Development and cross-amplification of novel SSR markers for population genetic analysis of Kitti’s hog-nosed bat (Craseonycteris thonglongyai) in Thailand

Kitti's hog-nosed bat or Craseonycteris thonglongyai is the only species in the family Craseonycteridae genus Craseonycteris and is considered as Endangered on the IUCN Red List of near-threatened vulnerable animals. This study aimed primarily to develop and characterize novel SSR markers specific to C. thonglongyai and secondarily to apply these markers for a preliminary assessment of genetic diversity within the species to develop a strategic conservation management plan. A total of 86 simple sequence repeats (SSR) primer pairs were developed for C. thonglongyai using an enriched-genomic DNA library with (GT)<sub>12</sub>/(CTG)<sub>9</sub> and (AG)<sub>12</sub>/(CAG)<sub>9</sub> probes. Of these, six loci showed polymorphisms within the tested C. thonglongyai samples. Genetic diversity estimates of 57 C. thonglongyai samples were based on 10 polymorphic SSR loci, including 6 newly developed loci from this study and 4 loci previously reported. In total, 48 alleles with an average of 4.8 alleles per locus were identified. The mean observed heterozygosity, expected heterozygosity, and polymorphic information content were 0.506, 0.486, and 0.494, respectively. Although no linkage disequilibrium was observed, three loci showed significant deviations from the Hardy-Weinberg equilibrium. Based on the analysis of 10 polymorphic SSR loci across 57 C. thonglongyai samples, the population in Thailand exhibited a moderate level of genetic diversity. The clustering observed in the phylogenetic tree and principal coordinate analysis did not correspond to the geographic locations of the caves. Moreover, cross-transferability of the polymorphic SSR loci from C. thonglongyai was successful in other bat species. Among the 10 polymorphic SSR loci tested across four bat families, 6 loci successfully amplified in at least one species of the Hipposideridae, Vespertilionidae, and Rhinolophidae, with polymorphic patterns observed in these amplified loci.

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Journal
Scientific Reports
Published
2025-11-29
DOI
https://doi.org/10.1038/s41598-025-30435-1
Primary Topic
Bat Biology and Ecology Studies
Type
article
Field-Weighted Citation Impact
0.00

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article

Development and cross-amplification of novel SSR markers for population genetic analysis of Kitti’s hog-nosed bat (Craseonycteris thonglongyai) in Thailand

P. P. Chareonsap, Ruangrat Buddhirongawatr, Siriporn Tungsudjai, Sarin Suwanpakdee et al.
Scientific Reports
Bat Biology and Ecology Studies
article

Development and cross-amplification of novel SSR markers for population genetic analysis of Kitti’s hog-nosed bat (Craseonycteris thonglongyai) in Thailand

P. P. Chareonsap, Ruangrat Buddhirongawatr, Siriporn Tungsudjai, Sarin Suwanpakdee, Nawarat Suksee, Nareerat Sangkachai, Thekhawet Weluwanarak, Nattaya Srisawad, Piengtawan Tappiban, Sukuman Rittem, Kridsada Chaichoun, Surachit Waengsothorn, Poonyapat Sedwisai, Kanokporn Triwitayakorn, Tatiyanuch Chamsai, Supajit Sraphet, Duncan R. Smith
article en

Abstract

Kitti's hog-nosed bat or Craseonycteris thonglongyai is the only species in the family Craseonycteridae genus Craseonycteris and is considered as Endangered on the IUCN Red List of near-threatened vulnerable animals. This study aimed primarily to develop and characterize novel SSR markers specific to C. thonglongyai and secondarily to apply these markers for a preliminary assessment of genetic diversity within the species to develop a strategic conservation management plan. A total of 86 simple sequence repeats (SSR) primer pairs were developed for C. thonglongyai using an enriched-genomic DNA library with (GT)<sub>12</sub>/(CTG)<sub>9</sub> and (AG)<sub>12</sub>/(CAG)<sub>9</sub> probes. Of these, six loci showed polymorphisms within the tested C. thonglongyai samples. Genetic diversity estimates of 57 C. thonglongyai samples were based on 10 polymorphic SSR loci, including 6 newly developed loci from this study and 4 loci previously reported. In total, 48 alleles with an average of 4.8 alleles per locus were identified. The mean observed heterozygosity, expected heterozygosity, and polymorphic information content were 0.506, 0.486, and 0.494, respectively. Although no linkage disequilibrium was observed, three loci showed significant deviations from the Hardy-Weinberg equilibrium. Based on the analysis of 10 polymorphic SSR loci across 57 C. thonglongyai samples, the population in Thailand exhibited a moderate level of genetic diversity. The clustering observed in the phylogenetic tree and principal coordinate analysis did not correspond to the geographic locations of the caves. Moreover, cross-transferability of the polymorphic SSR loci from C. thonglongyai was successful in other bat species. Among the 10 polymorphic SSR loci tested across four bat families, 6 loci successfully amplified in at least one species of the Hipposideridae, Vespertilionidae, and Rhinolophidae, with polymorphic patterns observed in these amplified loci.

Scientific ReportsVol. 16(1)
Thailand Institute of Scientific and Technological Research (TH), Mahidol University (TH), Royal Forest Department (TH), Chulabhorn Hospital (TH)
Mahidol University
Openalex Percentile: Top 72%
Bat Biology and Ecology Studies
DOIOpen Access PDFOpenAlex
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