AUTHOR=Pan Rui , Hua Tian , Guo Qixin , Bai Hao , Jiang Yong , Wang Zhixiu , Bi Yulin , Chen Guohong , Wu Xinsheng , Chang Guobin 

TITLE=Identification of SNPs in MITF associated with beak color of duck

JOURNAL=Frontiers in Genetics

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1161396

DOI=10.3389/fgene.2023.1161396

ISSN=1664-8021

ABSTRACT=<p><bold>Introduction:</bold> Beak color—a pigment-related trait—is an important feature of duck breeds. Recently, little research has addressed genetic mechanism of the beak colors in poultry, whereas the process and the regulation factors of melanin deposition have been well described.</p><p><bold>Methods:</bold> To investigate the genetic mechanism of beak colors, we conducted an integrated analysis of genomic selection signatures to identify a candidate site associated with beak color. For this, we used black-billed (Yiyang I meat duck synthetic line H1, H2, H3&amp;HF) and yellow-billed ducks (Cherry Valley ducks and white feather Putian black duck). Quantitative real-time PCR and genotyping approaches were used to verify the function of the candidate site.</p><p><bold>Results:</bold> We identified 3,895 windows containing 509 genes. After GO and KEGG enrichment analysis, nine genes were selected. Ultimately, <italic>MITF</italic> was selected by comparing the genomic differentiation (F<sub>ST</sub>). After loci information selection, 41 extreme significantly different loci were selected, which are all located in intron regions of <italic>MITF</italic> and are in almost complete linkage disequilibrium. Subsequently, the site ASM874695v1:10:g.17814522T &gt; A in <italic>MITF</italic> was selected as the marker site. Furthermore, we found that MITF expression is significantly higher in black-beaked ducks than in yellow-beaked ducks of the F<sub>2</sub> generation (<italic>p</italic> &lt; 0.01). After genotyping, most yellow-billed individuals are found with homozygous variant; at the same time, there are no birds with homozygous variant in black-billed populations, while the birds with homozygous and heterozygous variant share the same proportion.</p><p><bold>Conclusion:</bold><italic>MITF</italic> plays a very critical role in the melanogenesis and melanin deposition of duck beaks, which can effectively affect the beak color. The <italic>MITF</italic> site, ASM874695v1:10:g.17814522T &gt; A could be selected as a marker site for the duck beak color phenotype.</p>