Crop weediness, especially that of weedy rice (Oryza sativa f. spontanea), remains mysterious. Weedy rice possesses robust ecological adaptability; however, how this strain originated and gradually formed proprietary genetic features remains unclear. Here, we demonstrate that weedy rice at Asian high latitudes (WRAH) is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice. We also identified novel quantitative trait loci underlying weedy-specific traits, and revealed that a genome block on the end of chromosome 1 is associated with rice weediness. To identify the genomic modifications underlying weedy rice evolution, we generated the first de novo assembly of a high-quality weedy rice genome (WR04-6), and conducted a comparative genomics study between WR04-6 with other rice reference genomes. Multiple lines of evidence, including the results of demographic scenario comparisons, suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication. A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.

作物杂草，尤其是杂草稻（的水稻˚F。spontanea），仍然是神秘的。杂草稻具有很强的生态适应性。然而，尚不清楚该菌株如何起源并逐渐形成专有的遗传特征。在这里，我们展示了在亚洲的高纬度地区（即杂草稻WRAH）的系统发育明确界定，并在杂草与栽培稻之间有许多分歧地区拥有未选择的基因组特征。我们还确定了潜在的杂草特异性性状的新的数量性状基因座，并揭示了染色体1末端的基因组区与水稻的杂草性有关。为了确定杂草水稻进化的基础基因组修饰，我们产生了第一个从头开始组装高质量的杂草水稻基因组（WR04-6），并在WR04-6与其他水稻参考基因组之间进行了比较基因组学研究。多方面的证据，包括人口统计学情况的比较结果，表明，杂草稻和栽培稻之间的分化是由栽培稻的遗传改良引起的，杂草的本质是通过半驯化而出现的。植物高度模型进一步暗示了WRAH的起源可以被建模为进化博弈，并表明由适应性驱动的基于策略的选择影响了其基因组多样性。