DataSheet1_The Association Between Genomic Heterozygosity and Carcass Merit in Cattle.docx

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.

本研究旨在量化系谱与基于基因组的全局杂合性指标和胴体性状之间的关联，并鉴定与这些性状存在非加性关联的单核苷酸多态性（single nucleotide polymorphisms, SNPs）。本研究所关注的胴体性状包括胴体重（carcass weight, CW）、胴体体型评分（carcass conformation, CC）及胴体脂肪含量（carcass fat, CF）。为明确基于基因组的杂合性指标，并量化SNPs与胴体性状间的非加性关联，本研究使用了来自27213头牛只的经过基因型填充的高密度基因型数据，该数据集包含619158个SNPs。基于系谱的杂种优势系数与三种基因组杂合性指标间的相关系数范围为0.18至0.76。不同杂合性指标与胴体性状间的关联生物学效应均较弱：胴体重与胴体体型评分呈正相关，而胴体脂肪含量呈负相关。此外，即便校正了个体的系谱杂种优势系数，部分胴体性状的剩余变异仍可通过基因组杂合性指标予以捕捉。这提示，同时纳入基于系谱信息的杂种优势系数与基于基因组的杂合性指标，或可有效降低加性遗传值预测中的偏差。最终，位于普通牛（Bos taurus, BTA）5号染色体上的1个SNPs呈现出与胴体重的非加性关联。另有182个SNPs（其中180个位于BTA 2号染色体，2个位于BTA 21号染色体）与胴体体型评分存在非加性关联；而分布于BTA 2、5、11、13、14、18、19及21号染色体的231个SNPs，与胴体脂肪含量存在非加性关联。研究结果表明，无论是全局层面还是单个基因座层面的杂合性，对胴体性能的变异贡献均较小。