Genome wide association studies for milk production traits in Chinese Holstein population

Abstract

Genome-wide association studies (GWAS) based on high throughput SNP genotyping technologies open a broad avenue for exploring genes associated with milk production traits in dairy cattle. Motivated by pinpointing novel quantitative trait nucleotide (QTN) across Bos Taurus genome, the present study is to perform GWAS to identify genes affecting milk production traits using current state-of-the-art SNP genotyping technology, i.e., the Illumina BovineSNP50 BeadChip. In the analyses, the five most commonly evaluated milk production traits are involved, including milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP) and milk protein percentage (PP). Estimated breeding values (EBVs) of 2,093 daughters from 14 paternal half-sib families are considered as phenotypes within the framework of a daughter design. Association tests between each trait and the 54K SNPs are achieved via two different analysis approaches, a paternal transmission disequilibrium test (TDT)-based approach (L1-TDT) and a mixed model based regression analysis (MMRA). In total, 105 SNPs were detected to be significantly associated genome-wise with one or multiple milk production traits. Of the 105 SNPs, 38 were commonly detected by both methods, while four and 63 were solely detected by L1-TDT and MMRA, respectively. The majority (86 out of 105) of the significant SNPs is located within the reported QTL regions and some are within or close to the reported candidate genes. In particular, two SNPs, ARS-BFGL-NGS-4939 and BFGL-NGS-118998, are located close to the DGAT1 gene (160bp apart) and within the GHR gene, respectively. Our findings herein not only provide confirmatory evidences for previously findings, but also explore a suite of novel SNPs associated with milk production traits, and thus form a solid basis for eventually unraveling the causal mutations for milk production traits in dairy cattle.

Figure 1. Genome-wide plots of −log₁₀(p-values) for association of SNP loci with five milk production traits in sequential order.

Chromosomes 1–29 and X are shown separated by color. Fig. 1-a1, 1-a2, 1-a3, 1-a4 and 1-a5 refer to plots generated by L1-TDT for MY, FY, PY, FP and PP, respectively. Fig. 1-b1, 1-b2, 1-b3, 1-b4 and 1-b5 refer to plots generated by MMRA for MY, FY, PY, FP and PP, respectively. The corresponding horizontal lines indicate the genome-wise significance levels (−log₁₀(1.28×10⁻⁶) for L1-TDT and −log₁₀(1.24×10⁻⁶) for MMRA).

Figure 2. Quantile-quantile (Q-Q) plots of genome-wide association results by MMRA for five milk production traits.

Under the null hypothesis of no association at any SNP locus, the points would be expected to follow the slope lines. Deviations from the slope lines correspond to loci that deviate from the null hypotheses.