Whole Genome Resequencing Revealed the Genetic Relationship and Selected Regions among Baicheng-You, Beijing-You, and European-Origin Broilers
Author:
Yang Kai1, Zhang Jian2ORCID, Zhao Yuelei1, Shao Yonggang3, Zhai Manjun3, Liu Huagui2, Zhang Lifan1ORCID
Affiliation:
1. College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China 2. Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China 3. College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
Abstract
As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens.
Funder
Beijing Indigenous Animal Genetic Resources Protection Project Jiangsu Agricultural Science and Technology Innovation Fund Accurate Identification Project of Livestock and Poultry Germplasm Resources
Subject
General Agricultural and Biological Sciences,General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology
Reference74 articles.
1. China National Commission of Animal Genetic Resources (2011). Animal Genetic Resources in China Poultry, China Agriculture Press. 2. Estimation of genetic parameters for contents of intramuscular fat and inosine-5′-monophosphate and carcass traits in Chinese Beijing-You chickens;Chen;Poult. Sci.,2008 3. Comparison of carcass yields and meat quality between Baicheng-You chickens and Arbor Acres broilers;Sarsenbek;Poult. Sci.,2013 4. A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes;Esmailizadeh;Genet. Sel. Evol.,2021 5. Qanbari, S., Rubin, C.J., Maqbool, K., Weigend, S., Weigend, A., Geibel, J., Kerje, S., Wurmser, C., Peterson, A.T., and Brisbi, I.L. (2019). Genetics of adaptation in modern chicken. PLoS Genet., 15.
|
|