Anaerobic Germination Tolerance: QTL Discovery, Validation, and Deployment for Bangladesh Sustainable Rice Production

• Cereal: Rice
• Abiotic Stressor: Flood
• Principal Investigator: Endang Septiningsih, Texas A&M University

Improving rice establishment under flooded conditions requires identifying the genetic mechanisms that enable seeds to germinate and survive in low-oxygen environments. In direct-seeded rice systems, flooding during germination—referred to as anaerobic germination (AG)—is a major constraint, particularly in regions like Bangladesh where erratic rainfall and poor drainage are common. While one major AG locus (AG1) has been identified and deployed, its effects are limited under more severe stress conditions, highlighting the need to discover and validate additional loci.

This effort focuses on identifying novel AG-associated QTLs from a highly tolerant deepwater rice landrace, Shishumati, using an existing mapping population. High-resolution genotyping and phenotyping will be used to map QTL regions associated with seedling survival under flooded conditions, while whole-genome sequencing and transcriptomic analyses will support candidate gene identification and functional characterization. These approaches enable the dissection of genetic variation underlying AG tolerance and provide insight into the molecular pathways that regulate early-stage survival under hypoxic stress.

Key outputs include newly identified AG QTLs, candidate genes, validated genetic markers, and characterized germplasm carrying combinations of AG-related genes, including AG1 and SUB1. In addition, functional validation through transcriptomic analysis and gene editing will strengthen understanding of gene function and regulatory pathways associated with AG tolerance. Together, these resources support allele discovery, validation, and integration into breeding pipelines, providing a foundation for improving rice adaptation to direct-seeded and flood-prone production systems.