Analyzing Salt Stress Response in Rice Using Phenomic and Genomic Approaches

Soil salinity is a major constraint affecting crop productivity worldwide. Thus, salinity tolerance research aims to reduce effects of this stress on growth and yield, and a better understanding of this complex trait is required.

Asian rice (Oryza sativa L.) is one of the most salt sensitive cereal crops, and previous work analyzed the natural variation of key genes in rice response to salinity [1]. For this, 59 accessions with diverse responses to salt stress were phenotypically characterized. The characterization consisted of measurements of Na⁺ and K⁺ concentrations in shoots and roots, osmotic potential, chlorophyll a and b content, as well as other biomass parameters. We analyzed this multilevel phenotype data and found significant genome-environment interactions for almost all traits, and that Na⁺concentration in shoots and shoot biomass were the traits most correlated with presence/absence of salinity stress.

Additionally, we re-sequenced the whole genomes of fifty-eight (out of 59) accessions to ~10X coverage using Illumina HiSeq2000. We aligned the reads to the Nipponbare reference genome and called SNPs. Now we are filtering over 10,000,000 raw SNPs and using the filtered set to perform a pilot genome-wide association study (GWAS). We will present the SNP-calling and GWAS results, which will provide insights into the genetic architecture of rice salt tolerance.

1. Negrão, S., Almadanim, M.C., Pires, I.S., Abreu, I.A., Maroco, J., Courtois, B., Gregorio, G.B., McNally, K.L., and Oliveira, M.M. (2013). New allelic variants found in key rice salt-tolerance genes: an association study. Plant Biotechnol Journal 11, 87-100.