Genome-wide association study for the primary feather color trait in a native Chinese duck

Abstract

<b>Background:</b> To reveal candidate genes and the molecular genetic mechanism underlying primary feather color trait in ducks, a genome-wide association study (GWAS) for the primary feather color trait was performed based on the genotyping-by-sequencing (GBS) technology for a native Chinese female duck, Longyan Shan-ma ducks. <b>Methods:</b> Blood genomic DNA from 314 female Longyan Shan-ma duck were genotyped using GBS technology. A GWAS for the primary feather color trait with genome variations was performed using an univariate linear mixed model based on all SNPs in autosomes. <b>Results:</b> Seven genome-wide significant single nucleotide polymorphisms (SNPs, Bonferroni-adjusted <i>p</i>-value <8.03 × 10^-7) within the introns of the genes <i>STARD9</i>, <i>ZNF106</i>, <i>SLC7A5</i>, and <i>BANP</i> genes were associated with the primary feather color trait. Twenty-two genome-wide suggestive SNPs (Bonferroni-adjusted <i>p</i>-value <1.61 × 10^-5) of 17 genes (besides <i>ZNF106</i> and <i>SLC7A5</i>) were also identified. Seven SNPs were located at one 0.22 Mb region (38.65-38.87 Mb) on chromosome 5, and six SNPs were located at one 0.31 Mb region (19.53-19.84 Mb) on chromosome 11. The functions of <i>STARD9</i>, <i>SLC7A</i>5, <i>BANP</i>, <i>LOC101798015</i>, and <i>IPMK</i> were involved pigmentation and follicle development, especially, <i>STARD9</i> upregulated expression in black feather (haplotype-CCCC) bulb tissue compared with in pockmarked feather (haplotype-TGTT) bulb tissue, implicating these genes as candidate genes for primary feather color trait. <b>Conclusion:</b> The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.