Peppers (Capsicum) are a valuable commodity throughout the world. They provide food, coloring additives, vitamins, and ornamental aesthetics. Peppers can be grown in many different areas of the world and their success is based on variety selection. Breeding cultivars for superior performance is critical to success. Recent consumer desire for less chemical use throughout the growing process has resulted in new cultivar developments.. The objective of this research was to investigate how cultivar and type affect the yield and weight of field grown peppers. This study provides valuable information for growers in determining which cultivars are suitable for production in Kentucky. The research was conducted at the Western Kentucky University Agriculture Research and Education Complex in Bowling Green, Kentucky in 2016. Plants were provided by Ball Horticultural and Pan American Seed, Elburn, Illinois. The experimental design was a random design, with a 12 plant experimental unit consisting of four three plant rows. Thirty-six cultivars were divided into groups based on the type of pepper produced. Harvest occurred approximately every 7 days and were grouped into 3 periods. Data were obtained on yield, weight, and mean weight. Individual group selection is determined by the producers and their goals for production. There were wide differences in the types of peppers, including size, shape, and color. When comparing all groups, two of the thirty six cultivars, Cultivar 23 (Tapered) and Cultivar 34 (Chili) performed best for both yield and mean weight.

New soybean lines have been developed with significantly higher oil, protein + oil and higher meal protein. These soybeans contain a VgD1 gene (highly active acyl-CoA:diacylglycerol acyltransferase, DGAT from Vernonia galamensis (VgDGAT1A) produces much higher oil synthesis and accumulation activity in soybean. Soybean with active DGAT from Vernonia galamensis (VgDGAT1A) has active TAG biosynthesis relative to other DGATs including from soybeans and Arabidopsis. DGATs catalyze the final step of TAG synthesis: DAG (diacylglycerol) + acyl-CoA → TAG + CoASH (Coenzyme A is notable for its role in the synthesis and oxidation of fatty acids, and the oxidation of pyruvate in the citric acid cycle). A thorough analysis of the major components in VgD1 lines, especially those of nutritional or anti-nutritional value including what else changed (decreased); and what remained at normal levels was conducted. A field study was conducted in Spindletop and Princeton KY, reviled no reduction in yield nor protein, and about 4 % (DW) more oil was obtained in Princeton and 2% (DW) in Spindeltop. No consistent reduction in the other seed composition.VgDGAT1A soybean lines indicated noticeably early maturation compared to the parental line. This is associated with higher expression of the flowering genes FT2 (FLOWERING LOCUS T2) and FT5 (FLOWERING LOCUS T5), for the high oil lines. A single recessive mutation in soybean (MIPS) myo-inositol 1-phosphate synthase, confers a seed phenotype of increase inorganic phosphate (Pi) crossed with high oil lines expressing a DGAT from Vernonia galamensis (VgDGAT1A) (VgD). The oil and protein were maintained compart to VgD. VgD X MIPS (VM), had 21.2, and 22 % oil in 2015, and 23.3 and 24.0 oil in 2016, and protein 46, 49 in 2015, and 37 and 39 % in 2016. Phosphate results suggesting the cross MV is still segregating for MIPS and more selection and planting are needed. Measurement of seed phosphate levels is an established technique for screening for low phytate mutants but to date, it has not been performed non-destructively from single soybean seeds. A protocol was developed greatly reducing the sample size thereby reducing the cost and time and saving a generation in the selection of low phytate mutant seeds based on the high Pi phenotype. Genotyping single seeds are useful in breeding and genetics while maintaining high germination rates. Nondestructive single-seed genomic DNA extraction protocols using 12 mg cotyledon tissue with a modified cetyl trimethyl ammonium bromide (CTAB) technique and a commercial seed DNA extraction kit using 1 mg cotyledon tissue were developed for dry soybean seeds and cross-verified with leaf DNA analysis.

