Abstract
Guangxi chickens play a crucial role in promoting the high-quality development of the broiler industry in China, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Guangxi indigenous chicken, we analyzed the whole genomes of 185 chickens from 8 phenotypically and geographically representative Guangxi chicken breeds, together with 12 RJFt, 12 BRA and 12 WL genomes available from previous studies. Calculation of heterozygosity (Hp), nucleotide diversity (π), and LD level indicated that Guangxi populations were characterized by higher genetic diversity and lower differentiation than RJFt and commercial breeds except for HGFC. Population structure analysis also confirmed the introgression from commercial broiler breeds. Each population clustered together while the overall differentiation was slight. MA has the richest genetic diversity among all varieties. Selective sweep analysis revealed BCO2, EDN3 and other candidate genes had received strong selection in local breeds. These also provided novel breeding visual and data basis for future breeding.
Highlights
single nucleotide polymorphisms (SNPs) with MAF < 0.05, call rate < 0.8 and individual call rate < 0.9 were excluded, 13,245,769 high-quality SNPs and 3,790,305 indels were utilized for downstream analysis (Fig 1A)
The Guangxi indigenous chickens harbored a higher number of SNPs and indels than that of Red jungle fowl population from Thailand (RJFt) except for Dongzhongai chicken (DZAC), while WL exhibited the lowest ones
Our results showed that Guangxi chickens have a mosaic structure of isochores, the major isochores are the GC content of 36–42%, comprising a part of L2 and H1, which is the main source of variation
Summary
Chickens are the most widely distributed livestock species globally; more than half the total (53%) is found in Asia, one of the largest producers in China [1]. In China, poultry meat consumption accounts for the second-largest proportion after pork. People in different regions have different preferences for the appearance, flavor, and cooking methods of chickens. Guangxi Zhuang Autonomous Region is in mountainous terrain in the far south of China, and its unique climate has created unique and rich chicken germplasm resources. Three-yellow chicken (SHC) with yellow feathers, skin and shank, is a favorite choice for traditional broths and soups in southern China. Nandanyao chickens (NDYC) are famous for lower fat deposition and better meat quality [2].
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