AUTHOR=Sun Yanfa , Wu Qiong , Lin Rulong , Chen Hongping , Zhang Min , Jiang Bingbing , Wang Yaru , Xue Pengfei , Gan Qiuyun , Shen Yue , Chen Feifan , Liu Jiantao , Zhou Chenxin , Lan Shishi , Pan Haozhe , Deng Fan , Yue Wen , Lu Lizhi , Jiang Xiaobing , Li Yan 

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

JOURNAL=Frontiers in Genetics

VOLUME=Volume 14 - 2023

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1065033

DOI=10.3389/fgene.2023.1065033

ISSN=1664-8021

ABSTRACT=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 up-regulated 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. 
Conclusions: The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.