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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #399321

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: Validation of yield component QTLs identified by Genome-Wide Association Mapping in a tropical japonica × tropical japonica Rice Biparental Mapping Population

item Eizenga, Georgia
item Rice, Adam
item Huggins, Trevis
item SHAKIBA, EHSAN - University Of Arkansas
item Edwards, Jeremy
item Jackson, Aaron
item Jia, Melissa
item ALI, LIAKAT - University Of Arkansas

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 8/8/2022
Publication Date: 11/9/2022
Citation: Eizenga, G.C., Rice, A.D., Huggins, T.D., Shakiba, E., Edwards, J., Jackson, A.K., Jia, M.H., Ali, L. 2022. Validation of yield component QTLs identified by Genome-Wide Association Mapping in a tropical japonica × tropical japonica Rice Biparental Mapping Population. ASA, CSSA, SSSA International Meeting, Baltimore, Maryland. November 6-9, 2022.

Interpretive Summary:

Technical Abstract: Cultivated rice (Oryza sativa L.) is comprised of two subspecies, Indica and Japonica that further divide into five subpopulations (indica, aus, the aromatic, temperate japonica and tropical japonica). The Rice Diversity Panel 1 (RDP1) includes over 400 accessions with representation from all five subpopulations and is a resource for genome-wide association (GWA) studies to explore O. sativa genetic and phenotypic diversity. Previously collected phenotypic data for over 25 yield-related traits in RDP1 was reanalyzed using a recently released 4.8 million SNP dataset to enhance GWA mapping precision. GWA mapping revealed numerous GWA quantitative trait loci (QTLs) which were specific to one or more of the subpopulations or subspecies. Most all U.S. cultivars are classified as tropical japonica or admixtures, thus the tropical japonica subpopulation was the focus for validating RDP1 GWA QTLs. Two diverse tropical japonica accessions, L-202 originating from California, USA, and Trembese from Indonesia, were selected for developing a recombinant inbred line (RIL) population. This RIL population was characterized for 20 yield component traits, 16 of which were measured in RDP1 including six agronomic, six panicle architecture and four seed traits. Genotyping with 1,439 polymorphic markers and QTL mapping revealed 43 RIL QTLs. Examination of the GWA QTLs in the RIL QTL regions identified 175 GWA QTLs co-located with 36 RIL QTLs. A significant overlap was on chromosome 7 (22.56-29.66 Mb) where the well-known yield related genes, FRIZZY PANICLE (FZP), and GRAIN WEIGHT (GW7) are located and specific to the tropical japonica subpopulation. In this region, ten RIL QTLs were co-located with 36 GWA QTLs for panicle architecture or seed traits, especially increased secondary branching which increases the number of spikelets and seeds produced. The RIL QTL with high R2 values (>15%) co-located with GWA QTL are targets for developing SNP markers that can be utilized in cultivar development.