Doctor of Philosophy (PhD)


Plant, Environmental Management and Soil Sciences

Document Type



We have evaluated the potential of discriminant analysis (DA) to detect candidate markers associated with twelve economically important traits in a large population of unrelated U.S. and Asian inbred lines of rice. Associated marker alleles detected by DA mapped within the same genetic intervals when compared with previous traditional QTL mapping experiments that evaluated progeny derived from various controlled crosses. New markers identified by DA suggest that the procedure can also uncover relevant genetic regions not possible by standard genetic tests. With the same dataset, we also compared different modern regression approaches for selecting molecular markers associated with the twelve agronomic traits. These methods included stepwise forward regression (SFR), least angle regression (LAR) and least absolute shrinkage and selection operator (LASSO) selection. The epistatic model based on stepwise forward regression did successfully identify several interacting loci that explained a relatively high proportion of the observed variation for all the twelve agronomically important traits. Moreover, the loci identified by the epistatic model mapped within previously known QTL regions that underscores the genetic basis of the selected markers. It was concluded that stepwise forward regression with consideration for population structure, epistatic interactions, and missing data (multiple imputation) was a robust method, compared to the general linear model, to identify markers associated with complex agronomic traits. Acetolactate synthase (ALS), also known as acetohydroxy acid synthase (AHAS), which catalyzes the first step in the biosynthesis of the branched-chain amino acids valine, leucine and isoleucine in plants, is a target of five herbicide groups, including sulfonylurea and imidazolinone. A recently discovered group of Coreopsis tinctoria Nutt. mutants from the field showed high levels of resistance to both sulfonylurea and imidazolinone herbicides. In this study the mutants were compared by chemical, genetic, and molecular analyses with “normal” or wild-type Coreopsis. A phylogenetic analysis revealed that the ALS gene can serve as a useful molecular tool for evaluating evolutionary relationships among plant species. Due to pending patent applications by the Louisiana State University Agricultural Center and restrictions of patent applications, specific results from this research cannot be presented in this dissertation.



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Committee Chair

James H. Oard