Upland and lowland rices (Oryza sativa) are the two most important rice ecotypes adapted to agricultural ecosystems of contrasting soil water conditions. Consequently, they have distinguished genetic features associated with drought resistance. As they are essential germplasm resources for breeding water-saving and drought-resistant rice, effective methods for discriminating rice ecotypes and evaluating their drought resistances are required. Five and three selective SSR loci respectively for japonica and indica, located in the drought-responding expression sequence tags (EST), were involved in this study. The discriminating index was calculated from the allele frequencies of these EST-SSRs between the two ecotypes. The discriminating index of upland rice was significantly higher than that of lowland rice. Moreover, the discriminating index had distinct distribution patterns between upland and lowland ecotypes. There were ecotype-like gradients of the discriminating index in which most landraces of the corresponding ecotype were located. Using the ecotype-like gradients, we can accurately distinguish upland and lowland rice with a discriminating power of 0.89 in japonica and 0.82 in indica. Noticeably, the discriminating index was significantly correlated with rice drought resistance; therefore, it greatly facilitates the process of drought-resistance screens. As these drought-resistance-associated EST-SSRs were divergently selected among upland and lowland rice, the discriminating index can be well applied in the practices of germplasm collection and breeding. The findings bridge the knowledge gaps between population genetics and breeding practice. Once more informative loci have been involved, the powers for ecotype discrimination and drought-resistance prediction will be improved.
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This research was supported by the Natural Science Foundation of China (grant no. 31200279), Postdoctoral Science Foundation, Shanghai (no. 12R21421300), and the National High-Tech Research and Development Program of China (863 Plan) (grant no. 2014AA10A601-2). Rice materials in this study were kindly provided by the Rice Research Institute of the Guangxi Academy of Agricultural Science, Hebei Academy of Agricultural Science, Yunnan Academy of Agricultural Science, and Jiangsu Academy of Agricultural Science.
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