Identification of Drought Tolerance Markers in a Diverse Population of Rice Cultivars by Expression and Metabolite Profiling

Rice provides about half of the calories consumed in Asian countries, but its productivity is often reduced by drought, especially when grown under rain-fed conditions. Cultivars with increased drought tolerance have been bred over centuries. Slow selection for drought tolerance on the basis of phenotypic traits may be accelerated by using molecular markers identified through expression and metabolic profiling. Previously, we identified 46 candidate genes with significant genotype × environment interaction in an expression profiling study on four cultivars with contrasting drought tolerance. These potential markers and in addition GC-MS quantified metabolites were tested in 21 cultivars from both indica and japonica background that varied in drought tolerance. Leaf blades were sampled from this population of cultivars grown under control or long-term drought condition and subjected to expression analysis by qRT-PCR and metabolite profiling. Under drought stress, metabolite levels correlated mainly negatively with performance parameters, but eight metabolites correlated positively. For 28 genes, a significant correlation between expression level and performance under drought was confirmed. Negative correlations were predominant. Among those with significant positive correlation was the gene coding for a cytosolic fructose-1,6-bisphosphatase. This enzyme catalyzes a highly regulated step in C-metabolism. The metabolic and transcript marker candidates for drought tolerance were identified in a highly diverse population of cultivars. Thus, these markers may be used to select for tolerance in a wide range of rice germplasms.