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. 2022 Feb 24:13:789270.
doi: 10.3389/fgene.2022.789270. eCollection 2022.

The Association Between Genomic Heterozygosity and Carcass Merit in Cattle

David Kenny  1   2 , Tara R Carthy  3 , Craig P Murphy  2 , Roy D Sleator  2 , Ross D Evans  4 , Donagh P Berry  1
Affiliations

The Association Between Genomic Heterozygosity and Carcass Merit in Cattle

David Kenny et al. Front Genet. .

Abstract

The objective of the present study was to quantify the association between both pedigree and genome-based measures of global heterozygosity and carcass traits, and to identify single nucleotide polymorphisms (SNPs) exhibiting non-additive associations with these traits. The carcass traits of interest were carcass weight (CW), carcass conformation (CC) and carcass fat (CF). To define the genome-based measures of heterozygosity, and to quantify the non-additive associations between SNPs and the carcass traits, imputed, high-density genotype data, comprising of 619,158 SNPs, from 27,213 cattle were used. The correlations between the pedigree-based heterosis coefficient and the three defined genomic measures of heterozygosity ranged from 0.18 to 0.76. The associations between the different measures of heterozygosity and the carcass traits were biologically small, with positive associations for CW and CC, and negative associations for CF. Furthermore, even after accounting for the pedigree-based heterosis coefficient of an animal, part of the remaining variability in some of the carcass traits could be captured by a genomic heterozygosity measure. This signifies that the inclusion of both a heterosis coefficient based on pedigree information and a genome-based measure of heterozygosity could be beneficial to limiting bias in predicting additive genetic merit. Finally, one SNP located on Bos taurus (BTA) chromosome number 5 demonstrated a non-additive association with CW. Furthermore, 182 SNPs (180 SNPs on BTA 2 and two SNPs on BTA 21) demonstrated a non-additive association with CC, while 231 SNPs located on BTA 2, 5, 11, 13, 14, 18, 19 and 21 demonstrated a non-additive association with CF. Results demonstrate that heterozygosity both at a global level and at the level of individual loci contribute little to the variability in carcass merit.

Keywords: association analysis; carcass traits; dominance; genomic heterozygosity; heterosis; non-additive.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Manhattan plots showing–log10 (q-values) of the association between the additive [(A) graph] and dominance [(B) graph] effect of each single nucleotide polymorphism (SNP) from each Bos taurus (BTA) chromosome and the adjusted carcass weights. The red lines represent the threshold for significant (q values ≤0.01) SNPs.
FIGURE 2
FIGURE 2
Manhattan plots showing–log10 (q-values) of the association between the additive [(A) graph] and dominance [(B) graph] effect of each single nucleotide polymorphism (SNP) from each Bos taurus (BTA) chromosome and the adjusted carcass conformation scores. The red lines represent the threshold for significant (q values ≤0.01) SNPs.
FIGURE 3
FIGURE 3
Manhattan plots showing–log10 (q-values) of the association between the additive [(A) graph] and dominance [(B) graph] effect of each single nucleotide polymorphism (SNP) from each Bos taurus (BTA) chromosome and the adjusted carcass fat scores. The red lines represent the threshold for significant (q values ≤0.01) SNPs.
See this image and copyright information in PMC

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