Cultivated tomato plants are extremely susceptible to the two-spotted spider mite Tetranychus urticae Koch. Selection for pest resistance is usually a crucial step required to achieve successful genetic resistance transfer from wild into cultivated tomato genotypes. S. habrochaites LA2329, a wild relative of tomato, is highly resistant to arthropods. Its resistance has been attributed to the presence of a high density of type IV and type VI trichomes and abundant production of 7-epi-zingiberene, a sesquiterpene hydrocarbon. The interspecific backcross hybrids used in this research were derived from the cross between the wild relative tomato, S. habrochaites LA2329, and the cultivated tomato, S. lycopersicum ‘Zaofen 2’ (ZH2). This population has been directly selected for type IV trichome density and zingiberene. The arthropod resistance status of the backcross hybrids was unknown when this research was initiated. Thus, the main objective of the research was to verify the transfer of arthropod resistance from S. habrochaites to cultivated tomato. The effects of glandular trichome densities and leaf zingiberene contents on spider mite behavior and biology were also explored. Also, the chemical composition of the trichome secretions in the wild tomato donor is segregating for presence and abundance of sesquiterpenoids related to zingiberene. The bioactivity of these sesquiterpenoids was explored in this research. To evaluate the relative bioactivities of zingiberene alcohol and 7-epizingiberene, extracted from glandular trichomes of Solanum habrochaites accession LA2329, as well as alpha-zingiberene obtained from ginger oil, these were purified by silica gel chromatography and bioassayed with two-spotted spider mites, Tetranychus urticae Koch (Acari: Tetranychidae) using a bean leaf disc bioassay. Zingiberene alcohol was most efficacious and alpha-zingiberene, was least efficacious, while the efficacy of 7-epizingiberene was intermediate. Thus, tomato breeders should consider introgression of the genes responsible for the oxidation of 7-epizingiberene into zingiberene alcohol to potentially improve the spider mite resistance of cultivated tomato. Also, it is possible that this compound may be exploited as eco-biopesticide approach for integrated pest management against a broad spectrum of herbivorous pests. To verify transfer of arthropod resistance, a bioassay utilizing whole leaves was employed. Nine hybrids (BC3F3 and BC3F4) were chosen for this bioassay, based on variation of type IV trichome density and zingiberene concentration among the hybrids. The experiment also included three susceptible and three resistant control plants. Mite responses on some of the hybrids were similar to those on the resistant wild donor parent, S. habrochaites, as indicated by number of leaflet surfaces infested by mites, degree of mite webbing and feeding damage. Egg density on four backcross hybrids was similar to that on the S. habrochaites resistant controls. Based these results, we concluded that resistance had been successfully transferred from the wild accessions to the hybrids by deployment of backcrossing and indirect selection. There was a significant negative correlation of almost all mite behavioral and biological responses with Type IV trichome density and zingiberene content. This bioassay illuminated behavioral variations of mites associated with presence or absence of leaf compounds and glandular trichome densities. Also, the results support the idea that introgression of type IV trichomes and zingiberene has led to effective spider mite resistance. In another bioassay-based experiment to verify transfer of resistance, seven interspecific backcross hybrids (BC3F2), the resistant parent LA2329, and two susceptible cultivated tomato lines, the recurrent parent ZH2 and ‘Small Roma’, were used in thumbtack bioassays. Mite movement was measured by imaging bioassayed leaves at 15, 20, 30, 45, and 60 min intervals. In addition to confirming transfer of spider mite resistance, other objectives included determination of the relative contributions of type IV and VI trichome densities and leaf compounds to mite behavior over time intervals. Our findings confirmed the transfer of mite repellency from the wild resistant parent to advanced backcross hybrids. Several backcross hybrids performed similarly to the wild donor parent, displaying shorter distances traveled on the leaves after 15 and 30 min. The type IV and type VI trichome densities as well as zingiberene contents had a significant positive correlation with the number of spider mites remaining on tack. There was a significant negative correlation of type IV density and zingiberene concentration with the total distance travelled by mites for both the abaxial and adaxial surfaces across most time intervals. Stepwise multiple regression analysis showed that the type IV trichome density was the most critical factor, and zingiberene content was a secondary factor across over most time intervals. T. urticae remained longer on the thumbtack heads and traveled shorter distances on the leaf surface of the wild donor parent LA2329 and the interspecific hybrids compared to S. lycopersicum leaves. These results indicated that introgression of genetic resistance, especially repellence, against spider mite from the wild relative into cultivated tomato varieties has been successfully achieved. In conclusion, trichome type IV and/or zingiberene content has been successfully transferred from the wild relative into interspecific tomato hybrids, and the hybrids show significant adverse impact on spider mite behavior and/or biology in whole leaf and thumbtack bioassays. Type IV trichome density is the most crucial factor in mite deterrence while zingiberene seemed to be a second key factor across most of time durations for both surfaces. Collectively, several backcross hybrids had similar leaf characteristics to the S. habrochaites LA2329, also may be a potential source of resistance to other insect pests.

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.

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.