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

Many different crop species were selected for a common suite of ‘domestication traits’, which facilitates their use for studies of 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 independently evolved 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 6016 and 13 730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and 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. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. 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.

研究人员选取了多种作物物种，以共同的一套‘驯化性状（domestication traits）’作为筛选标准，为平行演化（parallel evolution）相关研究提供了便利。在栽培稻（Oryza sativa）中，不同栽培品种还独立演化出了杂草型株系，这使得我们能够探究杂草型演化的遗传基础，以及该过程在多大程度上依托共享的遗传机制实现。本研究利用两个重组自交系（recombinant inbred line, RIL）群体开展杂草化相关性状的比较数量性状位点（quantitative trait locus, QTL）定位，这两个群体分别由籼型（indica）栽培稻品种与美国稻田中发现的两种独立演化的杂草型株系——稻草色稃壳株系（S）和黑稃带芒株系（B）——杂交构建得到。采用测序分型（Genotyping-by-sequencing, GBS）技术获得高密度分子标记，用于连锁图谱构建（平均标记间隔<0.25 cM）；在S群体和B群体的F5代株系中，分别定位到6016个和13730个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记。针对部分杂草化性状（芒长、稃壳色素沉着与果皮色素沉着），通过QTL定位及候选基因测序证实，相关性状的变异主要由单个基因座所致。但对于抽穗期、穗长及落粒性等更为复杂的数量性状，我们仅检测到多个QTL，未发现S与B群体间存在共享遗传基础的证据，也未在以往杂草稻研究中观察到此类共享的遗传机制。候选基因测序明确了27个已定位QTL中8个的因果遗传基础。综合上述研究结果表明，尽管水稻驯化过程中曾经历遗传瓶颈（genetic bottleneck），该栽培作物仍具备充足的遗传变异，可通过多种遗传机制演化成为农业杂草。