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Author ORCID Identifier



Campus-Only Access for Five (5) Years

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Plant Biology

Year Degree Awarded


Month Degree Awarded


First Advisor

Ana L. Caicedo

Second Advisor

Li-jun Ma

Third Advisor

Jeffrey L. Blanchard

Fourth Advisor

Michelle DaCosta

Subject Categories

Apiculture | Evolution | Genetics | Genomics | Molecular Genetics | Population Biology


Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O.sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the ‘agricultural weed syndrome’, making this an ideal model to study the genetic basis of parallel evolution. Using population genetics analyses of South Asian and US weedy rice, my research reveals multiple independent evolution events giving rise to weed groups in the two geographic areas. Weeds in South Asia have highly heterogenous genetic backgrounds, with contributions from both cultivated varieties (aus and indica) and wild rice. Weeds in US evolved from independent single colonization events from South Asian cultivars (aus and indica). I phenotyped a more complete list of potential iconic weedy traits and assessed the polymorphisms on candidate genes underlying them. Among the traits I surveyed, seed shattering and red pericarps are the most essential weedy traits that converge among weedy rice worldwide with diverse ancestries. For the seed shattering candidate gene, sh4, almost all cultivar-like weeds inherited the non-shattering allele from cultivar ancestors, and thus there is another mechanism causing re-acquisition of shattering phenotype in cultivar-like weeds. However, genotypes of the the pericarp color candidate gene, Rc, is mostly sufficient to explain the red pericarp phenotype in weedy rice. I also performed physiological measurements and RNA-seq analysis to assess the competitiveness of weedy rice when compared to cultivar ancestors at vegetative growth stage, and to discover possible genetic mechanisms underlying competitiveness. Under low nitrogen environment, both US and South Asian weeds seem to allocate less or similar nitrogen to leaf area, while still have overall higher photosynthesis rate. Under optimal nitrogen environment, when compared to cultivars, US weedy rice grow faster and accumulate more sugar with less nitrogen accumulation in leaves. Certain sugar derivative pathway, plant growth and phytohormone related genes are detected to differentially express between weedy rice and their cultivar ancestors.