Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana.
Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana.
复制标题
DOI：
10.1371/journal.pgen.1000890
复制
发表时间：
2010-03-26
期刊：
影响因子：
4.5
通讯作者：
Weigel D
中科院分区：
文献类型：
--
作者：
Bomblies K;Yant L;Laitinen RA;Kim ST;Hollister JD;Warthmann N;Fitz J;Weigel D
随着拟南芥越来越多地被用于进化和生态学研究，了解自然遗传变异的模式和塑造它们的力量是至关重要的。以往的工作主要侧重于全球和区域范围，表明了诸如长途移徙和殖民等历史事件的重要性。关于当代因素或环境异质性在地方尺度上产生多样性格局中的作用，人们知之甚少。我们从德国图宾根周围不同环境下的77个紧密排列的林分中抽取了1005只个体。一组436个SNP标记被用来描述全基因组的关联和重组模式。相邻的遗传类型通常共享交替的标记同一性和差异性的镶嵌块。我们在大部分纯合的重组子中检测到最近的异交以及剩余杂合性的延伸。正如对其他几个自交物种所观察到的那样，在多样性和异交方面，不同地点之间存在着相当大的异质性，农村林分表现出比城市林分更大的多样性和杂合度。细尺度空间结构也很明显。在林分内，空间结构与观察到的杂合度呈负相关，这表明天然柳杉的高纯合度可能部分归因于近缘个体的近邻交配。这里使用的大量标记和广泛的本地采样为表征当地遗传模式提供了不同寻常的力量。当代过程，如正在进行的异交，在决定遗传多样性在这种规模上的分布方面发挥着重要作用。当地的“异交热点”似乎以令人惊讶的速度重新洗牌遗传信息，而其他林分的贡献相对较小。我们的研究结果对海桑种质资源的多样性取样和解释具有重要意义。受欢迎的模式植物拟南芥越来越多地被用于研究进化和生态学的问题。因此，在与单一植物相关的尺度上了解野生种群的动态是很重要的。我们分析了来自德国西南部图宾根附近77个生态多样性林地的1000多只个体。通过分析它们基因组中的数百个独立标记，我们生成了关于局部相关性和重组模式的前所未有的详细视图。正如之前对拟南芥和其他自交亲和植物所观察到的那样，即使是邻近的林分也有很强的分化。然而，个体往往与近邻关系最密切，最近重组事件的足迹是显而易见的。林分内结构明显，表明分散范围较短，最近邻居交配可能会降低杂合度。我们还观察到了农村和城市环境中林分的差异：物种丰富的农村立地的林分比物种丰富的城市立地的林分具有更高的平均遗传多样性，并提供了更多过去和正在进行的异交的证据。因此，新的基因组合可能主要出现在充当“异交热点”的一部分林分中，而其他基因组合对增加遗传多样性几乎没有贡献。
As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local “outcrossing hotspots” appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions. The popular model plant Arabidopsis thaliana is increasingly used to investigate questions in evolution and ecology. Thus it is important to understand the dynamics of wild populations at a scale relevant to single plants. We analyzed over 1,000 individuals from 77 ecologically diverse stands near Tübingen in Southwestern Germany. By assaying hundreds of independent markers in their genomes, we generated an unprecedentedly detailed view of local relatedness and recombination patterns. As has been observed previously for Arabidopsis thaliana and other self-compatible plants, even closely neighboring stands were strongly differentiated. Nevertheless, individuals tended to be most closely related to near neighbors, and footprints of recent recombination events were apparent. Structure was evident within stands, suggesting short dispersal ranges and the potential for nearest neighbor mating to reduce heterozygosity. We also observed differences between stands in rural and urban settings: stands in species-rich rural sites had higher average genetic diversity and presented more evidence of past and ongoing outcrossing than their species-poor urban counterparts. Thus novel combinations of genes may primarily arise in a subset of stands that act as “outcrossing hotspots,” while others contribute little to increasing genetic diversity.
登录
查看更多内容
影响因子：
5.7
作者：
Akinola, MO;Thompson, K;Buckland, SM
通讯作者：
Buckland, SM
影响因子：
3.8
作者：
F He;D Kang;H Gu
通讯作者：
H Gu
影响因子：
2.3
作者：
Allard, R. W.;Bradshaw, A. D.
通讯作者：
Bradshaw, A. D.
影响因子：
56.9
作者：
Clark, Richard M.;Schweikert, Gabriele;Weigel, Detlef
通讯作者：
Weigel, Detlef
影响因子：
4.5
作者：
François O;Blum MG;Jakobsson M;Rosenberg NA
通讯作者：
Rosenberg NA