Genome-wide association study for mild-salt tolerance in rice

Soil salinity is one of the environmental constraints that affect crop cultivation worldwide. Among cereals, rice (Oryza sativa L.) is one of the most salt-sensitive although cultivars can differ in their response to salt stress. In European coastal rice areas, salty raining and the salt wedge intrusion phenomenon caused by the rise in the sea levels consequent to the ongoing climate changes are provoking a tendency toward salinization in the adjacent paddy fields 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 genes involved in salt tolerance. In this context, a phenotyping activity has been performed in a greenhouse to study the natural variation of a worldwide japonica rice collection (281 cultivars) in the responses to mid-salt stress. Plants were grown, under submerged conditions, in pots containing paddy soil and measurement of some physiological traits such as, seedling emergence percent; plant height, chlorophyll a fluorescence on the flag leaf 10 days after flowering, delay in flowering; infrared thermography, was assessed. Moreover, visual salt injuries at vegetative stage were determined by using the Standard Evaluation Score (SES) proposed by IRRI To identify significant loci putatively involved in salt tolerance a genome wide association study (GWAS) was performed. For this purpose the stress susceptibility index (SSI) was calculated for all the phenotypic traits analyzed by using the following formula: SSI = (1 − Ys/Yp)/D, where Ys is the mean performance of a genotype under stress, Yp is the mean performance of the same genotype without stress, D (stress intensity) = 1 − (mean Ys of all genotypes/mean Yp of all genotypes). Results highlighted a variability among the genotypes in response to the treatment, suggesting that the rice population used might be a good resource for the discovery of traits related to salt stress response. Moreover, the GWAS identified several significant associations between SNPs and the analyzed salt stress-related traits. In particular 24 most significant loci were identified. The analysis of these gene is still in progress.