期刊
G3-GENES GENOMES GENETICS
卷 3, 期 6, 页码 1049-1059出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.113.006395
关键词
weedy rice; adaptation; crop mimicry; quantitative trait locus; haplotype
资金
- United States Department of Agriculture-National Research Initiative [2008-35301-19058]
- National Science Foundation (IOS) [0641376, 1021382]
- South Dakota Agricultural Extension Station and Drought Center
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [0641376] Funding Source: National Science Foundation
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [1021382] Funding Source: National Science Foundation
- NIFA [2008-35301-19058, 583579] Funding Source: Federal RePORTER
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 F-2 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 similar to 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.
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