RESEARCH-PGR: Systems Genomics of Rice Stress Adaptation

New York University, New York NY

Investigators

Abstract

Adaptation of crop plants like rice to environmental stress is an essential requirement to ensure high yields under those conditions. Salinity is among the major environmental stresses that crop plants face, and it is currently threatening rice cultivation due to increasing land pressure and climate change, which are pushing agriculture to marginal lands. Rice is a major world crop comprising two species: one from Asia (Oryza sativa), and one from Africa (O. glaberrima). This project aims to identify genes associated with adaptation to saline soils through comparative analyses of rice varieties that have contrasting adaptation to salt stress, within and between the two species. The discovery of more than one adaptive strategy will increase the options rice breeders could implement in their programs. This project will use several approaches to identify genes that have a uniquely coordinated pattern of expression when the plant is exposed to elevated salt, and at the same time are correlated with vigorous growth and productivity. This project will also undertake public outreach programs using the New York City BioBus. This is a transit bus equipped as a mobile educational laboratory that has been on the road reaching 115,000 people at more than 420 schools and communities. Plant biology laboratory modules will be developed for deployment across New York City on the BioBus. These modules will primarily target schoolchildren in underserved communities, and also the general public in street fairs. Salinity is one of the growing stress challenges crop plants face. In this systems genomics proposal, we will dissect the adaptive response of O. sativa (Asian rice) and O. glaberrima (African rice) to salt stress. First, we will infer the gene regulatory interaction network for salt stress in Asian and African rice using time-series transcriptome and chromatin accessibility data, coupled with state-of-the-art network inference methods. Second, we will use phenotypic selection analysis on gene expression levels to determine the strength and pattern of selection on stress response genes. Finally, we will map expression genome-wide association (GWAS) loci accompanying gene expression variation under salt stress, focusing on the genes that have been identified in phenotypic selection analysis as undergoing positive, stabilizing or disruptive selection. Moreover, we will also identity GWAS loci for plant fitness and fitness-related traits under saline conditions in both rice species, and integrate the results of these mapping analyses and phenotypic selection analyses with evidence for selective sweeps in whole genome sequence data from Asian and African rice. Our work will identify genes, genetic networks and genomic variants that affect gene expression differences in key loci in response to an environmental perturbation - salt stress -and explicitly connect gene regulatory variation to plant fitness.