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Can Malayan tapir's extinction be prevented? A genetic approach to its conservation

马来貘的灭绝可以避免吗？

基本信息

批准号：
21J15064
负责人：
LIM QILUAN
金额：
$ 0.96万
依托单位：
Kyoto University
依托单位国家：
日本
项目类别：
Grant-in-Aid for JSPS Fellows
财政年份：
2021
资助国家：
日本
起止时间：
2021-04-28 至 2023-03-31
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21J15064/
关键词：
genomics Malay tapir microsatellite SNP markers Japan Peninsular Malaysia conservation demographic history genetic diversity short tandem repeat d-loop genome Asian tapir bioinformatics SNP marker

项目摘要

From May to August 2022, a research trip was made to Peninsular Malaysia to conduct microsatellite analysis of 41 wild tapir samples using 38 novel microsatellite markers developed in this study. Genomic analyses of six Malayan tapirs from Japan institutions, each two with putative origins from Peninsular Malaysia, Thailand, and Sumatra, was conducted to infer the changes in historical effective population size that was as low as 2000-4000 upon entering Holocene and a population split between the mainland Southeast Asia and Sumatran populations >10k years ago. Using the six genomes and two public genomes, a custom panel of 24k single nucleotide polymorphism was developed, which targets mutations that are of moderate to high impacts to the gene functions. It was found that Sumatran samples showed a significantly higher loss-of-function mutations than the Peninsular Malaysian- and Thailand-origin samples. Malaysian and Sumatran samples also show higher inbreeding coefficients from the analysis of runs of homozygosity. More samples are required to clarify this. These results were presented three international conferences and a best poster prize was won. A scientific article was published in Global Ecology and Conservation. A Wildlife Conservation and Bioinformatics Workshop was held in March 2023. A Malaysian government wildlife research officer was invited to Japan to participate in the workshop as a mean for capacity building and for fostering the research connection between Wildlife Research Center of Kyoto University and the department of wildlife in Peninsular Malaysia.

2022年5月至8月，研究人员前往马来西亚半岛，使用本研究开发的38个新型微卫星标记对41个野生貘样本进行微卫星分析。对来自日本机构的6只马来貘进行了基因组分析，每两只都假定起源于马来西亚半岛、泰国和苏门答腊，以推断进入全新世后历史有效种群规模的变化，即低至2000-4000，以及1万年前东南亚大陆和苏门答腊种群之间的种群分裂。使用六个基因组和两个公共基因组，开发了24 k单核苷酸多态性的定制面板，其靶向对基因功能具有中度至高度影响的突变。结果发现，苏门答腊样本显示出显着更高的功能丧失突变比半岛马来西亚和泰国的起源样品。马来西亚和苏门答腊的样本也显示出较高的近交系数的纯合性运行的分析。需要更多的样本来澄清这一点。这些成果在三次国际会议上发表，并获得了最佳海报奖。一篇科学文章发表在《全球生态与保护》上。2023年3月举办了野生动物保护和生物信息学工作坊。一名马来西亚政府野生动物研究官员应邀前往日本参加讲习班，作为能力建设和促进京都大学野生动物研究中心与马来西亚半岛野生动物系之间研究联系的一种手段。

项目成果

期刊论文数量（0）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Genome-wide runs of homozygosity analysis in six captive Malayan tapirs in Japan

日本六只圈养马来貘的全基因组纯合性分析

DOI：
发表时间：
2022
期刊：
影响因子：
0
作者：
Lim;Q. L.;Rosli;N.;& Murayama;M.
通讯作者：
M.

Genetic assessment of the captive Malayan tapir in Japanese zoos

日本动物园圈养马来貘的遗传评估

DOI：
发表时间：
2021
期刊：
影响因子：
0
作者：
QL Lim;G Annavi;M Inoue-Murayama
通讯作者：
M Inoue-Murayama

Genetic diversity and phylogenetic relationships of Malayan tapir (Tapirus indicus) populations in the Malay Peninsula based on mitochondrial DNA control region

基于线粒体DNA控制区的马来半岛马来貘（Tapirus indicus）种群遗传多样性和系统发育关系

DOI：
10.1007/s10531-021-02202-x
发表时间：
2021
期刊：
Biodiversity and Conservation
影响因子：
3.4
作者：
Lim Qi Luan;Yong Christina Seok Yien;Ng Wei Lun;Ismail Ahmad;Rovie-Ryan Jeffrine J.;Rosli Norsyamimi;Annavi Geetha
通讯作者：
Annavi Geetha

Whole-genome resequencing of endangered Malayan tapir for novel discovery of genome-wide single nucleotide polymorphism loci

濒危马来貘全基因组重测序新发现全基因组单核苷酸多态性位点