TY - JOUR
T1 - Preserving Pure Siamese Crocodile Populations
T2 - A Comprehensive Approach Using Multi-Genetic Tools
AU - Panthum, Thitipong
AU - Ariyaraphong, Nattakan
AU - Wongloet, Wongsathit
AU - Wattanadilokchatkun, Pish
AU - Laopichienpong, Nararat
AU - Rasoarahona, Ryan
AU - Singchat, Worapong
AU - Ahmad, Syed Farhan
AU - Kraichak, Ekaphan
AU - Muangmai, Narongrit
AU - Duengkae, Prateep
AU - Fukuda, Yusuke
AU - Banks, Sam
AU - Temsiripong, Yosapong
AU - Ezaz, Tariq
AU - Srikulnath, Kornsorn
N1 - Funding Information:
This research was financially supported in part by the Thailand Science Research and Innovation through the Kasetsart University Reinventing University Program 2021 (3/2564), which was awarded to T.P. and K.S.; the High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA) (6417400247), which was awarded to T.P. and K.S.; the Center of Excellence on Agricultural Biotechnology, Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation. (AG-BIO/MHESI) (No. 60-005-021), which was awarded to K.S.; the Higher Education for Industry Consortium (Hi-FI) (6414400777), which was awarded to N.A.; and funding from the Office of the Ministry of Higher Education, Science, Research, and Innovation. International SciKU Branding (ISB), Faculty of Science, Kasetsart University, which was awarded to W.S., S.F.A., and K.S.
Publisher Copyright:
© 2023 by the authors.
PY - 2023/11
Y1 - 2023/11
N2 - Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00–26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs.
AB - Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00–26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs.
KW - conservation
KW - hybrid
KW - reintroduction
KW - saltwater crocodile
KW - Siamese crocodile
KW - SNP
UR - http://www.scopus.com/inward/record.url?scp=85188536306&partnerID=8YFLogxK
U2 - 10.3390/biology12111428
DO - 10.3390/biology12111428
M3 - Article
AN - SCOPUS:85188536306
SN - 2079-7737
VL - 12
SP - 1
EP - 20
JO - Biology
JF - Biology
IS - 11
M1 - 1428
ER -