DataSheet1_Genome-wide association study for the primary feather color trait in a native Chinese duck.pdf

Background: 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.
Methods: 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.
Results: Seven genome-wide significant single nucleotide polymorphisms (SNPs, Bonferroni-adjusted p-value <8.03 × 10−7) within the introns of the genes STARD9, ZNF106, SLC7A5, and BANP genes were associated with the primary feather color trait. Twenty-two genome-wide suggestive SNPs (Bonferroni-adjusted p-value <1.61 × 10−5) of 17 genes (besides ZNF106 and SLC7A5) 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 STARD9, SLC7A5, BANP, LOC101798015, and IPMK were involved pigmentation and follicle development, especially, STARD9 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.
Conclusion: The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.

研究背景：为揭示鸭初级羽毛颜色性状相关的候选基因及其分子遗传机制，本研究以中国地方雌性鸭品种龙岩山麻鸭（Longyan Shan-ma ducks）为研究对象，基于测序分型（Genotyping-by-Sequencing, GBS）技术开展了初级羽毛颜色性状的全基因组关联分析（Genome-Wide Association Study, GWAS）。
研究方法：采用GBS技术对314只雌性龙岩山麻鸭的血液基因组DNA进行分型。基于常染色体上的所有单核苷酸多态性（Single Nucleotide Polymorphism, SNPs），采用单变量线性混合模型对基因组变异与初级羽毛颜色性状开展全基因组关联分析。
研究结果：在STARD9、ZNF106、SLC7A5及BANP基因的内含子区域中，共鉴定到7个与初级羽毛颜色性状显著相关的全基因组水平SNPs（Bonferroni校正后P值<8.03×10⁻⁷）。此外，还鉴定到17个基因（不含ZNF106与SLC7A5）的22个全基因组水平提示性SNPs（Bonferroni校正后P值<1.61×10⁻⁵）。其中7个SNPs位于5号染色体的0.22 Mb区域（38.65~38.87 Mb），6个SNPs位于11号染色体的0.31 Mb区域（19.53~19.84 Mb）。STARD9、SLC7A5、BANP、LOC101798015及IPMK基因的功能涉及色素沉着与毛囊发育；与麻斑羽毛（单倍型TGTT）的毛囊组织相比，STARD9在黑色羽毛（单倍型CCCC）的毛囊组织中表达上调，提示上述基因为鸭初级羽毛颜色性状的候选基因。
研究结论：本研究初步筛选得到雌性鸭初级羽毛颜色性状的候选基因及基因组区域，为解析该性状的分子遗传基础提供了重要理论依据。