Domestication history and geographical adaptation inferred from a SNP map of African rice
Domestication history and geographical adaptation inferred from a SNP map of African rice
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DOI：
10.1038/ng.3633
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发表时间：
2016-09-01
期刊：
影响因子：
30.8
通讯作者：
Purugganan, Michael D.
中科院分区：
文献类型：
--
作者：
Meyer, Rachel S.;Choi, Jae Young;Purugganan, Michael D.
非洲稻（Oryza glaberrima Steud.）是与亚洲稻（Oryza sativa L.）但在西非独立驯化类似于3,000年前（1-3）。非洲水稻很少在撒哈拉以南非洲以外种植，但由于其对非生物胁迫的耐受性而受到全球关注（4，5）。在这里，我们描述了一个232万SNPs的非洲水稻全基因组重测序的93个地方品种的地图。种群基因组分析显示，该物种的种群瓶颈始于13，000 - 15，000年前，有效种群规模达到3，500年前的最小值，这表明种群规模的长期减少可能始于驯化前的管理和/或栽培。对6个耐盐性状的全基因组关联研究（GWAS）发现了11个显著的位点，其中4个位点位于300 kb左右的基因组区域内，具有正选择的特征，表明该物种的耐盐性具有适应性地理差异。
African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa similar to 3,000 years ago(1-3). African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses(4,5). Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began similar to 13,000-15,000 years ago with effective population size reaching its minimum value similar to 3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within similar to 300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species.