Identification of useful genomic regions in a Tropical Japonica Core collection for U.S. rice breeding programs

Authors: Huggins, Trevis; Edwards, Jeremy; Jia, Yulin; Jia, Melissa; Jackson, Aaron; Sells, Laduska

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/14/2024
Publication Date: 1/5/2026
Citation: Huggins, T.D., Edwards, J., Jia, Y., Jia, M.H., Jackson, A.K., Sells, L.J. 2026. Identification of useful genomic regions in a Tropical Japonica Core collection for U.S. rice breeding programs. Rice Technical Working Group Meeting Proceedings. New Orleans, Louisiana. February 14-17, 2025.

Interpretive Summary:

Technical Abstract: Most rice varieties grown in USA through the past 100 years belong to the tropical japonica subpopulation and have pedigrees that trace back to only about 40 founder parents. A panel of 740 globally diverse cultivars believed to be tropical japonica were selected from US pedigrees, USDA-ARS World Rice Collection and diversity panels to create a tropical japonica (TRJ) Core panel. The accessions were first screened with 13 microsatellite markers to verify subpopulation membership, which resulted in a final number of 529 accessions from 61 countries. The TRJ Core addresses the lack of genetic diversity in modern US breeding programs for yield and quality improvement as well as sustainability of US rice. A portion of the TRJ Core, 398 accessions, plus non TRJ controls were sequenced using skim sequencing with 3X average coverage. Google DeepVariant and GLnexus were used to call single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels) on the USDA-ARS SCINet High Performance Computing (HPC) system which resulted in 2,465,592 variants among the TRJ accessions. The variants were subsequently imputated using Beagle 5.0. After filtering with a minor allele frequency (maf)>0.05, 807,735 variants remained, and after linkage disequilibrium (LD) pruning with an r-squared threshold of 0.9 and a window size of 1000kb, 111,401 variants remained. Genome wide association analysis was performed with these variants on the USDA-ARS SCINet HPC system using GAPIT3 software with Mixed Linear Model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) methods. The TRJ Core was evaluated for reaction to one of the most common US blast races, IB49 under greenhouse conditions and under field conditions for days to heading, plant height, chlorophyll concentration, leaf pubescence, growth rate, flag leaf length and width, panicle length, number of seed per panicle, seed weight per panicle, number of primary and secondary panicle branches, and grain length and width. The GWA analysis identified genomic regions associated with apiculus color (1), hull color (2), leaf chlorophyll concentration by SPAD meter (2), leaf length (3), leaf width (3), primary branches per panicle (3), secondary branches per panicle (1), panicle seed density (4), seeds per panicle (2), and blast IB49 (4). The candidate gene narrow leaf 1 (NAL1), a gene that regulates leaf growth and controls panicle number, was identified for leaf length, leaf width and SPAD measurements. The traits panicle seed density, secondary panicle branches, and seed per panicle associated with the candidate gene frizzy panicle (FZP), while shortened pedicel 1 (sped1), a gene that regulates inflorescence branch development, was identified for panicle seed density and seed per panicle. Primary branches per panicle were associated with candidate genes for photoperiod sensitivity. Semi-dwarf, flowering and leaf length were associated with photoperiod sensitivity and auxin related candidates. One of the significant SNPs detected on chromosome 12 was associated with Sekiguchi Lesion (SL), a disease resistance and cell death regulator locus on chromosome 12 for blast IB49. The TRJ Core shows that it can be an excellent resource to mine allelic diversity for the development of improved tropical japonica rice varieties.