Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds

SIMPLE SUMMARY: There are five indigenous chicken breeds in Henan Province, China; however, comprehensive knowledge of their genetic basis is lacking. Therefore, using whole genome resequencing, we examined the genetic make-up, genomic diversity, and migration history of the indigenous Henan chicken populations as well as the selection factors and genes behind the distinct phenotypes of Henan gamecocks. These results will make it easier to comprehend the traits of the germplasm and the potential for using native breeds from Henan. 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.