Genome-Wide Association Study for Screening and Identifying Potential Shin Color Loci in Ducks

Genes (Basel). 2022 Aug 4;13(8):1391. doi: 10.3390/genes13081391.

Abstract

Shin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F2 population consisting of 275 ducks crossed between Runzhou crested-white ducks and Cherry Valley ducks. We obtained 12.6 Mb of single nucleotide polymorphism (SNP) data, and the three shin colors were subsequently genotyped. Genome-wide association studies (GWASs) were performed to identify candidate and potential SNPs for the three shin colors. According to the results, 2947 and 3451 significant SNPs were associated with black and yellow shins, respectively, and six potential SNPs were associated with spotted shins. Based on the SNP annotations, the MITF, EDNRB2, POU family members, and the SLC superfamily were the candidate genes regulating pigmentation. In addition, the isoforms of EDNRB2, TYR, TYRP1, and MITF-M were significantly different between the black and yellow tibiae. MITF and EDNRB2 may have synergistic roles in the regulation of melanin synthesis, and their mutations may lead to phenotypic differences in the melanin deposition between individuals. This study provides new insights into the genetic factors that may influence tibia color diversity in birds.

Keywords: GWAS; duck; melanin; shin color.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Birds / genetics
  • Ducks* / genetics
  • Genome-Wide Association Study*
  • Genotype
  • Humans
  • Melanins / genetics
  • Pigmentation / genetics

Substances

  • Melanins

Grants and funding

This research was funded by 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 study design, collection, analysis, or interpretation of data, writing of the manuscript, or decision to publish the results.