Unveiling Genetic Markers for Milk Yield in Xinjiang Donkeys: A Genome-Wide Association Study and Kompetitive Allele-Specific PCR-Based Approach

Abstract

Lactation traits are critical economic attributes in domestic animals. This study investigates genetic markers and functional genes associated with lactation traits in Xinjiang donkeys. We analyzed 112 Xinjiang donkeys using 10× whole genome re-sequencing to obtain genome-wide single nucleotide polymorphisms (SNPs). Genome-wide association analyses were conducted using PLINK 2.0 and GEMMA 0.98.5 software, employing mixed linear models to assess several lactation traits: average monthly milk yield (AY), fat percentage (FP), protein percentage (PP), and lactose percentage (LP). A total of 236 SNPs were significantly associated with one or more milk production traits (p < 0.000001). While the two-software identified distinct SNP associations, they consistently detected the same 11, 95, 5, and 103 SNPs for AY, FP, PP, and LP, respectively. Several of these SNPs are located within potential candidate genes, including glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 (GPIHBP1), FLII actin remodeling protein (FLII), mitochondrial topoisomerase 1 (TOP1MT), thirty-eight-negative kinase 1 (TNK1), polo like kinase 1 (PLK1), notch homolog 1 (NOTCH1), developmentally regulated GTP-binding protein 2 (DRG2), mitochondrial elongation factor 2 (MIEF2), glutamine-fructose-6-phosphate transaminase 2 (GFPT2), and dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2). Additionally, we validated the polymorphism of 16 SNPs (10 genes) using Kompetitive Allele Specific PCR, revealing that TOP1MT_g.9133371T > C, GPIHBP1_g.38365122C > T, DRG2_g.4912631C > A, FLII_g.5046888C > T, and PLK1_g.23585377T > C were significantly correlated with average daily milk yield and total milk yield in the studied donkeys. This study represents the first genome-wide association analysis of markers and milk components in Xinjiang donkeys, offering valuable insights into the genetic mechanisms underlying milk production traits. Further research with larger sample sizes is essential to confirm these findings and identify potential causal genetic variants.

Keywords: GWAS; SNPs; Xinjiang donkey; candidate gene; milk.

Figure 1

Population structure from the principal component analysis of the 112 Xinjiang donkeys.

Figure 2

Manhattan of SNPs associated with the milk production traits based on GEMMA. (A) AY; (B) FP; (C) PP; (D) LP. Note: The red diagonal line typically represents the reference line where the theoretical distribution perfectly matches the actual data. The black dots represent the actual data points. If the data points approximately fall along a straight line, it indicates that the data follows a normal distribution.

Figure 3

Manhattan of SNPs associated with the milk production traits based on PLINK. (A) AY; (B) FP; (C) PP; (D) LP.

Figure 4

Prediction of SNPs for lactation traits based on GEMMA and PLINK. (A) SNPs for AY. (B) SNPs for FP. (C) SNPs for PP. (D) SNPs for LP.

Figure 5

Prediction of candidate genes for lactation traits based on GEMMA and PLINK. (A) Genes for AY. (B) Genes for FP. (C) Genes for PP. (D) Genes for LP.

Figure 6

SNPs and candidate genes for four traits (AY, FP, PP, and LP) crossed over. (A) SNPs for four traits. (B) Candidate genes for four traits.