Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Wenting Li; Chaoqun Gao; Zhao Cai; Sensen Yan; Yanru Lei; Mengya Wei; Guirong Sun; Yadong Tian; Kejun Wang; Xiangtao Kang

Journal of Integrative Agriculture (Mar 2024)

Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Wenting Li,
Chaoqun Gao,
Zhao Cai,
Sensen Yan,
Yanru Lei,
Mengya Wei,
Guirong Sun,
Yadong Tian,
Kejun Wang,
Xiangtao Kang

Affiliations

Wenting Li: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China
Chaoqun Gao: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China
Zhao Cai: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
Sensen Yan: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China
Yanru Lei: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China
Mengya Wei: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
Guirong Sun: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China
Yadong Tian: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China
Kejun Wang: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China; Correspondence Kejun Wang
Xiangtao Kang: College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou 450002, China; Correspondence Xiangtao Kang

Journal volume & issue: Vol. 23, no. 3
pp. 975 – 987

Abstract

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Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations (GS1, 2010, ex-situ; GS2, 2019, ex-situ; GS3, 2019, in-situ; XB1, 2010, in-situ; and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs (in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

Published in Journal of Integrative Agriculture

ISSN: 2095-3119 (Print); 2352-3425 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Agriculture: Agriculture (General)
Website: https://www.journals.elsevier.com/journal-of-integrative-agriculture

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