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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #422243
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: Aus sub-population of Oryza sativa L. for bridging food security and water sustainability in rice

Author
item Rohila, Jai
item Huggins, Trevis
item Jackson, Aaron
item Sookaserm, Tiffany
item MITCHELL, JOHN - University Of Arkansas At Pine Bluff
item PONNIAH, SATHISH - University Of Arkansas At Pine Bluff
item Edwards, Jeremy

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/30/2024
Publication Date: 1/13/2025
Citation: Rohila, J.S., Huggins, T.D., Jackson, A.K., Sookaserm, T.B., Mitchell, J.R., Ponniah, S.K., Edwards, J. 2025. Aus sub-population of Oryza sativa L. for bridging food security and water sustainability in rice. Abstract. Plant and Animal Genome Conference. San Diego, California.

Interpretive Summary:

Technical Abstract: In the United States (US), Arkansas is the largest rice producer in the southern rice belt with over a million acres planted every year and plays a significant role towards global food security. Most of the rice acreage in Arkansas is irrigated by underground water. Thus, season-long flood irrigation hinders sustainable rice production in the region. To reduce the water footprint, irrigation management systems have been recommended such as alternate-wetting-drying (AWD) and furrow irrigation. Moreover, US rice germplasm has an extremely narrow genetic pool for improving stress tolerance traits, especially complex traits such as drought tolerance. To fill this knowledge gap and address the narrow genetic diversity, a global AUS diversity panel (ADP, n=198), which is a part of the 3K Rice Genome project, was assembled to incorporate stress tolerance traits in US rice breeding programs. Single nucleotide polymorphism (SNP) calling was performed using the USDA-ARS SCINet computing system. After imputation and filtering, 1,920,597 biallelic SNPs and genetic variations associated with the trait-of-interest under deficit irrigation were identified and used for downstream analyses. The ADP was divided into two sub-groups according to pericarp color: ADP1 (non-colored pericarp), and ADP2 (colored pericarp). Recently, we evaluated the ADP1 for agronomic and yield component traits for 3 seasons and ADP2 for one season under -80 kPa soil moisture measured at 15 cm below the soil surface. Genome wide association analysis on collected trait data using the R package “GAPIT” identified genomic regions associated with improved biomass at the early vegetative stage as well as the flowering stage in both greenhouse and field conditions. A preliminary analysis has identified several AUS accessions and multiple genomic regions harboring candidate genes, including one related to improved biomass under water deficit conditions. The candidate genes are being validated through CRISPR – Cas experiments and will be used to develop markers for early seedling vigor in future breeding programs. This study will narrow down potential candidate genes for improved deficit irrigation stress tolerance in the US elite rice germplasm.