Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds
Author:
Zhi Yihao1, Wang Dandan1, Zhang Ke1, Wang Yangyang1, Geng Wanzhuo1, Chen Botong1, Li Hong123, Li Zhuanjian123ORCID, Tian Yadong123, Kang Xiangtao123ORCID, Liu Xiaojun123
Affiliation:
1. College of Animal Science and Technologyw, Henan Agricultural University, Zhengzhou 450046, China 2. Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China 3. International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
Abstract
There are five indigenous chicken breeds in Henan Province, China. These breeds have their own unique phenotypic characteristics in terms of morphology, behavior, skin and feather color, and productive performance, but their genetic basis is not well understood. Therefore, we analyzed the genetic structure, genomic diversity, and migration history of Henan indigenous chicken populations and the selection signals and genes responsible for Henan gamecock unique phenotypes using whole genome resequencing. The results indicate that Henan native chickens clustered most closely with the chicken populations in neighboring provinces. Compared to other breeds, Henan gamecock’s inbreeding and selection intensity were more stringent. TreeMix analysis revealed the gene flow from southern chicken breeds into the Zhengyang sanhuang chicken and from the Xichuan black-bone chicken into the Gushi chicken. Selective sweep analysis identified several genes and biological processes/pathways that were related to body size, head control, muscle development, reproduction, and aggression control. Additionally, we confirmed the association between genotypes of SNPs in the strong selective gene LCORL and body size and muscle development in the Gushi-Anka F2 resource population. These findings made it easier to understand the traits of the germplasm and the potential for using the Henan indigenous chicken.
Funder
Key Project of NSFC-Henan Province Joint Grand Major Scientific and Technological Special Project of Henan Province Project of SANGAO Zhongyuan Scholars
Subject
General Veterinary,Animal Science and Zoology
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