Genetic dissection of seed shattering, agronomic, and color traits in American wildrice (Zizania palustris var. interior L.) with a comparative map

A comparative map of American wildrice (Zizania palustris var. interior L.) was used to identify loci controlling seed shattering, plant height, maturity, tiller number, plant habit, panicle length seed length, and color traits. Two to six significant quantitative-trait-loci (QTLs, P < 0.05) were detected for each trait evaluated, representing the first trait-mapping in wildrice. The chosen population was designed to emphasize the mapping of loci controlling the shattering trait, which is the most important trait in the management of this newly domesticated species. Three loci were detected that controlled the discretely categorized variation between shattering and non-shattering plants. Seed-shattering loci were detected and validated among the F₂ and F₃ generations. A multiple regression model with these three loci described 49.6% of the additive genetic variation. A genetic model with the same three loci including dominance and locus interactions predicted the shattering versus non-shattering phenotype at a success rate of 87%. The comparative map was based on mapped RFLP markers used in white rice (Oryza sativa L.) and other grass species. Anchor loci provided a reference point for the identification of potential orthologous genes on the basis of white rice mutant loci and consensus grass species QTLs. Candidate orthologous loci were identified among all traits evaluated. The study underscores the benefits of extending trait analysis through comparative mapping, as well as challenges of QTL analysis in a newly domesticated species.