Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape.
Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape.
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DOI：
10.1111/j.1365-294x.2011.05335.x
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发表时间：
2011-12
影响因子：
4.9
通讯作者：
Borevitz JO
中科院分区：
文献类型：
--
作者：
Morris GP;Grabowski PP;Borevitz JO
将遗传变异和种群结构的大规模模式与景观上的遗传多样性联系起来，是理解迁移和适应历史过程的关键一步。新的基因组学方法可以用来提高植物地理学研究的分辨率，同时减少位点取样效应和规避确定偏差。在这里，我们使用一种基于高通量测序的新方法来表征柳枝稷中完整叶绿体基因组和> 10，000个核位点的遗传多样性，跨越大陆和景观尺度。柳枝稷是一种北美高秆禾本科植物，广泛应用于保护区和多年生生物量生产，在整个大陆范围内表现出强烈的生态适应性和种群结构。我们对来自该物种范围内的24个个体和来自印第安纳州沙丘的20个个体的409亿个碱基对进行了测序。质体序列分析揭示了203个可变SNP位点，定义了8个单倍型群，这些单倍型群由4至127个SNP区分，并通过indel变异模式确认。这些包括三个分歧很大的单倍群，这对应于先前描述的低地-高地生态分裂和一个新的高地单倍群分裂，可追溯到中期Pleistoscene。大多数的质体单倍型组多样性存在于北方柳枝稷范围内，包括在印第安纳州沙丘，起源于中更新世或更新世之前，最近的冰后期冰化。此外，最近殖民景观功能（~150年）在印第安纳州沙丘包含几个深刻分歧的高地单倍群。核标记也支持深低地高地分裂，其次是有限的基因流，并显示广泛的基因流在当地人口的印第安纳州沙丘。
Connecting broad-scale patterns of genetic variation and population structure to genetic diversity on a landscape is a key step towards understanding historical processes of migration and adaptation. New genomic approaches can be used to increase the resolution of phylogeographic studies while reducing locus sampling effects and circumventing ascertainment bias. Here, we use a novel approach based on high-throughput sequencing to characterize genetic diversity in complete chloroplast genomes and >10,000 nuclear loci in switchgrass, across a continental and landscape scale. Switchgrass is a North American tallgrass species, which is widely used in conservation and perennial biomass production, and shows strong ecotypic adaptation and population structure across the continental range. We sequenced 40.9 billion base pairs from 24 individuals from across the species’ range and 20 individuals from the Indiana Dunes. Analysis of plastome sequence revealed 203 variable SNP sites that define eight haplogroups, which are differentiated by 4 to 127 SNPs and confirmed by patterns of indel variation. These include three deeply divergent haplogroups, which correspond to the previously described lowland-upland ecotypic split and a novel upland haplogroup split that dates to the mid-Pleistoscene. Most of the plastome haplogroup diversity present in the northern switchgrass range, including in the Indiana Dunes, originated in the mid- or upper-Pleistocene prior to the most recent postglacial recolonization. Furthermore, a recently colonized landscape feature (~150 ya) in the Indiana Dunes contains several deeply divergent upland haplogroups. Nuclear markers also support a deep lowland-upland split, followed by limited gene flow, and show extensive gene flow in the local population of the Indiana Dunes.