Genome-Wide Association Study Using Whole-Genome Sequencing Identifies a Genomic Region on Chromosome 6 Associated With Comb Traits in Nandan-Yao Chicken.

Zhuliang Yang,Linghu Zeng,Tiantian Sun,Yinhai Jia,Jixian Deng,Xiurong Yang,Jianping Jiang,Wenwen Xu,Leqin Zou

doi:10.3389/fgene.2021.682501

Abstract

Comb traits have potential economic value in the breeding of indigenous chickens in China. Identifying and understanding relevant molecular markers for comb traits can be beneficial for genetic improvement. The purpose of this study was to utilize genome-wide association studies (GWAS) to detect promising loci and candidate genes related to comb traits, namely, comb thickness (CT), comb weight (CW), comb height, comb length (CL), and comb area. Genome-wide single-nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) in 300 Nandan-Yao chickens were detected using whole-genome sequencing. In total, we identified 134 SNPs and 25 INDELs that were strongly associated with the five comb traits. A remarkable region spanning from 29.6 to 31.4 Mb on chromosome 6 was found to be significantly associated with comb traits in both SNP- and INDEL-based GWAS. In this region, two lead SNPs (6:30,354,876 for CW and CT and 6:30,264,318 for CL) and one lead INDEL (a deletion from 30,376,404 to 30,376,405 bp for CL and CT) were identified. Additionally, two genes were identified as potential candidates for comb development. The nearby gene fibroblast growth factor receptor 2 (FGFR2)—associated with epithelial cell migration and proliferation—and the gene cytochrome b5 reductase 2 (CYB5R2)—identified on chromosome 5 from INDEL-based GWAS—are significantly correlated with collagen maturation. The findings of this study could provide promising genes and biomarkers to accelerate genetic improvement of comb development based on molecular marker-assisted breeding in Nandan-Yao chickens.

Highlights

The Nandan-Yao chicken, with a single comb, is a typical indigenous breed in Guangxi Zhuang Autonomous Region (Yang et al, 2020)
Relatively few GWAS have been performed on comb traits, among which only two studies are established on the quantitative characters of combs
We identified 134 SNPs and 25 INDELs that were strongly associated with comb size, which could be helpful in the selection of Nandan-Yao chickens

Summary

Introduction

The Nandan-Yao chicken, with a single comb, is a typical indigenous breed in Guangxi Zhuang Autonomous Region (Yang et al, 2020). To meet the particular demand of local customers, chickens with a prominent ornament are preferred breeding targets for the local poultry industry. The comb is a sexual ornament in chickens, and its morphological characteristics, such as comb shape and size, are important in mating behavior in both sexes Males prefer to invest sperm in females with relatively large comb (Cornwallis and Birkhead, 2006); reciprocally, females preferentially like to copulate with dominant males with large combs (Graves et al, 1985; Zuk et al, 1990). It can be concluded that the comb has potential economic value in poultry breeding

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