Fusarium head blight (FHB) is a serious disease of wheat (Triticum aestivum) and other small grains; disease severity is affected by temperature and rainfall. This research comprised three studies: an artificially warmed experiment during 2016-2017, a morphology study and an FHB resistance screening study in 2015-2016, using approximately 250 wheat cultivars and breeding lines from programs in the eastern US. The location was the University of Kentucky Spindletop Research Farm in Lexington, KY. Higher levels of Fusarium damaged kernels and the toxin deoxynivalenol (DON) were observed in the warmed treatment compared to the control, and plant development was accelerated. In the FHB resistance screen, significant (p < 0.05) genotype differences for all traits were observed. A GWAS identified 16 SNPs associated with resistance and susceptibility, ranging from -2.14 to 4.01%. Three DON-associated SNPs reduced toxin levels by 3.2, 2.1, and 1.5 ppm. In the morphology study, negative correlations were observed among morphological and disease traits. Small effect SNPs were identified for all morphological traits, which might be useful in genomic selection; traits like spike length, spikelet number and inclination could be used in phenotyping. Response to warming indicates that existing resistance sources may be less effective in a warming climate.

Epigenetics is the study of heritable changes in phenotypes that are not the result of changes in DNA sequence. Examples of epigenetic affecters include methylation changes, chromatin modifications, transcription factors, and RNA-based changes. The molecular mechanisms behind epigenetic changes are not fully understood. Canalization is the buffering of gene expression against environmental changes over time, while habituation is semi-stable expression change over time due to selection. This work characterized the molecular changes associated with the kernel color changes of the R-sc:86-17pale allele at the maize red color1 (r1) locus to determine if the changes are epigenetic in nature. The research; 1) quantified the color differences between the progenitor and habituated sublines; 2) Determined that there are not sequence differences between the progenitor and habituated sublines at the 3` end of the Sc||nc1 gene that could account for changes in seed color; 3) and examined the cytosine methylation patterns at the 3` end of the Sc||nc1 gene of the habituated sublines and the progenitor to determine whether there are methylation differences that correspond with the kernel color changes. Quantification of the kernel colors of the R-sc:86-17pale selection sublines showed that there was a statistically significant difference in kernel color. The identical sequence of the R-sc:86 line and the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines at the 3` end of the Sc||nc1 gene is evidence that the kernel color change is not driven by differences in sequence within the r1 gene. The methylation data suggests that some methylation differences in the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines are present, and suggests that the molecular basis of the kernel color is epigenetic in nature.

Domesticated species are vital to global food security and have also been foundational to the formulation and advancement of evolutionary theory. My dissertation employs emerging molecular genomic tools to provide an evolutionary context for crop improvement. I begin by providing a contemporary perspective on two components of domestication biology that have long been used to improve crop production: wild relatives of crop species and grafted rootstocks. First, I propose a method to systematically introgress crop wild relative diversity into crop breeding programs. Then, I explore rootstocks, the lesser-known half of the perennial crop equation, documenting prevalence and diversity, cataloging rootstock traits under selection, and discussing recent advances in rootstock biology. Both crop wild relatives and rootstocks remain largely underutilized resources and hold great promise for agricultural innovation. While humans have domesticated thousands of plant species, research has largely focused on annual crops, to the exclusion of perennials. To improve our understanding of how tree species respond to domestication, I examine the evolution and domestication of one of the world’s most important perennial tropical fruit crops, the mango, Mangifera indica, and its wild and semi-domesticated relatives. I generated a dataset suitable for studying Mangifera across evolutionary time using double digest restriction site associated DNA sequencing (ddRADseq). I present a multilocus phylogeny that informs the classification of Mangifera and reveals, for the first time, the evolutionary relationships of wild, semi-domesticated, and domesticated species in the genus. Narrowing my focus to the intraspecific level, I examine how the introduction of M. indica into regions of the world impacted its genetic diversity. My results show M. indica maintained high levels of genetic diversity during its introduction into the Americas. However, the novel diversity I detect in Southeast Asian mango cultivars suggests that M. indica has a more complex domestication history than previously assumed. I also find evidence that M. indica hybridized with multiple congeners following its introduction into Southeast Asia, forming two hybrid lineages that may be maintained by clonal polyembryonic reproduction. Collectively, my research provides a comprehensive framework for understanding the evolution and domestication of a tropical tree crop of global economic importance.

