Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
College of Information and Electrical Engineering, Shenyang Agricultural University, Shenyang, China.
Mol Plant. 2019 May 6;12(5):632-647. doi: 10.1016/j.molp.2019.01.019. Epub 2019 Jan 30.
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.
铲除杂草，尤其是野生稻（Oryza sativa f. spontanea）的杂草，仍然是一个谜。野生稻具有很强的生态适应性；然而，这种菌株是如何起源并逐渐形成特有遗传特征的尚不清楚。在这里，我们证明了亚洲高纬度地区的野生稻（WRAH）在系统发育上是明确的，并且在野生稻和栽培稻之间的许多分化区域具有未经选择的基因组特征。我们还鉴定了与杂草特异性特征相关的新的数量性状位点，并揭示了 1 号染色体末端的一个基因组块与水稻杂草有关。为了鉴定野生稻进化的基因组修饰，我们首次对高质量野生稻基因组（WR04-6）进行了从头组装，并对 WR04-6 与其他水稻参考基因组进行了比较基因组学研究。包括人口统计情景比较结果在内的多种证据表明，野生稻和栽培稻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产生的。一个株高模型进一步表明，WRAH 的起源可以被建模为一个进化博弈，表明由适应性驱动的基于策略的选择塑造了其基因组多样性。
