Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs.
Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs.
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受威胁杜鹃花的保护基因组学：中性和选定 SNP 揭示的种群结构对比模式
DOI：
10.3389/fgene.2020.00757
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发表时间：
2020
影响因子：
3.7
通讯作者：
Ma Y
中科院分区：
文献类型：
--
作者：
Liu D;Zhang L;Wang J;Ma Y
虽然下一代测序技术（NGS）可以为植物保护管理提供比传统分子标记更深入的见解，但利用NGS来解决受威胁植物的保护基因组学和随后的保护策略的研究仍然很少。杜鹃花属是我国最大的木本植物属，许多物种受到威胁，但迄今为止还没有利用NGS对该属植物进行保护遗传学研究。本研究对红腹锦鸡儿的保护遗传学进行了研究。cyanocarpum，一种中国云南苍山特有的濒危物种，使用双酶切限制性位点相关DNA测序（ddRAD-seq）方法。由于有足够的SNPs，我们能够区分中性和非中性选择SNPs，并能够进一步研究R的遗传多样性，群体结构和分化。cyanocarpum，以及估计其人口统计历史。共获得6，584个SNP，其中5，729个为中性（使用Tajima's D检测）。在5，729个中性SNPs中，R. Rad-seq法分析表明，蓝果属植物的遗传多样性较高（π = 0.0702 ± 0.0017，He = 0.0675 ± 0.0016），但群体分化较弱（Fst为0.0314 ~ 0.0452）。有趣的是，从所有中性和选定的SNP中揭示了群体结构的对比模式，所有SNP和中性SNP形成了不同的遗传簇，但选定的SNP没有不同的亚组。此外，我们能够检测到有效种群大小（Ne）的变化。cyanocarpum从150，000年前，包括瓶颈事件CA。60，000年前，随后Ne在短时间内恢复，随后Ne逐渐下降。保留R的含义cyanocarpum基于这些主要结果进行了讨论。
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. Rhododendron is 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 of R. 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 in R. 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. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, He = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (Fst 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 (Ne) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of Ne over a short period, and a subsequent gradual decline in Ne to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.
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