2021 Fiscal Year Annual Research Report
Can Malayan tapir's extinction be prevented? A genetic approach to its conservation
| Project/Area Number |
21J15064
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| Research Institution | Kyoto University |
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Principal Investigator |
LIM QILUAN 京都大学, 理学研究科, 特別研究員(DC2)
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| Project Period (FY) |
2021-04-28 – 2023-03-31
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| Keywords | genetic diversity / short tandem repeat / d-loop / genome / Asian tapir / demographic history / bioinformatics / SNP marker |
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| Outline of Annual Research Achievements |
Thirty-one Malayan tapir samples collected from 10 Japanese zoos and 1 breeding centre were analysed using 38 novel and 9 cross-species microsatellite markers and mitochondrial DNA control region to investigate the population genetic structure. Three genetic clusters corresponding to three regions (i.e., Peninsular Malaysia, Thailand, Indonesia), were identified. Six of the samples, selected based on their putative origins, were sequenced on a next-generation sequencing platform. Historical effective population size of the Malayan tapir populations in Southeast Asia was investigated in the six genomes using Pairwise sequentially Markovian coalescent analysis. The results suggested that the population on the Sumatra island of Indonesia has been isolated from its counterpart in the Malay Peninsula, corresponding to the geographical barrier by the Straits of Malacca that has emerged since 10 thousand years ago post-Last Glacial Period. This information will provide genetic insights for the captive breeding programs in Japan and in other parts of the world, on whether breeding between Malayan tapirs from different regions should be encouraged for their conservation.
Adding two genomes retrieved from the short read archive, bioinformatic analysis was performed on the eight tapir genomes and identified >2 million potentially useful single nucleotide polymorphism (SNP) sites. These SNP sites are novel nuclear markers that will allow future SNP probe design for the Malayan tapir, which can be applied for genetic diversity analysis between populations worldwide on a genomic scale.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
Due to the Covid-19 situation, there was a delay in getting samples/visiting countries for DNA analysis. Samples from Europe have not been received. Visits to Malaysia, Thailand and Indonesia were not possible due to international border controls. However, whole-genome resequencing of six Malayan tapir samples obtained from the Japanese zoos was completed. Using the genome data, potentially useful single nucleotide polymorphism markers were identified, and historical effective population sizes of the Malayan tapir populations in Southeast Asia were deduced. Moreover, although my progress was slower than planned, I recovered my progress by publishing two scientific papers and presenting at six conferences.
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| Strategy for Future Research Activity |
Malayan tapir populations in Malaysia will be the main focus for the following DNA analysis using the novel microsatellite markers and mitochondrial DNA control region. This is because the necessary permit has already been obtained, and research plan has been acknowledged by the government. A research trip to Malaysia will be made during May-July. On the other hand, communications with Thailand, Indonesia, Europe and the USA for import of samples/visit to the countries will be continued to complete the DNA analysis on the samples from this regions. However, this will only be done when time and resources are reasonably adequate.
The whole-genome resequencing data that has been obtained will be further analysed for investigating the mutations in functional genes and for designing probes for the identified single nucleotide polymorphism. The probes will be applied for future population analysis on samples currently or will be available in Japan.
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[Journal Article] Microsatellite records for?volume 13, issue 42021
Author(s)
Chantra Rachawadee、Dai Yufei、Inoue-Murayama Miho、Kittiwattanawong Kongkiat、Lim Qi Luan、Rovie-Ryan Jeffrine J.、Sakornwimon Watchara、Wang Xianyan、Zhao Liyuan
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Journal Title
Conservation Genetics Resources
Volume: 13
Pages: 465～471
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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