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Link to original content: http://pubmed.ncbi.nlm.nih.gov/38674333/
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. 2024 Mar 24;15(4):398.
doi: 10.3390/genes15040398.

Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey

Wenping Zhang  1 , Kaixiong Lin  2 , Wenyuan Fu  3 , Junjin Xie  4 , Xueyang Fan  4 , Mingchun Zhang  5 , Hongxing Luo  2 , Yuzhong Yin  6 , Qiang Guo  1 , He Huang  4 , Tengteng Chen  2 , Xipan Lin  2 , Yaohua Yuan  7 , Cheng Huang  2 , Shizhang Du  1
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Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey

Wenping Zhang et al. Genes (Basel). .

Abstract

There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.

Keywords: South China tiger; genetic rescue; genome; hybrid.

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Conflict of interest statement

The authors declare that they have no conflicts of interest.

Figures

Figure 1
Figure 1
The results of assignment of individuals following the microsatellite genotype of 30 loci. Here, the population structure when K = 15, which produced the highest probability among other choices of K (Figure S1), and each individual were represented by a thin vertical bar. SCTs did not include the individuals and their offspring with an admixture of other tiger subspecies identified by Zhang et al. [10]. A total of 320 SCTs were included in this figure. #515 was identified as an admixture of other tiger subspecies.
Figure 2
Figure 2
The distributions of estimated individual inbreeding coefficients (fP and fM) and the heterozygous loci ratio based on microsatellite data. Here, A indicates the group including the individuals without the genetical materials of #140 and B indicates the group including the individuals with the genetical materials of #140. The p-value was obtained from an ANOVA test. fP: pedigree inbreeding coefficient, fM: microsatellite inbreeding coefficient.
Figure 3
Figure 3
Distribution of individual heterozygosity and genomic inbreeding coefficients (FROH). (A) Genome-wide heterozygosity and FROH per individual. (B) FROH based on different lengths of runs of homozygosity (ROH), with a minimum length of 100 kb, per individual.
Figure 4
Figure 4
Population genomic structure of tiger subspecies following autosomal variants. (A) Family tree of the 13 hybrid SCTs in Meihuashan are shown here. The number in the family tree is the studbook number or the code in Meihuashan. (B) Principal component analysis (PCA) of PC1 and PC3 indicates six distinct clusters corresponding to current subspecies designations and South China tigers including SCT and Mei. SCT denotes the 23 pureblood SCTs and Mei denotes the hybrid SCTs in Meihuashan. ptal: P. t. altaica, ptco: P. t. corbetti, ptja: P. t. jacksoni, ptsu: P. t. sumatrae, and ptti: P. t. tigris. (C) Population genetic structuring of different tiger subspecies inferred from the phylogenetic relationship and ADMIXTURE [37]. The phylogenetic tree was constructed using the domestic cat as an outgroup and all nodes are of 100% reliability. Each individual is represented by a thin vertical bar, which are partitioned into K colored segments and represent the individual affiliation to each cluster (K is set from 4 to 10).
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