A Genome-Wide Association Study of the Chest Circumference Trait in Xinjiang Donkeys Based on Whole-Genome Sequencing Technology

Abstract

Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (p < 1.61 × 10^-9). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including NFATC2 (Nuclear Factor of Activated T Cells 2), PROP1 (PROP Paired-Like Homeobox 1), UBB (Ubiquitin B), and HAND2 (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing.

Keywords: GWAS; PLINK; Xinjiang donkey; chest circumference; key genes.

Figure 1

Xinjiang donkey.

Figure 2

The QQ plot of the CC trait.

Figure 3

Distribution of read coverage.

Figure 4

The QQ plots for the GWAS analysis.

Figure 5

Manhattan plot of the CC trait. (A) GWAS conducted in PLINK. (B) GWAS conducted in GEMMA. (C) GWAS conducted in REGENIE. The black horizontal line indicates the threshold p < 1.61 × 10⁻⁹ and the blue line indicates p < 8.06 × 10⁻⁹.

Figure 6

SNPs and genes significantly associated with the CC trait in different software: (A) correlated SNPs (p < 8.06 × 10⁻⁹); (B) correlated SNPs (p < 1.61 × 10⁻⁹); (C) correlated genes.