Designing Climate-Resilient Rice Production Systems: Leveraging Genomics for Low-Emission Rice Varieties

Rice cultivation contributes up to 12% of global anthropogenic methane (CH 4 ) emissions, making it a significant climate concern. With rice demand projected to double by 2050, achieving the required 2.4% annual genetic gain must be balanced with emission reduction. This review synthesizes recent progress in three key areas: (1) mitigation strategies such as alternate wetting and drying and direct-seeded rice, which can reduce CH 4 emissions by 30%–40%; (2) identification of physiological and molecular traits, such as short duration, high harvest index, improved nitrogen use efficiency, optimized root architecture, and stress tolerance with reduced greenhouse gas (GHG) footprints; and (3) the potential of genomics-assisted breeding and high-throughput phenotyping to accelerate the development of climate-resilient rice varieties with lower CH 4 emissions. Specifically, we highlight how the synergistic integration of high-throughput phenotyping, genomic selection, and marker-assisted breeding can substantially improve the efficiency and precision of breeding programs targeting the development of climate-resilient rice varieties with reduced CH 4 emissions. This is exemplified through successful case studies utilizing multi-omics approaches, including the development of Green Super Rice varieties (GSR 2 and GSR 8), which have demonstrated up to a 37% reduction in GHG emissions. Crucially, we propose a stratified trait profile for low-GHG rice development and provide guidelines and metrics for integrating these traits into mainstream breeding pipelines. We conclude by proposing a strategic framework integrating carbon-efficient breeding, climate-adapted agronomy, and policy support, which is essential for scaling low-GHG rice systems globally.