Dataset Information

Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population.

ABSTRACT:

Background

The high narrow sense heritability of carcass traits suggests that the underlying additive genetic potential of an individual should be strongly correlated with both animal carcass quality and quantity, and therefore, by extension, carcass value. Therefore, the objective of the present study was to detect genomic regions associated with three carcass traits, namely carcass weight, conformation and fat cover, using imputed whole genome sequence in 28,470 dairy and beef sires from six breeds with a total of 2,199,926 phenotyped progeny.

Results

Major genes previously associated with carcass performance were identified, as well as several putative novel candidate genes that likely operate both within and across breeds. The role of MSTN in carcass performance was re-affirmed with the segregating Q204X mutation explaining 1.21, 1.11 and 5.95% of the genetic variance in carcass weight, fat and conformation, respectively in the Charolais population. In addition, a genomic region on BTA6 encompassing the NCAPG/LCORL locus, which is a known candidate locus associated with body size, was associated with carcass weight in Angus, Charolais and Limousin. Novel candidate genes identified included ZFAT in Angus, and SLC40A1 and the olfactory gene cluster on BTA15 in Charolais. Although the majority of associations were breed specific, associations that operated across breeds included SORCS1 on BTA26, MCTP2 on BTA21 and ARL15 on BTA20; these are of particular interest due to their potential informativeness in across-breed genomic evaluations. Genomic regions affecting all three carcass traits were identified in each of the breeds, although these were mainly concentrated on BTA2 and BTA6, surrounding MSTN and NCAPG/LCORL, respectively. This suggests that although major genes may be associated with all three carcass traits, the majority of genes containing significant variants (unadjusted p-value -?4) may be trait specific associations of small effect.

Conclusions

Although plausible novel candidate genes were identified, the proportion of variance explained by these candidates was minimal thus reaffirming that while carcass performance may be affected by major genes in the form of MSTN and NCAPG/LCORL, the majority of variance is attributed to the additive (and possibly multiplicative) effect of many polymorphisms of small effect.

SUBMITTER: Purfield DC

PROVIDER: S-EPMC6751660 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Publications

Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population.

Purfield D C DC Evans R D RD Berry D P DP

BMC genomics 20190918 1

<h4>Background</h4>The high narrow sense heritability of carcass traits suggests that the underlying additive genetic potential of an individual should be strongly correlated with both animal carcass quality and quantity, and therefore, by extension, carcass value. Therefore, the objective of the present study was to detect genomic regions associated with three carcass traits, namely carcass weight, conformation and fat cover, using imputed whole genome sequence in 28,470 dairy and beef sires fr ...[more]

PMID: 31533623

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Project description:BackgroundGenome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) dairy cattle. Whey protein (α-lactalbumin and β-lactoglobulin) and casein (αs1, αs2, β, and κ) contents were estimated by mid-infrared (MIR) spectrometry, with medium to high accuracy (0.59 ≤ R2 ≤ 0.92), for 848,068 test-day milk samples from 156,660 cows in the first three lactations. Milk composition was evaluated as average test-day measurements adjusted for environmental effects. Next, we genotyped a subset of 8080 cows (2967 MON, 2737 NOR, and 2306 HOL) with the BovineSNP50 Beadchip. For each breed, genotypes were first imputed to high-density (HD) using HD single nucleotide polymorphisms (SNPs) genotypes of 522 MON, 546 NOR, and 776 HOL bulls. The resulting HD SNP genotypes were subsequently imputed to the sequence level using 27 million high-quality sequence variants selected from Run4 of the 1000 Bull Genomes consortium (1147 bulls). Within-breed, multi-breed, and conditional GWAS were performed.ResultsThirty-four distinct genomic regions were identified. Three regions on chromosomes 6, 11, and 20 had very significant effects on milk composition and were shared across the three breeds. Other significant effects, which partially overlapped across breeds, were found on almost all the autosomes. Multi-breed analyses provided a larger number of significant genomic regions with smaller confidence intervals than within-breed analyses. Combinations of within-breed, multi-breed, and conditional analyses led to the identification of putative causative variants in several candidate genes that presented significant protein-protein interactions enrichment, including those with previously described effects on milk composition (SLC37A1, MGST1, ABCG2, CSN1S1, CSN2, CSN1S2, CSN3, PAEP, DGAT1, AGPAT6) and those with effects reported for the first time here (ALPL, ANKH, PICALM).ConclusionsGWAS applied to fine-scale phenotypes, multiple breeds, and whole-genome sequences seems to be effective to identify candidate gene variants. However, although we identified functional links between some candidate genes and milk phenotypes, the causality between candidate variants and milk protein composition remains to be demonstrated. Nevertheless, the identification of potential causative mutations that underlie milk protein composition may have immediate applications for improvements in cheese-making.

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Dataset Information

Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population.

Background

Results

Conclusions

Publications

Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population.

Similar Datasets

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