ARS | Publication request: Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under Salinity Stress during the Vegetative Growth Stage

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 2, 2005
Publication Date: September 23, 2005
Citation: Walia, H., Wilson, C., Condamine, P., Liu, X., Ismail, A.M., Zeng, L., Wanamaker, S.I., Mandal, J., Xu, J., Cui, X., Close, T.J. 2005. Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under Salinity Stress during the Vegetative Growth Stage. Plant Physiology. Vol 139:822-835

Interpretive Summary: Salinity is a major environmental constraint limiting crop yield for both irrigated and rain-fed agriculture. Irrigated agriculture supplies roughly one-third of the world’s food supply. With increases in the global population it is very important to address the problem of salinity. Genetic improvement of the salt tolerance of major cereals is needed. Rice, a salt-sensitive crop, is the most important cereal crop in many parts of the world. Fortunately though, rice has considerable genetic variation for salt tolerance within the cultivated gene pool. In this study, we exploited this genetic variability to identify genes which may be important in conferring salt tolerance to rice. Two indica rice genotypes, salt-tolerant FL478, a line bred from one salt-tolerant parent and one salt-sensitive parent, and IR29, the sensitive parent of the line were selected for this study. Using the recently released Affymetrix rice genome array, we found that gradual salinity stress induced a relatively large number of genes in salt-sensitive IR29 compared to tolerant FL478. Salinity especially induced a large number of genes involved in the flavenoid pathway in IR29, but not FL478. However, cell-wall related genes were induced in both genotypes, suggesting cell-wall processes are a general adaptive mechanism during salinity stress. One area of interest to many rice researchers is a part of chromosome 1 called “Saltol”. It is believe that this area is important in conferring salt tolerance in rice. We expected that this region in FL478 would have come from the salt-tolerant parent of FL478. Our analysis of the expression data, though, revealed that IR29 was the source of the Saltol region in FL478, contrary to expectation. In short, this study provides a genome-wide analysis of two well-characterized, genetically related rice genotypes differing in salinity tolerance during a gradually imposed salinity stress under greenhouse conditions.

Technical 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 flavenoid 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. Single-feature 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.