Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas

doi:10.3389/fgene.2021.717764

	Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas
	Wang, Quanchao 1,2; Liu, Ying 1,3; Yan, Lang 1; Chen, Linlin1,2 ; Li, Baoquan1,2
发表期刊	FRONTIERS IN GENETICS
	2021-08-19
卷号	12 页码:9
关键词	Mesocentrotus nudus single-nucleotide polymorphism discovery genetic diversity population structure China seas
DOI	10.3389/fgene.2021.717764
通讯作者	Li, Baoquan(bqli@yic.ac.cn)
英文摘要	Mesocentrotus nudus is an important commercially aquatic species because of its high edible and medicinal values. However, wild stocks have dramatically decreased in recent decades. Understanding the population structure and genetic diversity can provide vital information for genetic conservation and improvement. In the present study, the genotyping-by-sequencing (GBS) approach was adopted to identify the genome-wide single-nucleotide polymorphisms (SNPs) from a collection of 80 individuals consisting of five geographical populations (16 individuals from each population), covering the natural habitats of M. nudus in China seas. An average of 0.96-Gb clean reads per sample were sequenced, and a total of 51,738 biallelic SNPs were identified. Based on these SNPs, diversity index analysis showed that all populations have a similar pattern with positive F-is (0.136) and low Ne (724.3). Low genetic differentiation and high genetic connectivity among five geographical populations were detected by pairwise F-st, principal component analysis (PCA), admixture, and phylogenetic analysis. Besides, two YWL individuals originating from an isolated ancestor may imply that there is a genetically differentiated population in the adjacent sea. Overall, the results showed that GBS is an effective method to detect genome-wide SNPs for M. nudus and suggested that the protective measures and the investigation with larger spatial scale and sample size for M. nudus should be carried out in the future.
资助机构	Strategic Priority Research Program of the Chinese Academy of Sciences ; International Science Partnership Program of the Chinese Academy of Sciences ; Yantai Science and Technology Planning Project
收录类别	SCI
语种	英语
关键词[WOS]	STRONGYLOCENTROTUS-NUDUS ; R PACKAGE ; ADAPTATION ; CONSERVATION ; MANAGEMENT ; WEST ; REEF ; SET
研究领域[WOS]	Genetics & Heredity
WOS记录号	WOS:000724218400001
引用统计	被引频次：5[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.yic.ac.cn/handle/133337/30942
专题	海岸带生物学与生物资源利用重点实验室海岸带生物学与生物资源利用重点实验室_海岸带生物学与生物资源保护实验室
通讯作者	Li, Baoquan
作者单位	1.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Key Lab Coastal Biol & Bioresource Utilizat, Yantai, Peoples R China 2.Chinese Acad Sci, Ctr Ocean Megasci, Qingdao, Peoples R China 3.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Wang, Quanchao,Liu, Ying,Yan, Lang,et al. Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas[J]. FRONTIERS IN GENETICS,2021,12:9.
APA	Wang, Quanchao,Liu, Ying,Yan, Lang,Chen, Linlin,&Li, Baoquan.(2021).Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas.FRONTIERS IN GENETICS,12,9.
MLA	Wang, Quanchao,et al."Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas".FRONTIERS IN GENETICS 12(2021):9.