Origins and geographic diversification of African rice (Oryza glaberrima)
Origins and geographic diversification of African rice (Oryza glaberrima)
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DOI：
10.1101/398693
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发表时间：
2018-08
期刊：
影响因子：
3.7
通讯作者：
Margaretha A. Veltman;J. Flowers;J. Flowers;Tinde van Andel;Tinde van Andel;M. Schranz
中科院分区：
文献类型：
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作者：
Margaretha A. Veltman;J. Flowers;J. Flowers;Tinde van Andel;Tinde van Andel;M. Schranz
水稻是世界上不断增长的大多数人口的主食。亚洲稻（Oryza sativa L.）已被广泛研究，而非洲稻（Oryza glaberrima Steud.）的确切起源仍存在争议。先前的研究要么支持非洲稻驯化的单一起源说，要么支持非单一起源说。在此，我们通过对206个驯化和野生非洲稻的全基因组序列进行批判性重新评估，来审视这两种情况的证据。虽然遗传多样性分析表明驯化导致了严重的瓶颈效应，但近期强烈的正向选择特征并不能明确指向候选驯化基因，这表明非洲稻的驯化过程与亚洲稻不同——要么是对不同等位基因进行了选择，要么是选择模式不同。种群结构分析显示出五个位于不同地理区域的基因簇。在沿海种群中发现了距离隔离现象，这可以解释在地理上分离的种群中出现的平行适应。尽管全基因组系统发育关系支持起源于东部种植区，随后沿大西洋海岸多样化，但对驯化基因的进一步分析显示西南部存在独特的单倍型——这表明几个关键驯化性状中至少有一个可能起源于该地。这些发现通过强调非洲稻种植的不同根源，包括几内亚高地存在一个单独的驯化活动中心，为有关非洲植物驯化的长期争议提供了新的视角。因此，我们建议必须重新考虑普遍接受的非洲稻单一起源说，转而支持非单一起源或多起源的观点。
Rice is a staple food for the majority of our world’s growing population. Whereas Asian rice (Oryza sativa L.) has been extensively studied, the exact origins of African rice (Oryza glaberrima Steud.) are still contested. Previous studies have supported either a centric or a non-centric origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice – either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest - suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.