Genetic architecture of gene regulation under salinity stress in rice

We assessed gene expression variation in a population of 195 accessions of rice (Oryza sativa) belonging to the varietal group indica and japonica. The field experiment was conducted in the dry season of 2017 at IRRI in Los Banos, Laguna, Philippines. Seeds from each accession were sown on December 19, 2016, and seedlings were then transplanted into the experimental fields at 17 days after sowing (DAS), on January 5, 2017. The field experiments was conducted across two locations close-by: one non-salinized normal field and the other salinized field. Within each field environment, there were a total of three blocks each corresponding to a replicate, with each accession planted once per block, at a random location. Each plant was planted in a single-row plots for a total of one focal plant and seven neighboring plants (included in the experiment) per plot. Each experimental plot included the accessions NSICRC 222 and NSICRC 182 serving as border rows. The application of salt in Block L5 started on January 19, 2017 when the plants were 31 days old. The salinity level was monitored by recording electrical conductivity (EC), using EC meters installed in each of the parcels at a depth of 30 cm. The salinity levels were then maintained at 6 dS/m (considered mild to moderate salinity stress) until maturity. Management and maintenance of the fields included the application of basal fertilizer, spraying of insecticides against thrips and removal of plants potentially infected with the rice tungro virus disease. Tissue collection for transcriptome. Briefly, leaf collection was done at 38 DAS (8 days after the beginning of the salt treatment) in the non-saline and saline field. Transcript levels were measured using a liquid automation-based 3' mRNA-seq quantification approach. Samples were multiplexed in batches of 96 per library.