Isolated populations have potential to become new species that should have less genetic variation than their ancestors. Small populations are more likely to lose genetic variation, which is, thus, expected to be greater in ancestors. Aliciella caespitosa and A. tenuis, two endemic species, may be derived from small populations of A. subnuda, a widespread species. Chloroplast DNA sequences were used to test this hypothesis. Allozyme data were used to compare genetic variation and numbers of alleles. Chloroplast data do not support the proposed relationships between A. subnuda and the other two species. Allozyme data were not more variable in A. subnuda. The data suggest that A. tenuis is derived from A. caespitosa, although the former did not show lower allozyme diversity. I detected fewer alleles in A. tenuis. These data suggest that the original population of A. tenuis was not small enough to lose genetic variation relative to its progenitor.

Switchgrass (Panicum virgatum), a summer perennial grass native to North America, is currently being explored for its potential use in the production of biofuels. With these interests, genetic manipulation of switchgrass to produce plants that are easier to digest, have an increased resistance to diseases and stresses, and maintain viability longer in the field are required. Therefore, it was necessary to develop a reliable and efficient tissue culture system for the transformation of switchgrass. Current switchgrass tissue culture requires months for regeneration of transformants with relatively poor transformation efficiencies and are limited to derivatives of a single variety, Alamo. We have developed a tissue culture system, utilizing a novel media, LP9, which has demonstrated decreased time to the production of whole transgenic plants and with an increased efficiency. LP9 is not an MSO-based tissue culture system. It is comprised of both N6 macroelements and B5 microelements with the auxin, 2,4-D and does not include any cytokinin. After just 1 month on LP9 media, callus can be selected and used for Agrobacterium tumefaciens-mediated transformation or particle bombardment, and plants can be regenerated within 3 weeks of callus initiation. Our system is unique to previously explored MSO-based systems in that it is optimized for the production of type II callus, which has been shown to produce higher transformation efficiencies in other monocots. We have increased the transformation efficiency of switchgrass from to up to 4% to 34% efficiency by selecting for this type of callus.

The economic feasibility of producing biomass-based fuels requires high-yielding feedstocks to supply biomass to biorefineries. Populus trees are a potential biomass feedstock due to their high yield, but their high water requirement limits productivity under drought conditions. The number of genes controlling drought tolerance, and the long generation time for perennial species, slows cultivar development. Accelerated domestication proposes using the sequenced Populus genome to quickly incorporate target traits into productive clones by transgenesis. Six putative drought tolerance transcription factors: DREB2A, DREB2B, AtMYB, AREB1/ABF2, MYB, and NAC, had been previously identified and manipulated in eastern cottonwood (Populus deltoides). Three constructs of each gene were transformed into a P. deltoides background clone, including constitutive overexpression (OE), drought inducible OE, and knockdown. This greenhouse study examines the effect of these previously transformed constructs on drought tolerance by characterizing leaf abscission, leaf water potential, and growth under drought and well-watered conditions. AREB1/ABF2 constitutive OE lost significantly fewer leaves under drought than the Vector control, and had one of the lowest rates of leaf loss overall. Both DREB2A inducible OE and AREB1/ABF2 constitutive OE plants were more productive than the Vector control under drought conditions. MYB inducible OE was a productive construct and initially appeared to be drought tolerant. It is possible that this construct experienced xylem cavitation early on due to the severity of drought experienced by the large trees containing this construct. DREB2A inducible OE, AREB1/ABF2 constitutive OE, and MYB inducible OE were the most productive constructs as well as being likely to confer drought tolerance. Field trials would be the next step, providing a clearer picture of how these constructs would perform under natural conditions.

