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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #421949
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: Uncovering hidden introgressions: optimizing breeding strategies in US long-grain rice

Author
item Edwards, Jeremy
item Huggins, Trevis

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/13/2024
Publication Date: 1/5/2026
Citation: Edwards, J., Huggins, T.D. 2026. Uncovering hidden introgressions: optimizing breeding strategies in US long-grain rice. Rice Technical Working Group Meeting Proceedings. New Orleans, Louisiana. February 17-20, 2025.

Interpretive Summary:

Technical Abstract: Long-grain rice varieties grown in the United States are primarily developed from the tropical japonica (TRJ) rice subpopulation. Breeding programs have intentionally introduced genetic material from other rice subpopulations, such as indica, to improve traits like yield, disease resistance, and stress adaptability. However, these efforts have also resulted in unintended transfer of genomic regions, which may impact breeding outcomes in unforeseen ways. This study investigates recombination patterns surrounding introgressed regions and aims to uncover hidden introgressions in historical and modern US rice varieties. To trace the ancestry of chromosomal segments, local ancestry inference (LAI) was performed using Gnomix software. This analysis utilized publicly available sequence data from over 5,000 rice accessions, including all sequenced US rice varieties. Variants were identified through a DeepVariant/GLNexus pipeline run on USDA SCINet high-performance computational resources. Training data were prepared by selecting non-admixed individuals from each subpopulation using Admixture. The findings revealed notable patterns of linkage drag around key introgressed loci and identified previously unrecognized introgressions in US long-grain rice genomes. For instance, certain indica-derived introgressions on chromosome 1 include the sd1 gene for semidwarf stature and are associated with a linked locus conferring fissure resistance (qFIS1-2). This fissure resistance locus is positioned distal to sd1, however some introgressions carrying sd1 do not include this beneficial locus. On chromosome 12, an introgressed region containing the blast resistance gene Pi-ta displayed extremely limited recombination, resulting in a large, conserved segment. Characterizing these introgressed regions is critical for improving rice breeding. This knowledge enables breeders to address potential drawbacks of unintended introgressions while utilizing favorable genetic associations to enhance crop performance.