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

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.

Tigers of Sundarbans in India: Is the Population a Separate Conservation Unit?

“…Nine microsatellite loci, of which four loci were originally developed for Bengal tiger (PttA2, PttA4, PttC6, PttE5) [ 30 ], two (Pun82 and Pun327) for Snow leopard [ 31 ] and three (F41, Fca272 and Fca304) for domestic cat [ 32 ] were selected for the present study on the basis of small amplicon size, high amplification success and low genotyping error rate [ 33 , 34 ]. All PCR amplifications were performed as per Mishra et al [ 33 , 34 ]. All forward primers were fluorescently labelled.…”

Genetic Diversity and Population Structure in Captive Populations of Formosan Sambar Deer (Rusa unicolor swinhoei)

“…Additionally, parentage tests using microsatellites have become a valuable and widely adopted tool and gained significant importance in the breeding practices of various animals, including dogs [46], cats [47], horses [48], yak [49], and sika deer [50]. Previous studies recommended specific threshold values for PI (10 −3 to 10 −4 ) and PIsibs (<2 × 10 −2 ) for wildlife forensic applications [51,52]. These microsatellite DNA markers could also be applied to future cases related to the poaching of wild Formosan sambar deer populations or other deer species.…”

Forensic Analysis in Wildlife Crime Cases: Microscopy, DNA Profiling and Isotope Analysis

“…Generally, a panel of highly polymorphic microsatellite loci is first selected and used to generate the genetic profile of a test sample or forensic specimen [91,92]. This profile is assigned to a particular population by matching and comparing its observed alleles with the observed allele frequency in the population.…”