Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers

Xiao Zhao; Qiguan Qiu; Chang Li; Dongke Fu; Xuesong Hu; Shengjie Gao; Yugang Zhu; Haofang Mu; Runping Wang; Huanming Yang; Bo Li

doi:10.7717/peerj.8939

Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers

PeerJ. 2020 May 6:8:e8939. doi: 10.7717/peerj.8939. eCollection 2020.

Authors

Xiao Zhao^{1

2

3

4}, Qiguan Qiu⁵, Chang Li^{1

4

6}, Dongke Fu^{2

3

4}, Xuesong Hu^{2

4}, Shengjie Gao^{2

4}, Yugang Zhu⁷, Haofang Mu⁸, Runping Wang⁹, Huanming Yang^{1

4

10}, Bo Li⁴

Affiliations

¹ BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.
² Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.
³ Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen, China.
⁴ BGI-Shenzhen, Shenzhen, China.
⁵ Changsha Ecological Zoo, Changsha, China.
⁶ BGI-Qingdao, BGI-Shenzhen, Qingdao, China.
⁷ Changsha Sanzhen Tiger Park, Changsha, China.
⁸ Center of Forensic Sciences, BGI, Beijing, China.
⁹ BGI Shaanxi Xixian new area Institute of Forensic Science, Xi'an, China.
¹⁰ China National GeneBank, BGI-Shenzhen, Shenzhen, China.

Abstract

As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.

Keywords: Captive inbreeding; Forensic genetics; Genetic diversity; Microsatellites; Multiplex system; Parentage testing; Pedigree identification; Short tandem repeats; Tiger.

Grants and funding

This work was supported by the Shenzhen Municipal Government of China (No. ZDSYS201507301424148). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.