Genome–wide association study of carcass weight in commercial Hanwoo cattle

Edea, Zewdu; Jeoung, Yeong Ho; Shin, Sung-Sub; Ku, Jaeul; Seo, Sungbo; Kim, Il‐Hoi; Kim, Sang–Wook; Kim, Kwan‐Suk

doi:10.5713/ajas.17.0276

Cited by 26 publications

(21 citation statements)

References 46 publications

(60 reference statements)

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“…The QTL on BTA5 which contained the AMDHD1 gene, was located close to a QTL previously associated with carcass composition [43], whereas the QTL on BTA11 contains DYSF, a gene known to be linked with muscular dystrophy in humans [60]. The QTL on BTA14 contained the PREX2 gene which was previously linked to carcass weight in Hanwoo cattle [61].…”

Section: Other Candidate Genesmentioning

confidence: 83%

Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

et al. 2020

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Background: Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. Results:We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. Conclusions:The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future. © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article' s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article'

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Section: Other Candidate Genesmentioning

confidence: 83%

Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

et al. 2020

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“…On BTA12 the most frequent haplotype in Western Simmental cattle, with only a low frequency in the Russian population, contained five genes with different functions. From the production perspective, PARP4 influenced carcass weight in Hanwoo cattle (Edea et al, 2018), but also contributed to the environmental adaptation via DNA repair mechanisms (Edea et al, 2014). RNF17 was associated with fatty acid composition in Nelore cattle (Lemos et al, 2016), growth traits in Hanwoo cattle (Edea et al, 2018) and pigs (Puig-Oliveras et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

“…From the production perspective, PARP4 influenced carcass weight in Hanwoo cattle (Edea et al, 2018), but also contributed to the environmental adaptation via DNA repair mechanisms (Edea et al, 2014). RNF17 was associated with fatty acid composition in Nelore cattle (Lemos et al, 2016), growth traits in Hanwoo cattle (Edea et al, 2018) and pigs (Puig-Oliveras et al, 2014). MPHOSPH8 was up regulated in atretic follicles in cattle (Hatzirodos et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

Elevated haplotypes frequencies reveal similarities for selection signatures in Western and Russian Simmental populations

Mészáros¹,

Fornara²,

Reyer³

et al. 2019

JCEA

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This paper shows a straightforward, but surprisingly effective approach to detect genomic regions of importance, illustrated on two Simmental cattle populations. Medium density genomic data of 42 German/Austrian (denoted as "Western") and 38 Russian Simmental cattle were used to identify the most frequent haplotypes within the two populations. The haplotypes were defined as non-overlapping segments of ten single nucleotide ploymorphisms (SNP). The phasing was done with the SHAPEIT software, with a follow up analysis of haplotypes using the GHap package. Despite the low sample size a number of high frequency haplotypes could be identified accross the whole genome. The identified genes residing direcly in these high frequency haplotypes were extremely relevant for the dual purpose Simmental cattle. A large part of these genes influenced growth rate and carcass traits, others were relevant for the milk production. A smaller proportion was connected to the reproduction, immune system and cellular processes, with indirect influence on production traits.

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“…with hot carcass weight. Likewise, Edea et al [7] identified 17 and 16 QTLs that were significantly (p<0.01) associated with carcass weight under the additive and dominant models, respectively. They also mentioned that BTA 2, 6, 14, 22, and 24 loci were previously identified in several beef cattle breeds as QTL for carcass weight.…”

Section: Snp Marker 1)mentioning

confidence: 96%

“…Recently, genome-wide association studies using high density single nucleotide polymorphism (SNP) chips have been used to detect the genetics of quantitative trait loci (QTL) in several domestic livestock species [7]. For instance, carcass traits such as carcass weight, eye muscle area, back-fat thickness, and marbling score are the critical quantitative traits affecting beef cattle production [1].…”

Section: Introductionmentioning

confidence: 99%

Reduction of slaughter age of Hanwoo steers by early genotyping based on meat yield index

Jeong

Islam

Kim

et al. 2020

Asian-Australas J Anim Sci

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Objective: This study was conducted to determine early hereditary endowment to establish a short-term feeding program.Methods: Hanwoo steers (n = 140) were equally distributed into four groups (35/group) based on genetic meat yield index (MYI) viz. the greatest, great, low, and the lowest at Jukam Hanwoo farm, Goheung. All animals were fed in group pens (5 animals/pen) with similar feed depending on the growth stage. Rice straw was provided ad libitum, whereas concentrate was fed at 5.71 kg during the growing period (6 to 13 mo) and 9.4 kg during the fattening period (13 to 28 mo). Body weight (BW) was measured at two-month intervals, whereas carcass weight was determined at slaughtering at about 31 months of age. The Affymetrix Bovine Axiom Array 640K single nucleotide polymorphism (SNP) chip was used to determine the meat quantity-related gene in the blood.Results: After 6 months, the highest (p<0.05) BW was observed in the greatest MYI group (190.77 kg) and the lowest (p<0.05) in the lowest MYI group (173.51 kg). The great MYI group also showed significantly (p<0.05) higher BW than the lowest MYI group. After 16 and 24 months, the greatest MYI group had the highest BW gain (p<0.05) and were therefore slaughtered the earliest. Carcass weight was significantly (p<0.05) higher in the greatest and the great MYI groups followed by the low and the lowest MYI groups. Back-fat thickness in the greatest MYI group was highly correlated to carcass weight and marbling score. The SNP array analysis identified the carcass-weight related gene BTB-01280026 with an additive effect. The steers with the allele increasing carcass weight had heavier slaughter weight of about 12 kg.Conclusion: Genetic MYI is a potential tool for calf selection, which will reduce the slaughter age while simultaneously increasing carcass weight, back-fat thickness, and marbling score.

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Genome–wide association study of carcass weight in commercial Hanwoo cattle

Cited by 26 publications

References 46 publications

Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

Elevated haplotypes frequencies reveal similarities for selection signatures in Western and Russian Simmental populations

Reduction of slaughter age of Hanwoo steers by early genotyping based on meat yield index

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