Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck

Qixin Guo; Yong Jiang; Zhixiu Wang; Yulin Bi; Guohong Chen; Hao Bai; Guobin Chang

doi:10.3390/genes13071271

Genome-Wide Analysis Identifies Candidate Genes Encoding Beak Color of Duck

Genes (Basel). 2022 Jul 18;13(7):1271. doi: 10.3390/genes13071271.

Authors

Qixin Guo¹, Yong Jiang¹, Zhixiu Wang¹, Yulin Bi¹, Guohong Chen¹, Hao Bai¹, Guobin Chang^{1

2}

Affiliations

¹ Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
² College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.

Abstract

Beak color diversity is a broadly occurring phenomenon in birds. Here, we used ducks to identify candidate genes for yellow, black, and spotted beaks. For this, an F₂ population consisting of 275 ducks was genotyped using whole genome resequencing containing 12.6 M single-nucleotide polymorphisms (SNPs) and three beak colors. Genome-wide association studies (GWAS) was used to identify the candidate and potential SNPs for three beak colors in ducks (yellow, spotted, and black). The results showed that 2753 significant SNPs were associated with black beaks, 7462 with yellow, and 17 potential SNPs with spotted beaks. Based on SNP annotation, MITF, EDNRB2, members of the POU family, and the SLC superfamily were the candidate genes regulating pigmentation. Meanwhile, isoforms MITF-M and EDNRB2 were significantly different between black and yellow beaks. MITF and EDNRB2 likely play a synergistic role in the regulation of melanin synthesis, and their mutations contribute to phenotypic differences in beak melanin deposition among individuals. This study provides new insights into genetic factors that may influence the diversity of beak color.

Keywords: GWAS; beak color; duck; melanin.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Beak*
Ducks* / genetics
Genome-Wide Association Study
Humans
Melanins / genetics
Pigmentation / genetics

Substances

Melanins

Grants and funding

This research was funded by the Postgraduate Research and Innovation in Jiangsu Province (grant: KYCX21_3258), China Agriculture Research System of MOF and MARA (grant: CARS-42), and Jiangsu Agricultural Industry Technology System (grant: JATS [2021]326). The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.