Identification of molecular markers and association mapping of selected loci associated with agronomic traits in rice

Discriminate Analysis as a procedure was evaluated to select molecular markers associated with complex traits in US rice germplasm. Markers for percent head rice, percent total rice, and grain yield were identified with high levels of correct classification that mapped within or near traditional Quantitative Trait Loci (QTL).; Mixed model-regression procedure to identify molecular markers that predict phenotypic variance associated with four agronomic traits was created and validated in two distinct rice inbred populations. Main and epistatic effects were identified by standard hypothesis testing and Bayesian information criteria in a multivariate format. The new procedure increased power and enhanced prediction ability of markers in validation samples from both populations.; A new SNP discovery and genotyping protocol referred to as Alternative Ecotilling has identified four previously reported and 14 new SNPs in the alk and waxy genes among 57 accessions based on comparisons with sequencing results. The new procedure has been published in 2006 in the journal Plant Molecular Biology Reporter.; Application of haplotype-specific markers in exon 7 of the BAD2 gene for marker-assisted identification and introgression of the aroma gene in U.S. rice was evaluated. Aromatic/non-aromatic phenotypes were consistent with corresponding marker haplotypes for all progeny tested which shows the potential of this procedure for marker assisted breeding of new aromatic varieties.; Similarly, an allele-specific PCR assays were developed to distinguish between homozygous and heterozygous imazethapyr-resistant S653D and G654 SNP alleles of the rice ALS gene. Field collections were successfully screened for the presence of S653D SNP, and F2 progeny lines of natural CL 121 x red rice outcrosses were screened for the presence of the G654 SNP. These assays were proven successful and are currently used for detection of outcrossing and seed purity for the LSU AgCenter Rice Breeding Project.