ARS | Publication request: Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 30, 2010
Publication Date: February 1, 2011
Citation: Nelson, J.C., McClung, A.M., Fjellstrom, R.G., Moldenhauer, K.K., Boza, E., Jodari, F., Oard, J.H., Linscombe, S., Scheffler, B.E., Yeater, K.M. 2011. Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm. Theoretical and Applied Genetics. 122(2):291-309.

Interpretive Summary: The amount of whole versus broken kernels in harvested rice is a key crop value component, and the genetic control of grain breakage after milling (commonly called milling yield or head rice yield) is poorly understood. The goal of our studies was to characterize the mode of inheritance and determine rice gene regions providing control of milling yield, as well as identify DNA markers in these gene regions. We pursued these goals by making crosses between a high milling yield rice variety, called Cypress, with two different varieties with low milling yield, one derived from Asian rice, called RT0034, and one from the southern U.S., called LaGrue, and then measuring milling yields in progeny families derived from these genetic crosses. The progeny families were grown for three years, 2005 to 2007, in two rice production locations, Arkansas and Louisiana, using replicated trials, and, after harvesting, milled in a single location to reduce experimental milling technique errors. It was found that lines with high milling yield in LA often had low milling yield in AR, or vice-versa (low in LA was high in AR), so there were large growing location effects on milling yield in both genetic mapping populations. No outstandingly significant gene regions controlling milling yield were able to be identified, signifying that this trait has quite complex inheritance and that milling yield is primarily controlled by the environment and by a variety of genes interacting with the environment.

Technical Abstract: Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR U.S. japonica cultivar, with RT0034, a low-HR indica line (129 RILs) and LaGrue, a low-HR japonica cultivar (298 RILs), grown in two U.S. locations in 2005–2007. Early heading increased HR in the Louisiana (LA) but not the Arkansas (AR) location. Fitting QTL-mapping models to separate QTL main and QTL × environment interaction (QEI) effects and identify epistatic interactions revealed six main-effect HR QTLs in the two crosses, at four of which Cypress contributed the increasing allele. Multi-QTL models accounted for 0.36 of genetic and 0.21 of genetic × environment interaction of HR in MY1, and corresponding proportions of 0.25 and 0.37 in MY2. The greater HR advantage of Cypress in LA than in AR corresponded to a genomewide pattern of opposition of HR-increasing QTL effects by AR-specific effects, suggesting a selection strategy for improving this cultivar for AR. Treating year–location combinations as independent environments resulted in underestimation of QEI effects, evidently owing to lower variation among years within location than between location. Identification of robust HR QTLs in elite long-grain germplasm is suggested to require more detailed attention to the interaction of plant and grain development parameters with environmental conditions than has been given to date.