Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
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DOI：
10.1073/pnas.1217133110
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发表时间：
2013-05-14
影响因子：
11.1
通讯作者：
Akhunov, Eduard
中科院分区：
文献类型：
--
作者：
Cavanagh, Colin R.;Chao, Shiaoman;Akhunov, Eduard
驯化的作物经历了强有力的人为选择，目的是开发适应当地条件的高产品种。为了检测在改良过程中受到选择的小麦基因组区域，我们开发了一种高通量阵列，以询问全球2，994份六倍体小麦（包括地方品种和现代品种）样本中的9，000个基因相关单核苷酸多态性（SNP）。利用基于SNP的多样性图谱，我们描述了作物改良对遗传多样性的基因组和地理模式的影响。我们发现了一个小的人口瓶颈和广泛使用的祖先变异的证据，往往可追溯到创始人的品种来自不同的地理区域。分析群体间的遗传分化和单倍型共享程度，我们确定了在改良过程中进行选择的等位变异体。选择性扫描发现周围的基因参与调控开花时间和物候。通过基于单倍型的分析，检测到一个野生的相对来源的基因赋予抗真菌病原体的渐渗。比较选择性扫描确定在不同的人群中，我们表明，选择可能作用于不同的目标或多个功能等同的等位基因在不同的部分小麦的地理范围。大多数选择的等位基因在当地人群中的频率较低，这表明在育种过程中可能与不断变化的农业实践或环境条件有关的定向选择目标的选择压力或时间变化较弱。开发的SNP芯片和遗传变异图谱为推进小麦育种和支持未来小麦群体基因组和全基因组关联研究提供了资源。
Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.