Simple SummaryThe yak is a unique livestock species living in the Qinghai–Tibet Plateau. Investigating the morphological differences among different breeds of yaks is of paramount importance. However, due to the lack of effective communication of yak genetic information under natural and artificial selection, the genetic diversity of regional yaks is not effectively utilized for new breedings, and it is difficult for the existing analysis models to analyze such complex multi-species populations. Therefore, we extended the application scope of the current statistical model to perform whole-genome association analysis on multiple yak breeds and identified four genes significantly associated with body height. The findings of this study are of great significance for the development and improvement of yak morphological traits, as well as the expansion of statistical models.AbstractYaks have evolved several breeds or genetic resources owing to their geographical and ecological environment, and investigating the genetic construction of body size among breeds is key for breeding. Here, a genome-wide association study (GWAS) was performed for five body size traits in 31 yak breeds and genetic resources. The information from clustering individuals according to their habitats was used for kinship grouping in the compressed mixed linear model (CMLM). We named this approach the pCMLM method. A total of 3,584,464 high-quality single nucleotide polymorphisms (SNPs) were obtained, and six markers were found to be significantly associated with height by pCMLM. Four candidate genes, includingFXYD6,SOHLH2,ADGRB2, andOSBPL6, were identified. Our results show that when CMLM cannot identify optimal clustering groups, pCMLM can provide sufficient associated results based on population information. Moreover, this study provides basic information on the gene localization of quantitative traits of body size among yak breeds.