Date of Award

Winter 12-15-2021

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Evolution, Ecology & Population Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Just under one-half of the global population relies on cultivated rice (Oryza sativa) astheir primary source of calories, making the optimization of rice agriculture immensely important. One of the primary constraints to rice agriculture is the de-domesticated (feral) form of rice known as ‘weedy rice’ that aggressively competes for space, soil nutrients, and light. Heavy infestation can reduce crop yields by as much as 80%. As a closely-related weedy descendant of cultivated rice, chemical control is difficult in rice fields, and physical weeding is labor intensive, time consuming, and largely ineffective due to early life-stage mimicry of the crop.

Weedy rice occurs in almost every world region that cultivates rice and in most caseshas evolved from local cultivated varieties. This thesis focuses on two regions. The first is the southern United States, where two strains, black-hull awned (BHA) and straw-hull awnless (SH) have coexisted for >150 years at relatively equal frequencies. Historically, there has been minimal gene flow between these two independently-evolved strains or with cultivated varieties of rice. The other region is Thailand, where, unlike the US, the reproductively compatible wild rice ancestor (Oryza rufipogon) is present at the margins of fields. Both US and Thai weedy rice populations have been rapidly adapting to changing agricultural practices in recent decades. Using these two sampled regions, my dissertation research focused on three questions: 1) Do independently evolved strains of weedy rice use similar or different genetic mechanisms when evolving competitive growth traits — specifically, with respect to root system architecture? 2) How have weedy rice genomes adapted to rapidly changing 21st Century agricultural practices? And 3) How does the presence of an obligately outcrossing wild ancestor alter the gene flow dynamics of the predominantly selfing cultivated-weedy rice system?

Chapter One provides an overview of weedy rice and the evolutionary forces that haveshaped it worldwide.

In Chapter Two I used two large recombinant inbred line (RIL) populations to perform aQTL mapping study using root system architecture as my trait of interest. Both mapping populations were generated from a cultivated × weedy rice cross using the same cultivated plant as the paternal line (SH × cultivated and BHA × cultivated). Seedlings were grown for 13 days in an agarose gel, after which they were placed on a turntable and imaged at 5° increments in rotation. All 72 images were integrated to produce a 3D model of root system architecture. Over 100 root traits were measured on more than 600 seedlings. Mapping identified 10 traits that mapped to different genomic locations in each mapping population. Only a single trait, convex hull volume, mapped to the same genomic location in both populations. The results of this chapter suggest that different populations, experiencing the same selection pressures, rely on very different genetic mechanisms to evolve similar weedy phenotypes.

Chapter Three focuses on the effects of changing agricultural practices on the genomesof southern US weedy rice strains (SH and BHA). In 2002, herbicide resistant rice was commercialized. At the same time, hybrid rice technology was introduced as a high-yield alternative to traditional inbred cultivars. Due to the propensity of hybrid rice to drop its seed onto the soil before harvest, leading to crop volunteers, this technology became a bridge for gene flow between cultivated and weedy rice. Weedy rice populations became herbicide resistant by the mid 2000s, and experimentation showed this was due to adaptive introgression of the crop resistance allele. We collected 48 samples of weedy rice in 2018 and performed whole genome sequencing to determine the long-term genomic consequences of this event. We discovered that, while descendants of both the SH and BHA populations are represented, their genomes have been irrevocably altered from the strains that had existed prior to 2000. First, we find that most weedy rice plants (44/48) are of crop-weed hybrid origin and that BHA is the dominant weedy ancestor in these hybrid derivates. Moreover, a local ancestry analysis reveals that within the genomes of these contemporary weeds, most (~70%) of the genome is derived from the weedy ancestors, suggesting a selective advantage of the weed genome in contemporary hybrid-derived weeds. Lastly, we find that while herbicide resistance is primarily derived from herbicide resistant crop cultivars, the four weeds of non-hybrid origin also contain resistance alleles, suggesting that convergent evolution has played a part in the persistence of weedy rice.

Chapter Four seeks to identify the impact of local wild rice populations on gene flowdynamics of weedy rice in Thailand. We utilized two complementary data sets, twelve neutral microsatellite markers, and three domestication-associated genes, to track gene flow from wild and cultivated rice into weedy rice populations. Interestingly, while both data sets identified gene flow, there was little overlap between them in the accessions showing admixed ancestry. This suggests a temporal discordance (allowing for multiple generations of recombination between the gene flow events), with these historic introgression events occurring separately and quite long ago.


English (en)

Chair and Committee

Kenneth M. Olsen

Committee Members

Carlos A. Botero

Included in

Genetics Commons