Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study

Sudhanshu Mishra,Jouni Aspi,Ashok Kumar Munjal,Sujeet Kumar Singh,Surendra Prakash Goyal

doi:10.1186/2193-1801-3-4

Abstract

In India, six landscapes and source populations that are important for long-term conservation of Bengal tigers (Panthera tigris tigris) have been identified. Except for a few studies, nothing is known regarding the genetic structure and extent of gene flow among most of the tiger populations across India as the majority of them are small, fragmented and isolated. Thus, individual-based relationships are required to understand the species ecology and biology for planning effective conservation and genetics-based individual identification has been widely used. But this needs screening and describing characteristics of microsatellite loci from DNA from good-quality sources so that the required number of loci can be selected and the genotyping error rate minimized. In the studies so far conducted on the Bengal tiger, a very small number of loci (n = 35) have been tested with high-quality source of DNA, and information on locus-specific characteristics is lacking. The use of such characteristics has been strongly recommended in the literature to minimize the error rate and by the International Society for Forensic Genetics (ISFG) for forensic purposes. Therefore, we describe for the first time locus-specific genetic and genotyping profile characteristics, crucial for population genetic studies, using high-quality source of DNA of the Bengal tiger. We screened 39 heterologous microsatellite loci (Sumatran tiger, domestic cat, Asiatic lion and snow leopard) in captive individuals (n = 8), of which 21 loci are being reported for the first time in the Bengal tiger, providing an additional choice for selection. The mean relatedness coefficient (R = −0.143) indicates that the selected tigers were unrelated. Thirty-four loci were polymorphic, with the number of alleles ranging from 2 to 7 per locus, and the remaining five loci were monomorphic. Based on the PIC values (> 0.500), and other characteristics, we suggest that 16 loci (3 to 7 alleles) be used for genetic and forensic study purposes. The probabilities of matching genotypes of unrelated individuals (3.692 × 10-19) and siblings (4.003 × 10-6) are within the values needed for undertaking studies in population genetics, relatedness, sociobiology and forensics.

Highlights

The conservation of the tiger, among the large felids, has been a global issue because of the extinction of three subspecies (Luo et al 2004) and the decline of 93% of the habitat of the tiger (Karanth et al 2010)
Among the extant tiger subspecies, the largest population (1706) is that of the Bengal tiger (Jhala et al 2011), which is the national animal of India and an endangered species listed under Schedule I of the Wildlife (Protection) Act, 1972 of India
We describe for the first time the screening and genotyping profile characteristics of 39 microsatellite markers developed for the Sumatran tiger (Panthera tigris sumatrae), domestic cat (Felis catus), Asiatic lion (Panthera leo persica) and snow leopard using DNA from a high-quality source

Summary

Introduction

The conservation of the tiger, among the large felids, has been a global issue because of the extinction of three subspecies (Luo et al 2004) and the decline of 93% of the habitat of the tiger (Karanth et al 2010). Most of the studies undertaken so far on the Bengal tiger (Bhagavatula and Singh 2006; Mondol et al 2009b; Reddy et al 2012; Sharma et al 2013) fail to provide detailed information on locus-specific genetic characteristics (polymorphic information content [PIC] and probability of identity [PID]) and genotyping profile characteristics (stutter, allele to peak height etc.).

Results

Conclusion