Cette étude concerne la régulation de la dormance embryonnaire des semences de tournesol (Helianthus annuus L.) par le cyanure d'hydrogène (HCN), en relation avec les formes actives de l'oxygène (FAOs) et l'éthylène (C2H4). Les semences de tournesol fraîchement récoltées sont dormantes ce qui se caractérise par une germination difficile à des températures basses (10-15 °C). Un traitement de courte durée (3 h) des embryons dormants par du HCN gazeux élimine leur dormance et permet leur germination à 10°C. Cet effet stimulateur ne résulte pas d'une activation de la voie des pentoses phosphates ou de la voie insensible au cyanure, car d'autres inhibiteurs respiratoires ne permettent pas la germination des embryons dormants à 10°C. Après traitement par du HCN, les FAOs s'accumulent dans les cellules des axes embryonnaires ce qui s'accompagne d'une oxydation (carbonylation) de protéines spécifiques qui ont été en partie identifiées. Toutefois le cyanure ne modifie pas la transcription des gènes codant pour les enzymes impliqués dans la production et la signalisation des FAOs. L'effet stimulateur du cyanure sur la germination des embryons dormants n'est pas associé à une modification de la transcription des gènes impliqués dans la biosynthèse de l'éthylène, ACC synthétase et ACC oxydase, et ne résulte pas d'une augmentation de la production d'éthylène. En revanche, le HCN augmente nettement la transcription de ERF1 (ethylene response factor 1), mais n'a pas d'effet sur la transcription de ETR2 (ethylene response 2) et de CTR1 (constitutive triple response 1). Les résultats présentés permettent de proposer un nouveau mécanisme de régulation de la dormance des semences par le cyanure.

Invasive species are an increasing threat to biological diversity as well as a leading cause of recent species’ extinctions. Invasives spread quickly and efficiently, and the U.S spends millions of dollars annually in the control and eradication of these species. More information is necessary in order to predict which species may become invasive. Rubus (Rosaceae) was chosen for study because this genus includes various ploidy levels, reproductive modes, and species that are invasive as well as native. Three Rubus species were chosen to represent apomictic and tetraploid invasives (Rubus armeniacus), a sexual and diploid native species (R. occidentalis), and a sexual and diploid invasive species (R. phoenicolasius). Specimens were collected across the U.S. and two different genetic fingerprinting techniques were used; Amplified Fragment Length Polymorphism (AFLP) and Randomly Amplified Fingerprints (RAF). Using three AFLP primers and two RAF primers, genetic similarity was determined and phylograms were constructed. Through statistical analysis and phylogram data it was determined that there might be slightly more genetic diversity in native R. occidentalis than in invasive R. phoenicolasius. Genetic diversity between apomictic and tetraploid Rubus armeniacus and the two sexual and diploid Rubus species were so similar that no distinction could be made, although the mean pairwise distances and mean number of alleles were significantly different. It was also found that geographic distance and genetic similarity do not appear to be related in these three Rubus species. During the course of this study it was also observed that the AFLP technique produced more alleles than the RAF technique, although this difference was not significant.

The U.S. is the largest maize producer in the world with a production of 300 million tons in 2012. Approximately 86% of the maize production is focused on the Midwestern states. The rest of the production is focused in the Southern states, where Texas is the largest maize producer. Grain yield in Texas ranges from 18 tons/ha in the irrigated production zones to 3 tons/ha in the dryland production zones. As a result, grain yield has increased slowly because of the poor production in the non-irrigated acres. Methods to improve the grain yield in Texas is to breed for maize varieties adapted to Texas growing conditions, including mapping genes that can be incorporated into germplasm through marker assisted selection. This dissertation includes two separate projects that exploit historical data and maize diversity to increase grain yield in Texas. For the first project, a large dataset collected by Texas AgriLife program was analyzed to elucidate past trends and future hints on how to improve maize yield within Texas. This study confirmed previous reports that the rate of increase for grain yield in Texas is less than the rate observed in the Midwestern US. For the second project, a candidate gene and whole genome association mapping analysis was performed for drought and aflatoxin resistance in maize. In order to do so, maize inbred lines from a diversity panel were testcrossed to isogenic versions of Tx714. The hybrids were evaluated under irrigated and non-irrigated conditions. The irrigated trials were inoculated with Aspergillus flavus and the aflatoxin level was quantified. This study found that the gene ZmLOX4 was associated with days to silk, and the gene ZmLOX5 gene was associated with plant and ear height. In addition, this study identified 13 QTL variants for grain yield, plant height, days to anthesis and days to silk. Furthermore, this study shows that diverse maize inbred lines can make hybrids that out yield commercial hybrids under heat and drought stress. Therefore, there are useful genes present in these diverse lines that can be exploited in maize breeding programs

Abstract not available. / Thesis (Ph.D)-University of KwaZulu-Natal, Pietermaritzburg, 2008.