Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population.

Jihye Cha, Daehyeok Jin, Jae-Hwan Kim, Seung-Chang Kim, Jin A Lim, Han-Ha Chai, Seul A Jung, Jun-Heon Lee, Seung-Hwan Lee
Author Information
  1. Jihye Cha: Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea.
  2. Daehyeok Jin: Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea.
  3. Jae-Hwan Kim: Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea.
  4. Seung-Chang Kim: Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea.
  5. Jin A Lim: Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea.
  6. Han-Ha Chai: Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea.
  7. Seul A Jung: Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea.
  8. Jun-Heon Lee: Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea.
  9. Seung-Hwan Lee: Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea. Electronic address: slee46@cnu.ac.kr.

Abstract

Skin color in chickens is an economically important trait that determines the first impression of a consumer toward a broiler and can ultimately affect consumer choice in the market. Therefore, identification of genomic regions associated with skin color is crucial for increasing the sales value of chickens. Although previous studies have attempted to reveal the genetic markers associated with the skin coloration in chickens, most were limited to investigations of candidate genes, such as melanin-related genes, and focused on case/control studies based on a single or small population. In this study, we performed a genome-wide association study (GWAS) on 770 F2 intercrosses produced by an experimental population of 2 chicken breeds, namely Ogye and White Leghorns, with different skin colors. The GWAS demonstrated that the L* value among the 3 skin color traits is highly heritable, and the genomic regions located on 2 chromosomes (20 and Z) were detected to harbor SNPs significantly associated with the skin color trait, accounting for most of the total genetic variance. Particular genomic regions spanning a ∼2.94 Mb region on GGA Z and a ∼3.58 Mb region on GGA 20 were significantly associated with skin color traits, and in these regions, certain candidate genes, including MTAP, FEM1C, GNAS, and EDN3, were found. Our findings could help elucidate the genetic mechanisms underlying chicken skin pigmentation. Furthermore, the candidate genes can be used to provide a valuable breeding strategy for the selection of specific chicken breeds with ideal skin coloration.

Keywords

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MeSH Term

Animals
Skin Pigmentation
Genome-Wide Association Study
Chickens
Genome
Genomics
Phenotype
Polymorphism, Single Nucleotide

Word Cloud

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