IC4R001-GWAS-2011-21829395

Project Title

Genetic Architecture of Aluminum Tolerance in Rice( Oryza sativa ) Determined through Genome-Wide Association Analysis and QTL Mapping

The Background of This Project

While rice (Oryza sativa) is significantly more Al tolerant than other cereals, no genes underlying Al tolerance in rice have been reported. Using genome-wide association(GWA) and bi-parental QTL mapping, we investigated the genetic architecture of Al tolerance in rice. Japonica varieties were twice as Al tolerant as indica and aus varieties. Overall, 57% of the phenotypic variation was correlated with subpopulation, consistent with observations that different genes and genomic regions were associated with Al tolerance in different subpopulations. Four regions identified by GWA co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified quantitative trait loci(QTL). Haplotype and sequence analysis around the candidate gene, Nrat1, identified a susceptible haplotype explaining 40% of the Al tolerance variation within the aus subpopulation and three non-synonymous mutations within Nrat1 that were predictive of Al sensitivity. Using Indica 6 Japonica mapping populations, we identified QTLs associated with transgressive variation where alleles from a susceptible indica or aus parent enhanced Al tolerance in a tolerant japonica background. This work demonstrates the importance of subpopulation in interpreting and manipulating complex traits in rice and provides a roadmap for breeders aiming to capture genetic value from phenotypically inferior lines.

Corresponding Author

Akira Oikawa(oikawa@psc.riken.jp)