Chromosome‐scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger. (1st July 2022)

• Record Type: Journal Article
• Authors: Zhang, Le; Lan, Tianming; Lin, Chuyu; Fu, Wenyuan; Yuan, Yaohua; Lin, Kaixiong; Li, Haimeng; Sahu, Sunil Kumar; Liu, Zhaoyang; Chen, Daqing; Liu, Qunxiu; Wang, Aishan; Wang, Xiaohong; Ma, Yue; Li, Shizhou; Zhu, Yixin; Wang, Xingzhuo; Ren, Xiaotong; Lu, Haorong; Huang, Yunting; Yu, Jieyao; Liu, Boyang; Wang, Qing; Zhang, Shaofang; Xu, Xun; Yang, Huanming; Liu, Dan; Liu, Huan; Xu, Yanchun
• Is Part Of: Molecular ecology resources. Volume 23:Number 2(2023)
• Page Start: 330
• Page End: 347
• Publication Date: 2022-07-01
• Subjects: Amur tiger -- genetic management -- inbreeding depression -- South China tiger; Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.13669
• Languages: English
• ISSNs: 1755-098X

Abstract

Abstract: The South China tiger ( Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tiger due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first SCT genome and an improved Amur tiger ( P. t. altaica, AT) genome named AmyTig1.0 and PanTig2.0. The two genomes are the most continuous and comprehensive among any tiger genomes yet reported at the chromosomal level. By using the two genomes and resequencing data of 15 SCT and 13 AT individuals, we investigated the genomic signature of inbreeding depression of the SCT. The results indicated that the effective population size of SCT experienced three phases of decline, ~5.0–1.0 thousand years ago, 100 years ago, and since captive breeding in 1963. We found 43 long runs of homozygosity fragments that were shared by all individuals in the SCT population and covered a total length of 20.63% in the SCT genome. We also detected a large proportion of identical‐by‐descent segments across the genome in the SCT population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites and loss‐of‐function mutations were found across genomes with extensive potential influences, despite a proportion of these loads having been purged by inbreeding depression. Our research provides an invaluable resource for the formulation of genetic management policies for the South China tiger such as developing genome‐based breeding and genetic rescue strategy. Abstract : see also the Perspective by Anubhab Khan