Alvaro M. Pamplona

Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond

BACKGROUND AND AIMS Submergence is a recurring problem in the rice-producing rainfed lowlands of south and south-east Asia. Developing rice cultivars with tolerance of submergence and with agronomic and quality traits acceptable to farmers is a feasible approach to address this problem. The objectives of this study were to (a) develop mega varieties with Sub1 introgression that are submergence tolerant, (b) assess the performance of Sub1 in different genetic backgrounds, (c) determine the roles of the Sub1A and Sub1C genes in conferring tolerance, and (d) assess the level of tolerance in F(1) hybrids heterozygous for the Sub1A-1-tolerant allele. METHODS Tolerant varieties were developed by marker-assisted backcrossing through two or three backcrosses, and their performance was evaluated to determine the effect of Sub1 in different genetic backgrounds. The roles of Sub1A and Sub1C in conferring the tolerant phenotype were further investigated using recombinants identified within the Sub1 gene cluster based on survival and gene expression data. KEY RESULTS All mega varieties with Sub1 introgression had a significantly higher survival rate than the original parents. An intolerant Sub1C allele combined with the tolerant Sub1A-1 allele did not significantly reduce the level of tolerance, and the Sub1C-1 expression appeared to be independent of the Sub1A allele; however, even when Sub1C-1 expression is completely turned off in the presence of Sub1A-2, plants remained intolerant. Survival rates and Sub1A expression were significantly lower in heterozygotes compared with the homozygous tolerant parent. CONCLUSIONS Sub1 provided a substantial enhancement in the level of tolerance of all the sensitive mega varieties. Sub1A is confirmed as the primary contributor to tolerance, while Sub1C alleles do not seem important. Lack of dominance of Sub1 suggests that the Sub1A-1 allele should be carried by both parents for developing tolerant rice hybrids.

Stress Tolerant Rice Varieties for Adaptation to a Changing Climate

Rising temperatures due to accumulation of greenhouse gasses are expected to result in declining rice yields in the tropics. In addition to the direct effect of high temperature in reducing yields, a rise in sea level coupled with more erratic and extreme weather events will result in reduced yields and increase the risks of rice farming. The abiotic stresses that are anticipated to worsen as the consequences of climate change include high temperature, drought, flooding and salinity stresses. While high temperature is not currently a major problem, the other stresses are already widespread yield limiting factors in the unfavorable environments of tropical Asia. Incorporating stress tolerance into high-yielding varieties has proven to be a very effective approach to developing varieties that can cope with these situations. These successes provide optimism that the problem of climate change can be addressed partially through development and dissemination of adapted germplasm.

Comparison of phenotypic versus marker-assisted background selection for the SUB1 QTL during backcrossing in rice

Marker assisted backcrossing has been used effectively to transfer the submergence tolerance gene SUB1 into popular rice varieties, but the approach can be costly. The selection strategy comprising foreground marker and phenotypic selection was investigated as an alternative. The non-significant correlation coefficients between ranking of phenotypic selection and ranking of background marker selection in BC2F1, BC3F1 and BC3F2 generations indicated inefficiency of phenotypic selection compared to marker-assisted background selection with respect to recovery of the recipient genome. In addition, the introgression size of the chromosome fragment containing SUB1 was approximately 17 Mb, showing the effects of linkage drag. The significant correlation coefficient between rankings of phenotypic selection with the percentage of recipient alleles in the BC1F1 generation suggested that background selection could be avoided in this generation to minimize the genotyping cost. The phenotypically selected best plant of the BC3F1 generation was selfed and backcross recombinant lines were selected in the resulting BC3F4 generation. The selection strategy could be appropriate for the introgression of SUB1 QTL in countries that lack access to high-throughput genotyping facilities.