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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #420700

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 SCHAFER, SAM - Purdue University
item TING, TAO-CHIA - Purdue University
item Eizenga, Georgia
item HENRY, AMELIA - International Rice Research Institute
item WANG, DIANE - Purdue University

Submitted to: Crop Science Society of America
Publication Type: Abstract Only
Publication Acceptance Date: 11/8/2024
Publication Date: 11/14/2024
Citation: Schafer, S.E., Ting, T., Eizenga, G.C., Henry, A., Wang, D.R. 2024. Genome-Wide Association Study for drought response traits in a diverse tropical japonica rice panel. Crop Science Society of America. Abstract. ASA, CSSA, SSSA International Annual Meeting, San Antonio, Texas. November 10-13, 2024. https://scisoc.confex.com/scisoc/2024am/meetingapp.cgi/Paper/158147

Interpretive Summary:

Technical Abstract: Projected impacts of climate change include increases in both the prevalence and severity of drought and heat waves, which can have detrimental effects on rice production. In the United States, much of the rice production in the Midsouth lies along the Mississippi alluvial plain where many farms still rely on local aquifers, which poses challenges for the sustainability of rice production. Rice is divided into the Indica and Japonica varietal groups, with the latter further subdivided into the temperate japonica and tropical japonica (TRJ) subclades. The majority of Midsouth rice cultivars are TRJ. With aquifer resources being depleted, focus has shifted towards alternative management systems that use less water. 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 these were grown to study vegetative stress response. Available resources for accessions and associated genomic data included the Rice Diversity Panel 1 (RDP1), RDP2, 3,000 Rice Genomes Project, and USDA-ARS TRJ Core. Utilizing the rainout shelter at the International Rice Research Institute, 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) using the rMVP package in the R coding language was conducted to retrieve significant markers across key vegetative traits. Ongoing cross-referencing of publications to genes identified within linkage disequilibrium decay of significant markers will continually grow a shortlist of candidate genes for drought stress response. Currently, gene ontology of only 112 TRJ genotypes identified 17 candidate genes, including one tagged for water transport between cells. This gene may be the focus of developing markers for breeder use in the future.