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A Perspective on the Past and Future of Genetic Evaluations...
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A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 17029

Special Issue Editor

Prof. Dr. Deukhwan Lee

E-Mail Website
Guest Editor
Department of Animal Resource Science, Hankyong National University, Anseong, Korea
Interests: beef cattle breeding; genomic selection; computing program; swine breeding; quantitative genetics

Special Issue Information

Dear Colleagues,

Over the last half-century, genetic evaluations have undergone steady progress in animal breeding programs. The development of methodological in terms of genetic theory and statistics along with technological advances in computing has resulted in analyses with high power and performance. The application and development of genetic evaluations have played a pivotal role in successful and progressive selection in many important traits in the cattle industry. In the pre-genomic era, traditional selection using information on phenotypes and pedigree to predict breeding values were considered by long generation intervals. With the introduction of high-density SNP chips and the use of genomic information, breeding schemes are undergoing major restructuring worldwide. Additionally, the application of genomic evaluation has led to the inclusion of more traits in the selection indices so that there is growing interest in the introduction of novel traits. Therefore, the possibilities of recording phenotypic performance, breeding goals, and breeding programs need to be reassessed. Further, more studies are necessary to determine whether the genetic architecture of the traits of interest and the population structure can be influenced to improve genomic prediction accuracy. In this issue, we will describe the application of genetic evaluation when a trait in a population is evaluated for the first time; for this, it is important to compare the accuracy of predictions from several genomic models to those obtained with a pedigree-based model, and how these changes will affect the future of the cattle industry.

Prof. Dr. Deukhwan Lee
Guest Editor

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Keywords

  • genomic selection
  • cattle
  • breeding scheme
  • prediction accuracy
  • genetic parameters
  • heritability

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Published Papers (7 papers)

