Doctor of Philosophy (PhD)


School of Plant, Environmental, and Soil Sciences

Document Type



Rice breeders face the challenge to continually improve varieties for agronomic and quality traits. The first objective of my research was phenotypic and genotypic characterization of rice low endosperm chalk in US rice. A panel of 96 rice accessions and a set of 20 single nucleotide polymorphism (SNP) markers were used to evaluate low chalk kernels. Single marker analysis to detect main effect SNPs was performed to establish associations between markers and phenotype. A one-way ANOVA across the entire panel detected 3 SNP markers associated with low chalk values with R2 >10% on chromosomes 1 and 6. A U.S. rice germplasm panel (NTP) was used for validation. The SNP marker explaining the highest phenotypic variation (3.4%) was located at 20.5 Mbp on chromosome 10. Single marker analysis within genetic groups of the NTP detected two closely linked markers on chromosome 10 associated with chalk (R2=0.14). Results of this study confirmed that low chalk is a complex trait that may be addressed by other breeding techniques such as genomic selection.

The second objective of my research was the phenotypic and genotypic characterization of presence or absence of awns. Genetic analysis of awns was carried out using a segregating population developed from conventional and ProvisiaTM awnless parental lines and 127 genome-wide SNP markers. We mapped a 1557 Kb awn-related region on chromosome 3 that appears to be a major source of awn formation when ProvisiaTM material (indica-type) is used for crossing with U.S. elite varieties. Two single nucleotide polymorphism (SNP) markers, SNP261 and SNP1251 explained 26% and 28% of the phenotypic variation in awn formation and elongation. Contingency analysis of bulk generation 1, bulk generation 2, and bulk generation 3 showed that the awnless, short-awned, and low percentage of awns per panicle is explained by the presence of japonica alleles. When used together, these markers help differentiate awnless material.



Committee Chair

Oard, James



Available for download on Friday, January 19, 2029