Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla

doi:10.1111/1755-0998.13747

	Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla
	Sun, Jing-Jing ; Xia, Xiao-Mei ; Wei, Xiao-Xin ; Wang, Xiao-Quan
	2023
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
卷号	23 期号:4 页码:844-854
摘要	Genetic markers have emerged as one of the most promising tools for species identification and geographic traceability in biodiversity conservation and international trade of biological products. However, traditional molecular markers rarely have sufficient resolution at lower taxonomic levels, especially for discriminating closely related forest tree species and their populations. In this study, we developed a panel of RNA-Seq based single nucleotide polymorphism (SNP) markers for tracing the geographic origin of an endangered conifer, Cathaya argyrophylla, which is a paleoendemic restricted to four mountain regions in subtropical China. A total of 69 individuals from five populations (DLS, SHS, HP, BMS, and DYS) covering the entire range were used for transcriptome sequencing. Based on these transcriptomic data, we evaluated genetic variation and population structure of C. argyrophylla, and found extremely low nucleotide diversity but strong population differentiation. We also screened 113 population-specific SNP loci, including 96 for BMS, eight for DYS, six for SHS, two for HP, and one for one of the three subpopulations from DLS. According to these geographically diagnostic SNPs, we designed four population-specific molecular barcodes for PCR amplification. To test the utility and efficiency of the four markers in geographic discrimination, double-blind experiment was performed using 157 individuals labelled without any locality information. We found that almost all tested individuals could be successfully assigned to their geographic localities. Our study not only sheds some new light on the genetic profile of C. argyrophylla, but also provides a practical and cost-efficient solution for geographic traceability using transcriptome-derived SNPs.
关键词	Cathaya double-blind trial geographic traceability population genetics RNA-seq SNPs
学科领域	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
DOI	10.1111/1755-0998.13747
收录类别	SCI
语种	英语
WOS关键词	POPULATION-STRUCTURE ; TIMBER TRACKING ; DNA ; CONSERVATION ; PROGRAM ; BARCODE ; PROTEIN ; DISCRIMINATION ; MICROSATELLITE ; GENERATION
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000901547500001
出版者	WILEY
文献子类	Article
出版地	HOBOKEN
EISSN	1755-0998
资助机构	Chinese Academy of Sciences (CAS) [XDA23080000]
作者邮箱	weixx@ibcas.ac.cn ; xiaoq_wang@ibcas.ac.cn
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/29121
专题	系统与进化植物学国家重点实验室
作者单位	1.[Sun, Jing-Jing 2.Xia, Xiao-Mei 3.Wei, Xiao-Xin 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 5.China Natl Bot Garden, Beijing, Peoples R China 6.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Sun, Jing-Jing,Xia, Xiao-Mei,Wei, Xiao-Xin,et al. Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla[J]. MOLECULAR ECOLOGY RESOURCES,2023,23(4):844-854.
APA	Sun, Jing-Jing,Xia, Xiao-Mei,Wei, Xiao-Xin,&Wang, Xiao-Quan.(2023).Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla.MOLECULAR ECOLOGY RESOURCES,23(4),844-854.
MLA	Sun, Jing-Jing,et al."Tracing the geographic origin of endangered plant species using transcriptome-derived SNPs: An example of Cathaya argyrophylla".MOLECULAR ECOLOGY RESOURCES 23.4(2023):844-854.

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