Data from: Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that
competes aggressively with the crop and limits rice productivity
worldwide. Most genetic studies of weedy rice have focused on populations
in regions where no reproductively compatible wild Oryza species occur
(North America, Europe, northern Asia). Here we examined the population
genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be
found growing in close proximity to cultivated and weedy rice. Using 375
accessions and a combined analysis of 24 neutral SSR loci and two rice
domestication genes (sh4, controlling seed shattering, and Bh4,
controlling hull color), we addressed the following questions: 1) What is
the relationship of Malaysian weedy rice to domesticated and wild rice,
and to weedy rice strains in the US? 2) To what extent does the presence
of O. rufipogon influence the genetic and phenotypic diversity of
Malaysian weeds? 3) What do the distributions of sh4 and Bh4 alleles and
associated phenotypes reveal about the origin and contemporary evolution
of Malaysian weedy rice? Our results reveal: independent evolutionary
origins for Malaysian weeds and US strains, despite their very close
phenotypic resemblance; wild-to-weed gene flow in Malaysian weed
populations, including apparent adaptive introgression of seed-shattering
alleles; and a prominent role for modern Malaysian cultivars in the origin
and recent proliferation of Malaysian weeds. These findings suggest that
the genetic complexity and adaptability of weedy crop relatives can be
profoundly influenced by proximity to reproductively compatible wild and
domesticated populations.

杂草稻是栽培稻（Oryza sativa）的近缘种，与栽培稻竞争激烈，限制了全球水稻产量。大多数杂草稻遗传学研究集中于无生殖兼容野生稻属物种分布的区域（北美、欧洲、北亚）。本研究分析了马来西亚杂草稻的群体遗传学特征，该地区普通野生稻（O. rufipogon）常与栽培稻及杂草稻毗邻生长。利用375份材料，结合24个中性SSR位点与两个水稻驯化基因（sh4，控制种子落粒性；Bh4，控制颖壳颜色）的联合分析，我们探讨了以下问题：1）马来西亚杂草稻与栽培稻、野生稻及美国杂草稻品系的亲缘关系如何？2）普通野生稻（O. rufipogon）的存在对马来西亚杂草稻的遗传及表型多样性有何影响？3）sh4与Bh4等位基因的分布及其相关表型，能揭示马来西亚杂草稻起源与近期演化的哪些信息？研究结果表明：尽管马来西亚杂草稻与美国品系表型高度相似，但其演化起源独立；马来西亚杂草稻群体中存在野生稻向杂草稻的基因流，包括落粒性等位基因的适应性渐渗；现代马来西亚栽培品种在当地杂草稻的起源及近期扩散中扮演重要角色。这些发现提示，与生殖兼容的野生及栽培种群的毗邻分布，可对作物近缘杂草的遗传复杂性与适应性产生深远影响。