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Research

14 pages, 3615 KiB  
Article
Genetic Variations within the Bovine CRY2 Gene Are Significantly Associated with Carcass Traits
by Xuelan Li, Enhui Jiang, Kejing Zhang, Sihuan Zhang, Fugui Jiang, Enliang Song, Hong Chen, Peng Guo and Xianyong Lan
Animals 2022, 12(13), 1616; https://doi.org/10.3390/ani12131616 - 23 Jun 2022
Cited by 5 | Viewed by 2015
Abstract
As an important part of the circadian rhythm, the circadian regulation factor 2 of cryptochrome (CRY2), regulates many physiological functions. Previous studies have reported that CRY2 is involved in growth and development. However, the relationship between CRY2 gene polymorphism and cattle [...] Read more.
As an important part of the circadian rhythm, the circadian regulation factor 2 of cryptochrome (CRY2), regulates many physiological functions. Previous studies have reported that CRY2 is involved in growth and development. However, the relationship between CRY2 gene polymorphism and cattle carcass traits remains unclear. The aim of this study was to detect the possible variations of the CRY2 gene and elucidate the association between the CRY2 gene and carcass traits in the Shandong Black Cattle Genetic Resource (SDBCGR) population (n = 705). We identified a 24-bp deletion variation (CRY2-P6) and a 6-bp insertion variation (CRY2-P7) in the bovine CRY2 gene. The frequency of the homozygous II genotype is higher than the heterozygous ID genotype in both two loci. In addition, CRY2-P6 was consistent with HWE (p > 0.05). Importantly, the CRY2-P6 variant was significantly associated with 12 carcass traits, including gross weight, ribeye, high rib, thick flank, etc. and the II was the dominant genotype. The CRY2-P7 site was also significantly correlated with five traits (gross weight, beef-tongue, etc.). Collectively, these outcomes indicated that the two Indel loci in the CRY2 gene could be used for marker-assisted selection of cattle carcass traits. Full article
(This article belongs to the Special Issue A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle)
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13 pages, 2371 KiB  
Article
Runs of Homozygosity and Quantitative Trait Locus/Association for Semen Parameters in Selected Chinese and South African Beef Cattle
by Mamokoma Cathrine Modiba, Khathutshelo Agree Nephawe, Jun Wang, Nompilo Hlongwane, Khanyisile Hadebe, Wenfa Lu and Bohani Mtileni
Animals 2022, 12(12), 1546; https://doi.org/10.3390/ani12121546 - 14 Jun 2022
Cited by 2 | Viewed by 2147
Abstract
In this study, runs of homozygosity (ROH) and quantitative trait locus/association (QTL) for semen parameters in selected Chinese and South African beef cattle breed were estimated. The computed results showed 7516 ROH were observed between classes 0–5 Mb with no ROH observed in [...] Read more.
In this study, runs of homozygosity (ROH) and quantitative trait locus/association (QTL) for semen parameters in selected Chinese and South African beef cattle breed were estimated. The computed results showed 7516 ROH were observed between classes 0–5 Mb with no ROH observed in classes >40 Mb. Distribution of ROH showed high level of genomic coverage for ANG, NGU, CSI, and BEL breeds. Approximately 13 genomic regions with QTL were controlling sperm motility, sperm concentration, semen volume, sperm count, sperm head abnormalities, sperm tail abnormalities, sperm integrity, and percentage of abnormal sperm traits. Nine candidate genes, CDF9, MARCH1, WDR19, SLOICI, ST7, DOP1B, CFAF9, INHBA, and ADAMTS1, were suggested to be associated with above mentioned QTL traits. The results for inbreeding coefficient showed moderate correlation between FROH vs FHOM at 0.603 and high correlation between FROH 0–5 Mb 0.929, and lowest correlation for 0–>40 Mb 0.400. This study suggested recent inbreeding in CSI, BEL, ANG, BON, SIM, and NGU breeds. Furthermore, it highlighted varied inbreeding levels and identified QTL for semen traits and genes of association. These results can assist in implementation of genetic improvement strategies for bulls and provide awareness and proper guidelines in developing breeding programs. Full article
(This article belongs to the Special Issue A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle)
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18 pages, 4652 KiB  
Article
m6A Methylases Regulate Myoblast Proliferation, Apoptosis and Differentiation
by Xinran Yang, Chugang Mei, Xinhao Ma, Jiawei Du, Jianfang Wang and Linsen Zan
Animals 2022, 12(6), 773; https://doi.org/10.3390/ani12060773 - 18 Mar 2022
Cited by 13 | Viewed by 2708
Abstract
N6-methyladenosine (m6A) plays an important role in regulating gene expression. Previous studies found that m6A methylation affects skeletal muscle development. However, the effect of m6A methylases on bovine skeletal myogenesis is still unclear. Here, we [...] Read more.
