Genomic Approaches for Improving Flooding and Salt Stress Tolerance in Rice

Excess water and salt stress are major abiotic factors limiting rice production in rainfed lowlands, reducing yields to less than a third of that under irrigated areas. Developing varieties tolerant of these stresses will help improve the productivity of these areas.  Recent advances in genomics facilitated using novel breeding approaches to accelerate germplasm improvement. We present examples from rice where substantial progress was made in developing submergence and salt tolerant varieties, with the potential to transform agriculture in these less favorable areas. Rice varieties tolerant of anaerobic conditions during germination are being developed for direct seeding; a system increasing being adopted in recent years. Traits associated with tolerance were studied and major QTLs identified, two of them are being introgressed into popular varieties using molecular markers. Cloning of the SUB1A gene that confers tolerance of transient submergence for up to 18 d facilitated its subsequent deployment through high yielding varieties to over 4 million farmers in Asia within few years, with ensuing yield advantages of 1 to over 3 t/ha in affected areas. Contrary to submergence tolerance, numerous traits are required for high salt tolerance, and several major QTLs were identified. High yielding rice varieties carrying some of these major QTLs are being developed, providing opportunities for breeding highly tolerant varieties. Whole genome sequences of novel QTL donors are being explored to accelerate cloning of major QTLs and to develop reliable markers for combining them in suitable varieties. Developing varieties with tolerance of multiple stresses is also being pursued