Location: Responsive Agricultural Food Systems Research Unit
Project Number: 3093-10700-001-010-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2026
End Date: Jun 30, 2029
Objective:
The primary goal of this research is to implement a genetic analysis framework in rice to identify seed traits that influence microbial fermentation patterns within the human gut microbiome. By leveraging existing genetic resource populations, this study will use a combination of quantitative and functional genomics to systematically study how genetic and phenotypic variation in rice can influence fermentation patterns in the human gut microbiome. Integrating these microbiome traits into rice improvement programs will facilitate the development of biofortified varieties designed to optimize human nutritional outcomes.
Approach:
A quantitative genetics framework will be implemented using meta-analysis and parallel genome-wide association studies (GWAS) of Oryza sativa to characterize loci where genetic variation drives dramatic shifts in the composition and functional capacity of human gut microbial communities. In this project we will employ a rice diversity panel comprising 330 cultivars that represent broad global genetic and phenotypic variation, together with AiMS microbiome phenotyping, to detect genetic loci linked to changes in gut microbiome composition or function across multiple human donors. In parallel, we will map loci influencing this defined set of focal traits and assess whether multiple-effect loci (MEL) contribute both to trait variation and to microbiome responses. The novel rice traits (microbiome activity) and candidate genes and genomic markers identified through this work will support breeding strategies aimed at enhancing crop nutritional quality and promoting positive human health outcomes in rice and related species. Moreover, the integrated AiMS phenotyping and GWAS framework developed here will be applicable to a wide range of diverse crop systems.