Data from: Increased novel single nucleotide polymorphisms in weedy rice populations associated with the change of farming styles: Implications in adaptive mutation and evolution

Substantial genetic variation is found in weedy rice (Oryza sativa f. spontanea Roshev.) populations from different rice-planting regions with the change of farming styles. To determine the association of such genetic variation with rice farming changes is critical for understanding the adaptive evolution of weedy rice. We studied weedy-rice specific novel SNPs by genome-wide comparison between DNA sequences of weedy and cultivated rice, in addition to PCR fingerprinting at 22 selected novel SNP loci in weedy rice populations. A great number of novel SNPs were identified across the weedy rice genome. High frequencies of the novel SNPs were determined at the 22 selected loci, although with considerable variation among weedy rice populations in different rice-planting regions. The highest frequency (~57%) of novel SNPs was identified in weedy rice populations from Jiangsu that experienced the most dramatic changes in rice farming styles, including the shift from transplanting to direct seeding, and from indica to japonica varieties. The lowest frequency (~29%) was detected in weedy rice populations from Northeast China where rice farming has a relatively less change. The association between frequencies of novel SNPs in weedy rice populations and the extent of changes in rice farming styles suggests the critical role of adaptive mutation and accumulation of the mutation influenced by human activities in the rapid evolution of weedy rice.

不同水稻种植区的杂草稻（Oryza sativa f. spontanea Roshev.）种群中存在大量遗传变异，且该变异随耕作方式的改变而呈现差异。明确此类遗传变异与水稻耕作方式变革之间的关联，对于解析杂草稻的适应性演化机制至关重要。本研究通过杂草稻与栽培稻的全基因组DNA序列比对，结合对杂草稻种群中22个筛选得到的新型单核苷酸多态性（Single Nucleotide Polymorphism，简称SNP，复数形式SNPs）位点进行聚合酶链式反应（Polymerase Chain Reaction，简称PCR）指纹图谱分析，鉴定了杂草稻特异性的新型SNP。研究在杂草稻全基因组中鉴定出大量新型SNP。尽管不同水稻种植区的杂草稻种群间存在显著变异，但在上述22个筛选得到的位点中，新型SNP均呈现较高的检出频率。来自江苏的杂草稻种群中新型SNP检出频率最高（约57%），该区域的水稻耕作方式变革最为剧烈，包括从插秧移栽改为直播栽培，以及从籼稻（indica）品种替换为粳稻（japonica）品种。而来自东北地区的杂草稻种群中新型SNP检出频率最低（约29%），该区域的水稻耕作方式相对变化较小。杂草稻种群中新型SNP检出频率与水稻耕作方式变革程度之间的关联，表明适应性突变以及受人类活动影响的突变积累，在杂草稻的快速演化过程中发挥关键作用。