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.
Highlights
The tiger (Panthera tigris) was listed as an endangered (EN) species by the International Union for Conservation of Nature (IUCN) in 1986
A total of 139,967 valid STR loci were identified across the whole tiger genome and 31.48% and 12.76% of these STR loci display two and three to six alleles (Fig. S1A), respectively
We used the bioinformatics analysis method to identify tiger microsatellite loci on a genome-wide scale for the first time and screened 15 highly polymorphic microsatellite loci distributed on 11 chromosomes from the tiger genome
Summary
The tiger (Panthera tigris) was listed as an endangered (EN) species by the International Union for Conservation of Nature (IUCN) in 1986. As a recognized keystone species, tigers play a key role in maintaining healthy ecosystems (Cho et al, 2013). The World Wildlife Fund (WWF) worked in alliance with local governments and agencies to protect wild tiger populations. There has been an effort to conserve tigers through captive breeding programs and the efforts appeared to have paid off. The captive tiger population has greatly outnumbered the wild ones since 2007 (Luo et al, 2008). In China, the number of captive tiger population has grown rapidly since 2002 and has reached between 5,000 and 6,000 in the last 2 years (https://eia-international.org/where-are-the-tigers/)
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