A Study of Genomic Prediction of 12 Important Traits in the Domesticated Yak (Bos grunniens)

Abstract

Simple SummaryThe domesticated yak is among the most important livestock species on the Qinghai-Tibet Plateau. Breeders have the task of developing varieties that provide growth performance and disease resistance. Traditional breeding processes rely on complete family pedigree information and large numbers of data records. However, there are inevitably records that are missing, including incomplete pedigrees and long-term data tracking, resulting in prolonged breeding cycles, reduced breeding efficiency, and the lack of economic benefit. Genome selection (GS), also known as whole genomic selection (WGS), can significantly reduce the selection cycle of quantitative traits and accelerate genetic progression while displaying appropriate prediction accuracy (PA). It combines a reference population and single nucleotide polymorphism (SNP) loci rather than pedigrees to estimate the effect of all SNPs. Then breeding values of target traits are predicted. The key for GS is genomic prediction (GP) and an assessment of PA.AbstractThe aim of this study was to explore the possibility of applying GP to important economic traits in the domesticated yak, thus providing theoretical support for its molecular breeding. A reference population was constructed consisting of 354 polled yaks, measuring four growth traits and eight hematological traits related to resistance to disease (involved in immune response and phagocytosis). The Illumina bovine HD 770k chip was used to obtain SNP information of all the individuals. With these genotypes and phenotypes, GBLUP, Bayes B and Bayes Cπ methods were used to predict genomic estimated breeding values (GEBV) and assess prediction capability. The correlation coefficient of the association of GEBV with estimated breeding value (EBV) was used as PA for each trait. The prediction accuracy varied from 0.043 to 0.281 for different traits. Each trait displayed similar PAs when using the three methods. Lymphocyte counts (LYM) exhibited the highest predictive accuracy (0.319) during all GP, while chest girth (CG) provided the lowest predictive accuracy (0.043). Our results showed moderate PA in most traits such as body length (0.212) and hematocrit (0.23). Those traits with lower PA could be improved by using SNP chips designed specifically for yak, a better optimized reference group structure, and more efficient statistical algorithms and tools.

Genome-wide identification of SNPs associated with body weight in yak

“…Based on DSNPGA and GWAS, multiple genes related to little size trait in Pelibuey sheep [8], four candidate genes associated with body weight in Baluchi sheep [9], two genes associated with carcass weight in pig [10], and 105 SNPs potentially affecting milk production traits in Chinese Holstein population have been detected [11]. In yaks, Fu et al [12] genotyped yak SNP using an Illumina Bovine HD 770 K chip. However, the obtained results were not informative enough, since the used chip was designed against bovine genome, and there are great differences between yak and bovine genomes.…”

Accuracies of Genomic Prediction for Growth Traits at Weaning and Yearling Ages in Yak

“…Therefore, it is desirable to apply genomic selection to the yak population in order to facilitate gains in the overall level of production. To take full advantage of genomic selection, we have placed emphasis on selection for early growth traits compared to a previous study concerning the preliminary exploration of genomic prediction in yak [ 16 ]. Furthermore, genomic selection combined with early growth traits could lead to considerably decreased feeding costs, as genotyped animals could be procured when juvenile.…”