in poultry worldwide and has a hidden threat to public health. Escherichia coli type three secretion system 2 (ETT2), similar to the Salmonella pathogenicity island SPI1, is widely distributed in APEC [...] Read more.

Avian pathogenic Escherichia coli (APEC) is the leading cause of systemic infections in poultry worldwide and has a hidden threat to public health. Escherichia coli type three secretion system 2 (ETT2), similar to the Salmonella pathogenicity island SPI1, is widely distributed in APEC and associated with virulence. The function of YqeI, which is one of the hypothetical transcriptional regulators locating at the ETT2 locus of APEC, is unknown. In this study, we successfully obtained the mutant strain AE81ΔyqeI of the wild type strain AE81 and performed the transcriptional profiling assays. Additionally, the transcriptional sequencing results revealed that YqeI influenced localization, locomotion and biological adhesion and so on. The transmission electron microscope observation showed that the wild type strain AE81 possessed long curved flagella, whereas the mutant strain AE81ΔyqeI hardly had any. The strain AE81ΔyqeI exhibited lower motility than AE81 after culturing the dilute bacterial suspension on a semisolid medium. It was also found that the survival ability of AE81ΔyqeI weakened significantly when AE81ΔyqeI was cultured with 0%, 10%, 20%, 30%, 40% and 50% SPF serum in PBS, and AE81ΔyqeI had decreased adherence to DF-1 cells compared with AE81 in the bacterial adhesion assay. The bacterial colonization assay indicated that the virulence of AE81ΔyqeI was reduced in the heart, liver, spleen, and lung. These results confirmed that the transcription regulator YqeI is involved in APEC’s pathogenicity, and this study provides clues for future research. Full article

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13 pages, 1261 KiB

Open AccessCommunication

Maternal Origins and Haplotype Diversity of Seven Russian Goat Populations Based on the D-loop Sequence Variability

by Tatiana Deniskova, Nekruz Bakoev, Arsen Dotsev, Marina Selionova and Natalia Zinovieva

Animals 2020, 10(9), 1603; https://doi.org/10.3390/ani10091603 - 9 Sep 2020

Cited by 8 | Viewed by 3560

Abstract

The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai [...] Read more.

The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status. Full article

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11 pages, 376 KiB

Open AccessArticle

Analysis of Genetic Diversity in the Czech Spotted Dog

by Karolína Machová, Anita Kranjčevičová, Luboš Vostrý and Emil Krupa

Animals 2020, 10(8), 1416; https://doi.org/10.3390/ani10081416 - 14 Aug 2020

Cited by 10 | Viewed by 3174

Abstract

Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed—the Czech Spotted Dog (CSD). [...] Read more.

Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed—the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity—which was calculated based on the reference population and pedigree completeness—were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence. Full article

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