Data from: More than one way to evolve a weed: Parallel evolution of U.S. weedy rice through independent genetic mechanisms

Many crop species have been independently selected for a shared suite of “domestication traits,” facilitating studies on parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two major weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping-by-sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6,016 and 13,730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length and grain pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed a causal role for previously described molecular variation, with trait variation largely attributable to individual loci. However, for more complex quantitative traits (heading date, panicle length, seed shattering) we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.多种作物物种均经历了独立的选择过程，演化出一套共通的“驯化性状”，为平行进化相关研究提供了便利。在驯化水稻（Oryza sativa）中，不同栽培品种也独立演化出了杂草型品系，这使得我们得以探究杂草型平行演化的遗传基础，以及该过程在多大程度上依赖于共通的遗传机制。本研究针对杂草化性状开展了比较数量性状位点（Quantitative Trait Locus, QTL）定位分析，所用的两个重组自交系群体分别由籼稻栽培品种与美国稻田中两类主要杂草型菌株的代表株系杂交得到，这两类杂草菌株分别为稻草壳型（strawhull, S）和黑壳颖毛型（blackhull awned, B）。通过测序分型技术（Genotyping-by-Sequencing, GBS）获得了高密度分子标记用于连锁图谱构建（平均标记间距<0.25 cM）；在S群体和B群体的F5代株系中，分别定位到6016和13730个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）标记。针对部分杂草化性状（颖毛长度与籽粒色素沉着），QTL定位结合候选基因测序分析证实，此前报道的分子变异确实发挥了因果作用，且性状变异主要由单个位点决定。然而对于抽穗期、穗长、落粒性等更为复杂的数量性状，我们共检测到多个QTL，但未发现S与B群体间存在共通遗传基础的显著证据，且与此前针对杂草稻的相关研究也缺乏共通性。综合以上研究结果表明，尽管水稻驯化过程中曾经历遗传瓶颈，但该栽培作物仍拥有充足的遗传变异，能够通过多种遗传机制演化成为农业杂草。