Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis
Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis
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野生对马豹猫全基因组遗传多样性和遗传结构分析
DOI：
10.3390/ani10081375
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发表时间：
2020-08-01
期刊：
影响因子：
3
通讯作者：
Murayama, Miho
中科院分区：
文献类型：
--
作者：
Ito, Hideyuki;Nakajima, Nobuyoshi;Murayama, Miho
简单总结 对马豹猫（Prionailurus bengalensis euptilurus）是阿穆尔豹猫的一个小区域种群，仅分布于日本对马岛。育种计划需要有关该种群的亲缘关系、亲属关系和近亲繁殖的充分信息。因此，迫切需要开发这些信息以保护种群及其遗传多样性。我们进行了 GRAS-Di 分析来研究对马豹猫的遗传多样性和遗传结构。我们通过三种不同的基因分型方法鉴定了 133 至 158 个单核苷酸多态性 (SNP) 标记。这些 SNP 标记可用于识别个体和亲子关系。此外，使用这些标记的结构分析表明，48只对马豹猫的样本具有相似的遗传组成，并表明对马豹猫没有亚群。我们提供了对保护对马豹猫有用的遗传标记，例如个体识别和亲子关系。此外，我们还通过结构分析明确了对马豹猫种群的保护单位。对马豹猫（Prionailurus bengalensis euptilurus）生活在日本对马岛，是阿穆尔豹猫的一个地区种群；它面临灭绝的威胁。由于其种群规模较小，其遗传管理非常重要。我们使用随机扩增子直接测序 (GRAS-Di) 进行基因分型来开发基因组草案并探索单核苷酸多态性 (SNP) 标记。使用三种基因分型方法（从头映射、对马豹猫基因组草图和家猫基因组）对 SNP 进行分析。我们检查了对马豹猫的遗传多样性和遗传结构。基因组大小约为 2.435 Gb。鉴定出的SNP数量为133-158。这些标记的力量足以进行个体和亲子鉴定。这些SNP可以提供有关对马豹猫的生活和配对的有用信息，并为引入创始人通过异地保护来保护遗传多样性提供有用的信息。我们确定对马豹猫不存在亚群。确定的单位将有助于集中保护工作。 SNP 可应用于其他地区豹猫的分析，使其可用于种群间比较和其他小种群的保护。
Simple Summary The Tsushima leopard cat,Prionailurus bengalensis euptilurus, is a small regional population of the Amur leopard cat and is only found on Tsushima Island in Japan. A breeding program will require adequate information on parentage, kinship, and inbreeding for this population. Hence, there is an urgent need to develop this information in order to conserve the population and its genetic diversity. We performed GRAS-Di analysis to investigate the genetic diversity and genetic structure of the Tsushima leopard cat. We identified between 133 and 158 single-nucleotide polymorphism (SNP) markers in three different genotyping methods. These SNP markers can be used in identification of individuals and parentage. In addition, structure analysis using these markers demonstrated the similar genetic composition of the samples from 48 Tsushima leopard cats, and indicated Tsushima leopard cats have no subpopulations. We have provided genetic markers that are useful for conservation of the Tsushima leopard cat, such as individual identification and parentage. Moreover, we have also clarified units for conservation of the Tsushima leopard cat population from structure analysis. The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133-158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.