Genome-Wide Association Studies for Comb Traits in Chickens

PLoS One. 2016 Jul 18;11(7):e0159081. doi: 10.1371/journal.pone.0159081. eCollection 2016.


The comb, as a secondary sexual character, is an important trait in chicken. Indicators of comb length (CL), comb height (CH), and comb weight (CW) are often selected in production. DNA-based marker-assisted selection could help chicken breeders to accelerate genetic improvement for comb or related economic characters by early selection. Although a number of quantitative trait loci (QTL) and candidate genes have been identified with advances in molecular genetics, candidate genes underlying comb traits are limited. The aim of the study was to use genome-wide association (GWA) studies by 600 K Affymetrix chicken SNP arrays to detect genes that are related to comb, using an F2 resource population. For all comb characters, comb exhibited high SNP-based heritability estimates (0.61-0.69). Chromosome 1 explained 20.80% genetic variance, while chromosome 4 explained 6.89%. Independent univariate genome-wide screens for each character identified 127, 197, and 268 novel significant SNPs with CL, CH, and CW, respectively. Three candidate genes, VPS36, AR, and WNT11B, were determined to have a plausible function in all comb characters. These genes are important to the initiation of follicle development, gonadal growth, and dermal development, respectively. The current study provides the first GWA analysis for comb traits. Identification of the genetic basis as well as promising candidate genes will help us understand the underlying genetic architecture of comb development and has practical significance in breeding programs for the selection of comb as an index for sexual maturity or reproduction.

MeSH terms

  • Alleles
  • Animals
  • Breeding
  • Chickens / genetics*
  • Chickens / physiology
  • Female
  • Genetic Variation
  • Genome-Wide Association Study
  • Genotype
  • Male
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci
  • Sexual Maturation

Grant support

This work was supported in part by the National Science & Technology Pillar Program during the 12th Five-year Plan Period (2012BAD39B0401), and China Agriculture Research Systems (CARS-41-K02,, PR China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.