Distinguishing upland and lowland rice ecotypes by selective SSRs and their applications in molecular-assisted selection of rice drought resistance

Abstract

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.