Harnessing Molecular Markers for Developing Climate-smart Rice Varieties

Abstract

Rice production is increasingly constrained by climate-associated abiotic and biotic stresses, while conventional breeding is limited by dependence on phenotypic selection and lengthy breeding cycles. Climate-smart rice breeding seeks to develop high-yielding, resilient varieties with reduced environmental impact by integrating conventional approaches with molecular and genomic tools. This review synthesises the role of molecular markers in accelerating the development of climate-smart rice, with emphasis on marker-assisted selection, marker-assisted backcrossing, quantitative trait locus mapping, and gene pyramiding. Molecular markers enable the precise tracking and introgression of genes and quantitative trait loci associated with tolerance to drought, salinity, submergence, heat, cold, and major biotic stresses. Their use also supports the stacking of multiple stress-tolerance loci within elite genetic backgrounds while retaining desirable agronomic and grain-quality characteristics. The review further considers genomic selection, CRISPR-Cas9 genome editing, and haplotype-based breeding as complementary approaches for improving breeding efficiency and addressing complex traits. Advances in rice genomics and high-density marker systems continue to strengthen the identification and deployment of useful alleles. However, genotype × environment interactions, incomplete functional characterisation of some quantitative trait loci, and the integration of genomic data remain important constraints. Combining validated molecular markers with emerging precision-breeding tools offers a practical framework for developing resilient rice varieties suited to increasingly variable production environments.