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=14

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=<p><bold>Background:</bold> 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.</p><p><bold>Methods:</bold> 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.</p><p><bold>Results:</bold> Seven genome-wide significant single nucleotide polymorphisms (SNPs, Bonferroni-adjusted <italic>p</italic>-value &lt;8.03 × 10<sup>−7</sup>) within the introns of the genes <italic>STARD9</italic>, <italic>ZNF106</italic>, <italic>SLC7A5</italic>, and <italic>BANP</italic> genes were associated with the primary feather color trait. Twenty-two genome-wide suggestive SNPs (Bonferroni-adjusted <italic>p</italic>-value &lt;1.61 × 10<sup>−5</sup>) of 17 genes (besides <italic>ZNF106</italic> and <italic>SLC7A5</italic>) 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 <italic>STARD9</italic>, <italic>SLC7A</italic>5, <italic>BANP</italic>, <italic>LOC101798015</italic>, and <italic>IPMK</italic> were involved pigmentation and follicle development, especially, <italic>STARD9</italic> 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.</p><p><bold>Conclusion:</bold> The preliminarily findings suggested candidate genes and regions, and the genetic basis of primary feather color trait in a female duck.</p>