Marker-Assisted Breeding for Abiotic Stress Tolerance in Rice: Progress and Future Perspectives

Abstract

While global climate change threatens to increase the occurrence and intensity of production constraints such as abiotic stresses, new marker-assisted breeding techniques may enable the rapid development of stress-tolerant rice varieties to face these challenges. Through the mapping of quantitative trait loci (QTLs) and precise transfer of tolerant QTLs by marker-assisted backcrossing (MABC), improved varieties can be developed with beneficial traits. For example, salt stress is a major constraint across many rice-producing areas because of the high sensitivity of modern rice varieties. At IRRI, we are working towards combining QTLs conferring salt tolerance to develop robust cultivars for stress-prone environments. Previously, RILs from a cross between IR29 and an accession of the tolerant landrace Pokkali were used to map several salt tolerance QTLs, including Saltol, a major QTL on the short arm of chromosome 1. Near-isogenic lines were developed between IR29 and Pokkali, and subsequently multiple Pokkali alleles were identified between the original RILs and the NILs. The Pokkali introgressions in six advanced lines were also characterized using an Illumina GoldenGate assay developed at Cornell University to genotype 1,536 SNP loci across the rice genome. A precision marker-assisted backcrossing system is also being employed to efficiently transfer beneficial Pokkali introgressions into popular varieties such as BRRI dhan28, an important dry season variety in coastal Bangladesh, to increase production in saline prone areas. Future advances in new marker-assisted breeding strategies, rapid sequencing of multiple rice genomes, and SNP genotyping technologies also promise to increase the efficiency of marker development and integration of molecular tools into modern breeding programs.