Large-Scale Genome-Wide Association Analysis Reveals Candidate Genes in Yak Body Size Traits

Background The yak is a unique livestock species bred on the Qinghai-Tibet Plateau. We utilized genotypic data obtained from the yak sequencing chip "Qingxin-1" and phenotypic data measured from image photographs using conversion between pixel and distance. The primary objective of this study was to conduct genome-wide association studies (GWAS) using five models to analyze seven body size traits. Specifically, the goals were to (1) characterize the genetic structure of three major yak breeds: Maiwa, Yushu, and Huanhu; (2) identify candidate genes that significantly influence yak body size traits; and (3) compare the prediction accuracy of single-trait and multi-trait genomic selection(GS). Results A total of 94 markers were significantly ( P  < 1e-05) associated with yak body size traits. GWAS results revealed that PRKAA2 and SNX9 were important candidate genes affecting the body size traits of yaks. The GS results indicated that combining marker-assisted selection and best linear unbiased prediction significantly improved the accuracy of predicting body size traits, the average accuracy in multi-trait GS was higher than that in single-trait GS. Conclusions Our findings provide valuable insights into the genetic architecture underlying yaks, with implications for the development and selection of yak body size traits. The identification of key genes such as PRKAA2 and SNX9 offers promising targets for breeding programs aimed at optimizing body size traits, thereby supporting genetic improvements in yak populations.