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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #430154
Research Project: Broadening and Strengthening the Genetic Base of Rice for Adaptation to a Changing Climate, Crop Production Systems, and Markets

Location: Dale Bumpers National Rice Research Center

Title: Genome-Wide Association Study for drought response traits in a diverse tropical japonica rice panel

Author
item SHAFER, SAM - Purdue University
item TING, TO-CHIA - Purdue University
item EIZENGA, GEORGIA
item HENRY, AMELIA - International Rice Research Institute
item WANG, DIANE - Purdue University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/14/2025
Publication Date: 11/14/2025
Citation: Shafer, S.E., Ting, T., Eizenga, G.C., Henry, A., Wang, D.R. 2025. Genome-Wide Association Study for drought response traits in a diverse tropical japonica rice panel. Meeting Abstract. CANVAS 2025 Conference, Salt Lake City , Utah. November 9-12, 2025.

Interpretive Summary:

Technical Abstract: In the United States, much of the rice production in the mid-South lies along the Mississippi alluvial plain (MAP) region where many farms still rely on local aquifers, which poses challenges for the sustainability of rice production because the water is being depleted. Rice is divided into the Indica and Japonica varietal groups, with Japonica further subdivided into the temperate japonica (TEJ) and tropical japonica (TRJ) subclades. The majority of rice grown in the mid-South is TRJ cultivars. With aquifer resources being depleted, focus has shifted towards alternative management systems that use less water, thus there is a need to identify drought tolerant cultivars. Most cultivars are bred for flooded conditions and have only been evaluated for drought at reproductive stages, resulting in a research gap for stress at critical vegetative stages. For these reasons, a diverse panel of 198 TRJ accessions was selected from available genetic resources and grown out to study vegetative stress response. Available resources for genomic data included the Rice Diversity Panels 1 (RDP1), RDP2, 3,000 Rice Genomes Project (3KRG), and the USDA-ARS TRJ Core. Utilizing the rainout shelter at the International Rice Research Institute in the Philippines, data was collected for 15 field traits under drought-stressed and flooded conditions across two dry seasons. With this data, a genome-wide association study (GWAS) utilizing the rMVP package in the R coding language was conducted to retrieve significant markers across key vegetative traits. Through linkage disequilibrium (LD) decay and further cross-referencing of previously published data, genes nearby significant markers can be shortlisted for drought stress response, serving as a useful tool for future breeder resources. Preliminary analysis using gene ontology of 173 TRJ genotypes has identified few candidate genes tagged for water transport between cells.