Preserving Pure Siamese Crocodile Populations: A Comprehensive Approach Using Multi-Genetic Tools

Area of Science:

• Conservation genetics
• Molecular ecology
• Reptile biology

Background:

• Hybridization between Siamese crocodiles (Crocodylus siamensis) and saltwater crocodiles (C. porosus) in captivity poses a significant threat to conservation and reintroduction programs.
• Previous genetic methods using microsatellite and mitochondrial DNA were limited by biased allelic frequencies and genetic drift, necessitating more robust approaches.
• Anthropogenic activities exacerbate the challenges in managing these hybrid populations and ensuring the genetic integrity of endangered species.

Purpose of the Study:

• To identify genome-wide single nucleotide polymorphisms (SNPs) in Siamese and saltwater crocodiles using DArT sequencing.
• To develop and validate species-diagnostic SNP markers for accurate identification of parental species and their hybrids.
• To compare analytical approaches for diagnosing hybridization levels, including backcrossing events.

Main Methods:

• DArT sequencing was employed to identify genome-wide SNPs in both crocodile species.
• Species-diagnostic SNP loci were identified for Siamese crocodiles (8051 loci) and saltwater crocodiles (1288 loci).
• A PCR-based approach was used to validate selected SNP loci, with 3 loci successfully differentiating species and hybridization levels.

Main Results:

• Approximately 17.00-26.00% of loci were conserved between the genomes of Siamese and saltwater crocodiles.
• Species-diagnostic SNP markers were successfully identified and validated, enabling precise genetic identification.
• A novel combined method integrating mitochondrial and nuclear genetic information (microsatellite genotyping and diagnostic DNA markers) was developed.

Conclusions:

• The developed SNP markers and combined genetic approach provide a reliable tool for assessing hybridization in crocodile populations.
• This method can overcome limitations of previous genetic analyses, offering improved accuracy for conservation management.
• Accurate genetic assessment is crucial for conservation prioritization, ensuring sustainable genetic integrity and long-term species survival in reintroduction programs.