Genome-Wide Association Study for Mid-Salt Tolerance in Rice

Salt stress is one of the environmental constraints that affect crop cultivation worldwide, since more than 800 Mha of land throughout the world suffer from salinization problems. Among cereals, rice (Oryza sativa L.) is one of the most sensitive to salt stress, although cultivars can differ in their response to salinity. In Europe, due to scarce water availability and the rise in sea levels, there is a clear tendency toward salinization in the river deltas where rice is grown. Thus, the identification of rice cultivars tolerant to salt stress and the dissection of salt stress tolerance mechanisms are of high interest for European rice breeding. Plant response to salt stress is a complex trait, depending on the combination of many genes and metabolic pathways, and thus difficult to control and engineer. Exploiting natural variation occurring in worldwide genotypes may be a powerful approach to discover new traits to tolerate high salinity conditions. In this context, a phenotyping activity has been performed to study the natural variation of a worldwide japonica rice collection in response to mid-salt stress. A greenhouse experiment was carried out on 281 japonica rice cultivars subjected to salt stress and the measurement of physiological traits (i.e. seedlings emergence rate, plant growth, chlorophyll fluorescence, flowering delay) was assessed. A genome wide association study (GWAS) highlighted the presence of significant loci involved in salt tolerance. Analysis of candidate genes significantly associated to these loci is in progress.