Genome-Wide Survey on Genomic Variation, Expression Divergence, and Evolution in Two Contrasting Rice Genotypes under High Salinity Stress

Abstract

Expression profiling is one of the most important tools for dissecting biological functions of genes and the upregulation or downregulation of gene expression is sufficient for recreating phenotypic differences. Expression divergence of genes significantly contributes to phenotypic variations. However, little is known on the molecular basis of expression divergence and evolution among rice genotypes with contrasting phenotypes. In this study, we have implemented an integrative approach using bioinformatics and experimental analyses to provide insights into genomic variation, expression divergence, and evolution between salinity-sensitive rice variety Nipponbare and tolerant rice line Pokkali under normal and high salinity stress conditions. We have detected thousands of differentially expressed genes between these two genotypes and thousands of up- or downregulated genes under high salinity stress. Many genes were first detected with expression evidence using custom microarray analysis. Some gene families were preferentially regulated by high salinity stress and might play key roles in stress-responsive biological processes. Genomic variations in promoter regions resulted from single nucleotide polymorphisms, indels (1–10 bp of insertion/deletion), and structural variations significantly contributed to the expression divergence and regulation. Our data also showed that tandem and segmental duplication, CACTA and hAT elements played roles in the evolution of gene expression divergence and regulation between these two contrasting genotypes under normal or high salinity stress conditions.

Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress

“…First, proper controls have to be analyzed, which also means evaluating the biomass of plants both in control and salt stress conditions, and controlling for the biomass in control conditions when necessary. It is common to use rice cultivar Pokkali as a salt‐tolerant reference in salinity stress experiments (Bhowmik et al , Jiang et al , Jain et al ). However Pokkali was one of the biggest plants, among the 56 different rice genotypes we analyzed under control conditions.…”

Genetic Variation for Salinity Tolerance in Pakistani Rice (Oryza sativa L.) Germplasm

“…) from Pakistan, Nipponbare (Jiang et al. ) from Japan and Azucena (Awala et al ) from Philippines were previously reported as salt sensitive. Due to large number of genotypes, screening at germination stage was carried out in three sets of 33, 76 and 76 genotypes, whereas screening at vegetative stage was carried out in three sets of 70, 55 and 60.…”

“…Seeds of these genotypes were acquired from the Genebank of Plant Genetic Resources Institute, National Agricultural Research Centre, Islamabad, Pakistan, and other rice research institutes of Pakistan. Among the studied genotypes, Nona Bokra and Kharai Ganja (Khan et al 1987) and IR-6 from Pakistan were salt-tolerant (Gurmani et al 2006), whereas Basmati-370 (Yadav et al 2008) from Pakistan, Nipponbare (Jiang et al 2013) from Japan and Azucena (Awala et al 2010) from Philippines were previously reported as salt sensitive. Due to large number of genotypes, screening at germination stage was carried out in three sets of 33, 76 and 76 genotypes, whereas screening at vegetative stage was carried out in three sets of 70, 55 and 60.…”

Integrating omics analysis of salt stress-responsive genes in rice

“…Of these, the affymetrix microarray platform is the most popular, and to date, 2741 array data have been produced and deposited at NCBI gene expression omnibus (GEO, http://www.ncbi.nlm.nih.gov/ geo/) (Barrett et al 2011). Of these, seven GEO data series have been produced to explore genome-wide transcriptional profiles in response to salt stress (Cotsaftis et al 2011;Jain et al 2007;Jiang et al 2013;Pandit et al 2010;Walia et al 2005Walia et al , 2007Walia et al , 2009. These experiments suggest a number of candidate genes for salt-stress responses in rice, but genes show conserved expression patterns in response to salt stress throughout genetic backgrounds and regional diversities have not been studied.…”