Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under Salinity Stress during the Vegetative Growth Stage

Abstract

Rice (Oryza sativa), a salt-sensitive species, has considerable genetic variation for salt tolerance within the cultivated gene pool. Two indica rice genotypes, FL478, a recombinant inbred line derived from a population developed for salinity tolerance studies, and IR29, the sensitive parent of the population, were selected for this study. We used the Affymetrix rice genome array containing 55,515 probe sets to explore the transcriptome of the salt-tolerant and salt-sensitive genotypes under control and salinity-stressed conditions during vegetative growth. Response of the sensitive genotype IR29 is characterized by induction of a relatively large number of probe sets compared to tolerant FL478. Salinity stress induced a number of genes involved in the flavonoid biosynthesis pathway in IR29 but not in FL478. Cell wall-related genes were responsive in both genotypes, suggesting cell wall restructuring is a general adaptive mechanism during salinity stress, although the two genotypes also had some differences. Additionally, the expression of genes mapping to the Saltol region of chromosome 1 were examined in both genotypes. Singlefeature polymorphism analysis of expression data revealed that IR29 was the source of the Saltol region in FL478, contrary to expectation. This study provides a genome-wide transcriptional analysis of two well-characterized, genetically related rice genotypes differing in salinity tolerance during a gradually imposed salinity stress under greenhouse conditions. Salinity is a major problem for both irrigated and rainfed agriculture. Irrigated agricultural systems supply roughly one-third of the world's food supply (Munns, 2002). Therefore, there is a great urgency in addressing the problem of salinity, especially with an increasing global population. Salt stress also is a major problem for rainfed agriculture in coastal areas because of seawater ingress during high tide and the rising shallow saline groundwater, particularly during the dry season. The problem of salinity has been approached through better management practices and introduction of salt-tolerant varieties in the affected areas. Unfortunately, the use of improved irrigation management practices in salt-affected areas has generally proven to be uneconomical and difficult to implement on a large scale. Thus, genetic improvement of salt tolerance of major cereal crops like rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare) appears to be the most feasible and promising strategy for maintaining stable global food production.Rice, the most important cereal crop in many parts of the world, is considered to be salt sensitive (Maas and Hoffman, 1977). Sensitivity of rice to salinity stress varies with the growth stage. In general, rice plants are very sensitive to salinity stress at young seedling stages and less so at reproduction (Flowers and Yeo, 1981;Lutts et al., 1995). From an agronomic point of view, tiller number and number of spikelets per panicle have been reported to be the most sa...

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

“…There was an apparently delayed response to cold in K354 compared with C418, with 232 DEGs in C418 vs 83 in K354 at 2 h cold stress. Similar results were previously observed in rice under salinity stress; in that study, the sensitive genotype IR29 induced a relatively large number of genes compared to tolerant FL478 [18]. In addition, comparison of gene expression levels between K354 and C418 showed that there were 308 up-regulated and 209 down-regulated genes in K354 compared with C418 under control conditions.…”

“…Although high-throughput RNA sequencing has recently become popular as an alternative to microarray analysis, the microarray platform, with its robust sample process and data analysis pipelines, is still the preferred choice for transcriptomic profiling involving a large number of samples in model plants with well-annotated genomes [14,15]. Many microarray-based studies have been carried out to identify abiotic stress responsive genes in specific rice varieties and transgenic rice [9,10,16,17], and comparative transcriptional profiling of two contrasting rice genotypes under salinity and drought stress have revealed novel genetic regulatory mechanisms involved in stress tolerance [18,19]. Unfortunately, it is difficult to use the stress-related genes uncovered in those studies to improve modern varieties in rice breeding, because most of them already exist in elite rice varieties.…”

Cold stress affects antioxidative response and accumulation of medicinally important withanolides in Withania somnifera (L.) Dunal

“…The antioxidant potential is highly variable in different plant species and in different genotypes of the same species. Stress tolerant genotypes have often been reported to show higher expression of antioxidants as reported for salt (Walia et al, 2005), drought (Türkan et al, 2005), cold (Seppanen and Coleman, 2003,b;Kumar et al, 2008a,b;Mutlu et al, 2013) and heat stress (Snider et al, 2010;Almeselmani et al, 2009). The responsiveness and efficiency of scavenging systems of plants governs their performance, endurance, and survival capability under stress conditions (Seppanen and Coleman, 2003;Mishra et al, 2014).…”

Applying hyperspectral imaging to explore natural plant diversity towards improving salt stress tolerance

“…Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice shoots was used (Hairmansis et al, 2014). The imaging techniques for seed germination to identify salt-tolerant genotypes can be useful, especially when seeds have different colors and phenotype (Walia et al, 2005;Li et al, 2016). At the leaf scale, it was found that hyperspectral reflectance and chlorophyll fluorescence can be served as valuable tools for non-invasive measurements of photosynthetic parameters under salinity stress (Li et al, 2010).…”