Conservation priority and run of homozygosity pattern assessment of global chicken genetic resources

Chaoqun Gao; Kejun Wang; Xiaoyu Hu; Yanru Lei; Chunhong Xu; Yixiang Tian; Guirong Sun; Yadong Tian; Xiangtao Kang; Wenting Li

doi:10.1016/j.psj.2023.103030

Conservation priority and run of homozygosity pattern assessment of global chicken genetic resources

Poult Sci. 2023 Nov;102(11):103030. doi: 10.1016/j.psj.2023.103030. Epub 2023 Aug 22.

Authors

Affiliations

¹ Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China.
² College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China.
³ Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China. Electronic address: liwenting_5959@hotmail.com.

Abstract

The conservation of genetic resources is becoming increasingly important for the sustainable development of the poultry industry. In the present study, we systematically analyzed the population structure, conservation priority, runs of homozygosity (ROH) of chicken breeds globally, and proposed rational conservation strategies. We used a 600K Affymetrix Axiom HD genotyping SNP array dataset of 2,429 chickens from 134 populations. The chickens were divided into 5 groups based on their country of origin and sampling location: Asian chickens (AS-LOC), African chickens (AF), European local chickens (EU-LOC), Asian breeds sampled in Germany (AS-DE), and European breeds sampled in Germany (EU-DE). The results indicated that the population structure was consistent with the actual geographical distribution of the populations. AS-LOC had the highest positive contribution to the total gene (HT, 1.00%,) and allelic diversity (AT, 0.0014%), the lowest inbreeding degree and the fastest linkage disequilibrium (LD) decay rate; the lowest contribution are derived by European ex situ chicken breeds (EU-DE:HT = -0.072%, AT = -0.0014%), which showed the highest inbreeding and slowest LD decay. Breeds farmed in ex situ (AS-DE, EU-DE) conditions exhibited reduced genetic diversity and increased inbreeding due to small population size. Given limited funds, it is a better choice for government to conserve the breeds with the highest contribution to genetic diversity in each group. Therefore, we evaluated the contribution of each breed to genetic and allelic diversity in 5 groups. Among each group, KUR(AF), BANG(AS-LOC), ALxx(EU-LOC), BHwsch(AS-DE), and ARw(EU-DE) had the highest contribution to gene diversity in the order of the above grouping. Similarly, according to the allelic diversity standard (in the same order), ZIMxx, PIxx, ALxx, SHsch, and ARsch had the highest contribution. After analyzing ROH, we found a total of 144,708 fragments and 27 islands. The gene and genome regions identified by the ROH islands and QTLs indicate that chicken breeds have potential for adaptation to different production systems. Based on these findings, it is recommended to prioritize the conservation of breeds with the highest genetic diversity in each group, while paying more attention to the conservation of Asian and African breeds. Furthermore, providing a valuable reference for the conservation and utilization of chicken.

Keywords: ROH; chicken; conservation; genetic diversity; genome-wide SNP array.