Skip to main content
ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #422283
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: Using ontologies to identify genetic loci overlapping across multiple traits in a tropical Japonica rice core panel

Author
item Edwards, Jeremy

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/31/2024
Publication Date: 1/10/2025
Citation: Edwards, J. 2025. Using ontologies to identify genetic loci overlapping across multiple traits in a tropical Japonica rice core panel. Plant and Animal Genome Conference Proceedings. San Diego, California. January 9-14, 2026.

Interpretive Summary:

Technical Abstract: Tropical japonica rice dominates U.S. production, with most varieties tracing back to only about 40 founder parents, highlighting a need for greater genetic diversity. To address this, a tropical Japonica (TRJ) Core panel was developed, consisting of 529 accessions from 61 countries. Skim sequencing at 3X coverage identified over 2.4 million variants, which were filtered and pruned to 111,401 informative variants. Genome-wide association (GWA) analysis using GAPIT3 software identified loci associated with traits such as leaf morphology, panicle architecture, grain yield components, and disease resistance. The integration of ontologies enabled systematic exploration of genetic loci underlying multiple traits. For example, NAL1, a regulator of leaf growth and panicle development, was implicated in leaf length, width, and chlorophyll content. Similarly, the frizzy panicle (FZP) gene was associated with seed number and panicle density, while Sekiguchi Lesion (SL), a regulator of disease resistance, was linked to blast resistance. By organizing phenotypic data and candidate gene associations through ontologies, overlapping genetic regions across traits were efficiently identified, underscoring the TRJ Core’s utility for breeding programs. This panel provides a robust resource for mining allelic diversity to improve tropical japonica rice for yield, quality, and sustainability.