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Conservation Genomics of a ThreatenedRhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs

文献类型： 外文期刊

作者： Liu, Detuan 1 ; Zhang, Lu 2 ; Wang, Jihua 2 ; Ma, Yongpeng 1 ;

作者机构： 1.Chinese Acad Sci, Kunming Inst Bot, Yunnan Key Lab Integrat Conservat Plant Species E, Kunming, Yunnan, Peoples R China

2.Yunnan Acad Agr Sci, Flower Res Inst, Kunming, Yunnan, Peoples R China

关键词： Rhododendron cyanocarpum; ddRAD-seq; genetic diversity; population demography; conservation

期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.599； 五年影响因子：4.888 ）

ISSN：

年卷期： 2020 年 11 卷

页码：

收录情况： SCI

摘要： Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare.Rhododendronis the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics ofR. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation inR. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima's D). In terms of the 5,729 neutral SNPs,R. cyanocarpumhad a higher genetic diversity (pi = 0.0702 +/- 0.0017,H-e= 0.0675 +/- 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (F(st)from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (N-e) ofR. cyanocarpumfrom 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery ofN(e)over a short period, and a subsequent gradual decline inN(e)to date. Implications for conservingR. cyanocarpumbased on these main results are then discussed.

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