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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #422284
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: The history and hidden impacts of subpopulation introgressions in US rice breeding

Author
item Edwards, Jeremy

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/31/2024
Publication Date: 1/12/2025
Citation: Edwards, J. 2025. The history and hidden impacts of subpopulation introgressions in US rice breeding. Plant and Animal Genome Conference Proceedings. San Diego, California. January 10-15, 2025.

Interpretive Summary:

Technical Abstract: Long-grain rice in the United States predominantly derives from the tropical japonica (TRJ) subpopulation, with targeted introgressions from other subpopulations, such as indica, to enhance traits like yield, disease resistance, and stress tolerance. However, these breeding efforts have also led to unintended genomic introgressions, which may influence breeding outcomes in unexpected ways. This study employed local ancestry inference (LAI) using Gnomix software and sequence data from over 5,000 rice accessions, including all sequenced US varieties. Analysis revealed notable linkage drag and previously unrecognized introgressions in US rice genomes. For example, certain sd1-associated indica introgressions on chromosome 1 include a fissure resistance locus (qFIS1-2), though not all sd1 introgressions retain this beneficial trait. Similarly, an introgressed Pi-ta blast resistance region on chromosome 12 exhibited limited recombination, resulting in a conserved block. These findings underscore the importance of characterizing introgressed regions to optimize breeding strategies, mitigate drawbacks from unintended genomic transfer, and leverage favorable traits to improve rice performance.