Interaction of Genes That Enhance Anaerobic Germination and Submergence Tolerance in Rice

Sustainable growth in rice yield requires a second-generation of varieties that are productive in the face of one or multiple abiotic stresses over the course of the plant life cycle. Rice researchers have used the extensive diversity in rice germplasm to uncover genetic variation associated with greater resilience to abiotic stresses. The responsible loci are being exploited to limit the loss in yield due to unpredictable climatic conditions. Quantitative trait loci (QTLs) for submergence tolerance (Sub1A; Xu et al., 2006), anaerobic germination tolerance (AG1; Angaji et al., 2010) and salinity tolerance (Saltol; Bonilla et al., 2002) have been mapped on rice chromosomes 9S, 9L and 1S, respectively. These three QTLs have been introgressed into the widely-grown high-yielding cultivar IR64 at the International Rice Research Institute (IRRI) as single locus additions or as pyramided loci. The goal of this dissertation research was to examine the interconnections between AG1, Sub1 and Saltol, at physiological, biochemical and molecular levels. The central hypothesis was that if the mechanisms of abiotic stress resilience controlled by these loci are expressed in a developmentally distinct manner or are functionally distinct, then farmers could rely on a triply-pyramided genotype for direct seeding, submergence and salinity tolerance. During this analysis, my colleagues at IRRI successfully demonstrated that the AG1 locus encodes a functional trehalose-6-phosphate phosphatase, namely OsTPP7, that enhances anaerobic germination tolerance. The trait is absent in the IR64 variety due to a small interstitial chromosomal deletion.In the three separate chapters the combined and pyramided lines were evaluated for independent anaerobic germination, vegetative submergence and salinity stress treatments. These treatments showed that AG1, Sub1 and Saltol provide their tolerance trait in presence of other two loci. For example, when introgressed in the genetic background of Sub1 and Saltol, AG1 displayed the anaerobic germination phenotype. Similarly, the Sub1 showed the vegetative submergence tolerance in presence of AG1 and Saltol. Finally the Satlol exhibited salinity tolerance phenotype when combined with AG1 and Sub1, although there was little additional benefit to the already saline-insensitive IR64 genotype. These results demonstrate that interaction between loci, if any, does not have negative ramifications under the scenarios tested. Therefore these pyramided lines can be used in the farmer’s fields to cope with independent stresses throughout the growing season.Farmer’s also must cope with combined stresses, such as submergence with salinity or submergence following direct seedling. Therefore, combined stresses of vegetative submergence and salinity or anaerobic germination continuing with vegetative submergence, were investigated to evaluate possible negative interactions between AG1 and Sub1, and Sub1 and Saltol, respectively. To test the former, we improvised a combined salinity and submergence scenario that simulated a natural field condition in which roots were subjected to a saline stress accompanied by shoot submergence in fresh water. The data showed that the benefits of Saltol and Sub1 could be maintained in the same genotype. To test combined anaerobic germination and vegetative submergence stress, seed were planted in soil and the seedlings continually submerged from 0 through 16 d. Four genotypes, including the pyramided IR64(AG1 Sub1) line, were evaluated in a series of physiological, biochemical and molecular analyses. In this scenario, the pyramided line was less able to survive submergence than IR64, IR64(AG1) or IR64(Sub1) This was illuminated by the significant consequences on the global transcriptome at every timepoint assayed, reflecting antagonism between the coleoptile escape and shoot quiescence survival strategies characteristic of AG1 and Sub1, respectively, during seedling establishment. IR64(AG1 Sub1) displayed some transcript abundance features regulated by SUB1A-1, a few regulated by OsTPP7, and an overall delay in development that was manifested in a lower survival rate. Moreover, the analysis showed that Sub1 promotes the transition to photoautotrophy in seedlings cultured underwater from seed, an aspect of the traits provided by this locus that had previously not been described. These data indicate that the hydrology of the flood can impact the success of the combined IR64(AG1, Sub1) genotype. Altogether, this dissertation provides mechanistic knowledge of the independent function and interactions of three high-value genetic loci used to increase the yield stability of rice in South and Southeast Asia