N6-methyladenosine (m6A) plays an important role in regulating gene expression. Previous studies found that m6A methylation affects skeletal muscle development. However, the effect of m6A methylases on bovine skeletal myogenesis is still unclear. Here, we found that the expression of m6A demethylases (FTO and ALKBH5) was significantly higher in the longissimus dorsi muscle of adult cattle than in newborn cattle. In contrast, the expression of m6A methyltransferases (METTL3, METTL14 and WTAP) was reduced. The mRNA expression of all five genes was found to be increased during the myogenesis of myoblasts in vitro. Knockdown of FTO or METTL3 promoted myoblast proliferation, inhibited myoblast apoptosis and suppressed myogenic differentiation, whereas ALKBH5 knockdown had the opposite effect. METTL14 knockdown enhanced myoblast proliferation and impaired myogenic differentiation. WTAP knockdown attenuated proliferation and contributed to apoptosis but did not affect differentiation. Furthermore, the functional domains of these five m6A methylases are conserved across species. Our results suggest that m6A methylases are involved in regulating skeletal muscle development and that there may be a complex network of m6A methylation regulating skeletal myogenesis. Full article
(This article belongs to the Special Issue A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle)
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10 pages, 305 KiB  
Article
Evaluation of Genetic Parameters of Growth of Pelibuey and Blackbelly Sheep through Pedigree in Mexico
by Víctor Rodríguez Hernandez, Vicente Vega Murillo, Roberto Germano Costa, Conrado Parraguirre Lezama, Maria De Los Angeles Valencia de Ita and Omar Romero-Arenas
Animals 2022, 12(6), 691; https://doi.org/10.3390/ani12060691 - 10 Mar 2022
Cited by 5 | Viewed by 2329
Abstract
Birth weight (BW) and weaning weight (WW) data from Pelibuey and Blackbelly lambs belonging to the Asociación Mexicana de Criadores de Ovinos (AMCO) were used with the objective of estimating genetic parameters (heritability and genetic correlations) and analyzing the growth characteristics of ewes [...] Read more.
Birth weight (BW) and weaning weight (WW) data from Pelibuey and Blackbelly lambs belonging to the Asociación Mexicana de Criadores de Ovinos (AMCO) were used with the objective of estimating genetic parameters (heritability and genetic correlations) and analyzing the growth characteristics of ewes born and weaned at different times of the same year from different herds with pedigree registration. In the case of Pelibuey lambs, the animal model included the weaning weight at 75 days of age, considering the direct additive genetic effect, maternal additive genetic effect, covariance between direct and maternal effects, as well as the permanent environmental effect of the mother. The direct estimators of heritability for Pelibuey were BW = 0.01 ± 0.021 and WW = 0.31 ± 0.074 and for Blackbelly they were BW = 0.05 ± 0.042 and WW = 0.41 ± 0.146. In the case of the maternal heritability estimators in Pelibuey they were BW = 0.02 ± 0.040 and WW = 0.21 ± 0.121 and for Blackbelly they were BW = 0.12 ± 0.054 and WW = 0.28 ± 0.121. The magnitude of the estimates of genetic correlations between direct and maternal effects for adjusted weaning weight at 75 days of age indicate that genetic progress may be slow in a breeding program. However, these selection results could be included in the short term in the breeding programs for the Pelibuey and Blackbelly breeds in Mexico, for livestock development in low-income rural areas. Full article
(This article belongs to the Special Issue A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle)
10 pages, 285 KiB  
Article
Estimation of Genetic Correlations of Primal Cut Yields with Carcass Traits in Hanwoo Beef Cattle
by Masoumeh Naserkheil, Deukmin Lee, Kihoon Chung, Mi Na Park and Hossein Mehrban
Animals 2021, 11(11), 3102; https://doi.org/10.3390/ani11113102 - 30 Oct 2021
Cited by 6 | Viewed by 1997
Abstract
This study was carried out to estimate the variance components, heritability, and genetic correlations between the carcass traits and primal cut yields in Hanwoo cattle. Carcass traits comprising 5622 records included back fat thickness (BFT), carcass weight (CW), eye muscle area (EMA), and [...] Read more.
This study was carried out to estimate the variance components, heritability, and genetic correlations between the carcass traits and primal cut yields in Hanwoo cattle. Carcass traits comprising 5622 records included back fat thickness (BFT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS). The 10 primal cut yields from 3467 Hanwoo steers included the tenderloin (TLN), sirloin (SLN), striploin (STLN), chuck (CHK), brisket (BSK), top round (TRD), bottom round (BRD), rib (RB), shank (SK), and flank (FK). In addition, three composite traits were formed by combining primal cut yields as novel traits according to consumer preferences and market price: high-value cuts (HVC), medium-value cuts (MVC), and low-value cuts (LVC). Heritability estimates for the interest of traits were moderate to high, ranging from 0.21 ± 0.04 for CHK to 0.59 ± 0.05 for MS. Except genetic correlations between RB and other primal cut traits, favorable and moderate to high correlations were observed among the yields of primal cut that ranged from 0.38 ± 0.14 (CHK and FK) to 0.93 ± 0.01 (TRD and BRD). Moreover, the estimated genetic correlations of CW and EMA with primal cut yields and three composite traits were positive and moderate to strong, except for BFT, which was negative. These results indicate that genetic progress can be achieved for all traits, and selection to increase the yields of primal cuts can lead to considerable profitability in the Hanwoo beef industry. Full article
