Doctor of Philosophy (PhD)



Document Type



Rice is a staple food for over one-third of the world’s population. With the increasing population, plant breeders must continue to breed for improved varieties. The utilization of markers to applied breeding program can increase the efficiency of selection for key traits. The targeted traits for this research include grain aroma and resistance to the fungal disease narrow brown leaf spot (Cercospora janseana). Our objective was to characterize SNP diversity across the BADH2 gene in publicly available sequence data of a collection of 2,932 rice varieties was characterized to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, we detected 11 haplotype groups, and subsequently identified a minimal set of nine informative SNPs that uniquely identified all of the BADH2 haplotypes. These nine SNPs were developed into Kompetitive Allele Specific PCR assays and used to examine a panel of 370 U.S. rice accessions. Six haplotypes were detected within the U.S. panel, of which two were found in a majority (85%) of varieties. A representative set of 40 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines. One haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm. A recombinant inbred line population was scored for narrow brown leaf spot resistance under natural disease pressure in the field across three years. A single, large effect QTL was identified that explained 81.4% of the phenotypic variation across all three years. A set of 13 informative SNPs were selected across this region and used to characterize the haplotype diversity across a panel of 389 U.S. rice breeding lines that were phenotyped for Cercospora over two years. A total of 14 haplotypes were identified and Haplotype 1 was the only susceptible haplotype in the panel. A single SNP was identified that distinguishes the susceptible viii haplotype from all resistant haplotypes. This SNP explained 52.7% of the phenotypic variation for NBLS resistance in the panel across two years of phenotype data.



Committee Chair

Famoso, Adam