AUTHOR=Wang Huie , Wen Junhui , Li Haiying , Zhu Tao , Zhao Xiurong , Zhang Jinxin , Zhang Xinye , Tang Chi , Qu Lujiang , Gemingguli M. 

TITLE=Candidate pigmentation genes related to feather color variation in an indigenous chicken breed revealed by whole genome data

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.985228

DOI=10.3389/fgene.2022.985228

ISSN=1664-8021

ABSTRACT=<p>Chicken plumage color is an inheritable phenotype that was naturally and artificially selected for during domestication. The Baicheng You chicken is an indigenous Chinese chicken breed presenting three main feather colors, lavender, black, and yellow plumages. To explore the genetic mechanisms underlying the pigmentation in Baicheng You chickens, we re-sequenced the whole genome of Baicheng You chicken with the three plumage colors. By analyzing the divergent regions of the genome among the chickens with different feather colors, we identified some candidate genomic regions associated with the feather colors in Baicheng You chickens. We found that <italic>EGR1</italic>, <italic>MLPH</italic>, <italic>RAB17</italic>, <italic>SOX5</italic>, and <italic>GRM5</italic> genes were the potential genes for black, lavender, and yellow feathers. <italic>MLPH</italic>, <italic>GRM5</italic>, and <italic>SOX5</italic> genes have been found to be related to plumage colors in birds. Our results showed that <italic>EGR1</italic> is a most plausible candidate gene for black plumage, <italic>RAB17</italic>, <italic>MLPH</italic>, and <italic>SOX5</italic> for lavender plumage, and <italic>GRM5</italic> for yellow plumage in Baicheng You chicken.</p>