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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #400462
Research Project: Gene Discovery and Crop Design for Current and New Rice Management Practices and Market Opportunities

Location: Dale Bumpers National Rice Research Center

Title: USDA-ARS Aus Rice Panel: An untapped resource to enrich natural genetic variation for abiotic stress tolerance in US rice breeding programs

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

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/11/2023
Publication Date: 1/30/2024
Citation: Rohila, J.S., Sookaserm, T.B., Mitchell, J., Jackson, A.K., Edwards, J., McClung, A.M., Huggins, T.D., Ponniah, S. 2024. USDA-ARS Aus Rice Panel: An untapped resource to enrich natural genetic variation for abiotic stress tolerance in US rice breeding programs. Rice Technical Working Group Meeting Proceedings. February 20-23, 2023, Hot Springs, Arkansas. Electronic Publication. p. 81.

Interpretive Summary:

Technical Abstract: Aus is a subpopulation of rice that is historically cultivated in rainfed areas in north-east India and Bangladesh. The USDA-ARS Aus Rice Panel (hereafter called UARP) is a diverse global collection of approximately 100 purified, Aus accessions with seeds lacking pigmented pericarp. It was established as a genetic resource to discover genes and allelic variations that can be used to improve US rice varieties (primarily Japonica) for agronomic traits such as abiotic stress tolerance, climate resiliency and sustainability. Single-nucleotide polymorphism (SNP) data for the UARP was obtained from the publicly available 3000 Rice Genomes (3KRG) imputed resequencing data. Approximately two million SNPs were found to be variable in the UARP with a minor allele frequency greater than three percent. The dense genotype data is suitable for genome-wide association studies (GWAS) using phenotypes measured on the UARP. UARP phenotypes for major morphological, developmental, physiological and agronomic traits under severe drought conditions (-80 to -100 kPa) were determined over multiple years in a replicated field study conducted in Stuttgart, Arkansas. The UARP was found to have a wide range in traits under drought conditions, such as above ground biomass, thousand kernel weight, grain length, grain width, and total yield. GWAS revealed significant associations with known genes for seed length at GS3 and qLGY3/GW3p6/OsLG3b, for seed width at GW5, and for yield at GS2/GL2 and GWi7.1/ GWi7.2. Additional significant associations with other chromosomal regions were found across 22 traits, many of which have no previously reported candidate genes or trait associations. Among the genetic loci uncovered by GWAS, several have large estimated additive effects and explain a substantial percent of the phenotypic variation observed in the field. Identified loci are good potential targets for fine mapping and candidate gene verification in future studies and may be used for marker-assisted breeding aimed at improving water use efficiency and related stress tolerance traits in US rice production.