(This article belongs to the Special Issue A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle)
12 pages, 963 KiB  
Article
Combinations of Linear Type Traits Affecting the Longevity in Hungarian Holstein-Friesian Cows
by Evelin Török, István Komlósi, Viktor Szőnyi, Béla Béri, Gábor Mészáros and János Posta
Animals 2021, 11(11), 3065; https://doi.org/10.3390/ani11113065 - 27 Oct 2021
Cited by 9 | Viewed by 2028
Abstract
Several research studies confirm the association of the linear type traits with longevity, but only with one trait at a time. The aim of our study was to analyse the influence of combinations for linear type traits on longevity in the Hungarian Holstein-Friesian [...] Read more.
Several research studies confirm the association of the linear type traits with longevity, but only with one trait at a time. The aim of our study was to analyse the influence of combinations for linear type traits on longevity in the Hungarian Holstein-Friesian cows. Data were provided by four herds; the filtered dataset consisted of 17,717 cows. From the 14 available linear type traits, the most important combinations were identified based on principal components and cluster analysis. From the six identified combinations, only three (chest width-body depth, fore udder attachment-udder depth, angularity-rear udder height) proved to have a significant effect on longevity. A wide chest and deep body caused a high-risk ratio of culling. The lowest risk ratio was observed with cows having intermediate chest width and intermediate body depth. Very angular cows having low rear udder height were at the highest risk of culling. The lowest culling risk was found in cows with a lack of angularity and high rear udder height. Weak and loose fore udder along with deep udder had increased culling risk. Strong and tight fore udder subclasses were the most favourable as their risk ratios decreased towards the shallowing of udder depth. Full article
(This article belongs to the Special Issue A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle)
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9 pages, 257 KiB  
Article
Estimation of Genetic Parameters and Correlation between Yearling Ultrasound Measurements and Carcass Traits in Hanwoo Cattle
by Masoumeh Naserkheil, Deuk-Hwan Lee, Hong-Sik Kong, Jiyeon Seong and Hossein Mehrban
Animals 2021, 11(5), 1425; https://doi.org/10.3390/ani11051425 - 16 May 2021
Cited by 17 | Viewed by 2750
Abstract
Genetic parameters have a significant role in designing a breeding program and are required to evaluate economically important traits. The objective of this study was to estimate heritability and genetic correlation between yearling ultrasound measurements, such as backfat thickness (UBFT), eye muscle area [...] Read more.
Genetic parameters have a significant role in designing a breeding program and are required to evaluate economically important traits. The objective of this study was to estimate heritability and genetic correlation between yearling ultrasound measurements, such as backfat thickness (UBFT), eye muscle area (UEMA), intramuscular fat content (UIMF), and carcass traits, such as backfat thickness (BFT), carcass weight (CW), eye muscle area (EMA), marbling score (MS) at approximately 24 months of age, as well as yearling weight (YW) in Hanwoo bulls (15,796) and steers (5682). The (co) variance components were estimated using a multi-trait animal model. Moderate to high heritability estimates were obtained and were 0.42, 0.50, 0.56, and 0.59 for CW, EMA, BFT, and MS, respectively. Heritability estimates for yearling measurements of YW, UEMA, UBFT, and UIMF were 0.31, 0.32, 0.30, and 0.19, respectively. Favorable and strong genetic correlations were observed between UIMF and MS (0.78), UBFT and BFT (0.63), and UEMA and EMA (0.65). Moreover, the estimated genetic correlation between YW and CW was high (0.84) and relatively moderate between YW and EMA (0.43). These results suggest that genetic improvement can be achieved for carcass traits when using yearling ultrasound measurements as selection criteria in ongoing Hanwoo breeding programs. Full article
(This article belongs to the Special Issue A Perspective on the Past and Future of Genetic Evaluations for Economically Important Traits in Cattle)
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