Plant Science Department, South Dakota State University, Brookings, South Dakota 57007, USA.
G3 (Bethesda). 2013 Jun 21;3(6):1049-59. doi: 10.1534/g3.113.006395.
Conspecific weeds retained characteristics from wild ancestors and also developed crop mimicries for adaptation and competitiveness. This research was conducted to identify quantitative trait loci (QTL) associated with the wild and crop-mimic traits and to determine haplotype variants for QTL-rich regions in U.S. weedy rice. An F2 population from the cross between a cultivated (EM93-1) and a U.S. weedy (US1) rice line was evaluated for six wild and eight crop-mimic traits in a greenhouse to identify the QTL. A core collection of 27 U.S. weedy red rice lines and 14 AA-genome wild rice lines were determined for the haplotype variants. A total of 49 QTL were identified, with 45 collocated as clusters on 14 genomic segments. The number of haplotypes across the 14 segments was lower in the weedy (6.1 ± 2.4) than in the wild (7.5 ± 1.8) rice sample. Both samples shared ~50% haplotypes (wild-like). The EM93-1-like haplotypes accounted for a greater proportion (30 ± 26%) of the haplotypes in the weedy than in the wild (7 ± 10%) rice. Based on haplotype patterns for the 14 QTL cluster regions, 26 of the 28 red rice lines were clustered into two groups corresponding to the black-hull awned and straw-hull awnless morphological types, respectively. The QTL analysis demonstrated that conspecific weed-crop differentiation involved many genomic segments with multiple loci regulating natural variation for adaptation and competitiveness. The haplotype analysis revealed that U.S. weedy rice retained large blocks of linkage disequilibrium for the multiple loci from the wild relatives and also incorporated haplotypes from cultivars.
同种杂草保留了野生祖先的特征，并为适应和竞争力发展出作物模拟特征。本研究旨在鉴定与野生和作物模拟特征相关的数量性状位点（QTL），并确定美国杂草稻中富含 QTL 的区域的单倍型变异。在温室中，对来自栽培（EM93-1）和美国杂草（US1）水稻品系杂交的 F2 群体进行了六种野生和八种作物模拟特征的评估，以鉴定 QTL。对 27 个美国杂草红米系和 14 个 AA 基因组野生稻系进行了核心收集，以确定单倍型变异。共鉴定到 49 个 QTL，其中 45 个在 14 个基因组片段上簇集。杂草稻（6.1 ± 2.4）的单倍型数量低于野生稻（7.5 ± 1.8）。两个样本共享约 50%的单倍型（野生型）。EM93-1 样单倍型在杂草稻中的比例（30 ± 26%）高于野生稻（7 ± 10%）。根据 14 个 QTL 簇区域的单倍型模式，28 个红米系中的 26 个分别聚类为黑壳芒和稻草壳无芒两种形态类型。QTL 分析表明，同种杂草-作物分化涉及许多基因组片段，多个位点调节自然变异以适应和竞争力。单倍型分析表明，美国杂草稻保留了来自野生亲缘的多个位点的大量连锁不平衡块，并且还整合了来自品种的单倍型。
