Araucaria cunninghamii is an ancient tropical conifer with substantial value as a forestry species in Australia and Papua New Guinea, and has been subject to a genetic improvement program for more than 50 years. This study was undertaken to demonstrate the utility of quantitative genetic analysis in describing the genetic architecture of commercial traits in A. cunninghamii. Linkage maps were prepared using the pseudotestcross strategy in what was believed to be a wide interprovenance cross using microsatellites and AFLP. A very low rate of marker polymorphism and limited differentiation between the parental provenances was identified, resulting in low mapping efficiency. The population genetic structure of A. cunninghamii was assessed to establish the underlying causes for the limited differentiation and low marker heterozygosity and assess the implications for future analysis of quantitative traits. Despite the limited mapping efficiency, genetic maps were generated for both parents. The maternal map for individual H15 contained 14 linkage groups comprising of 51 AFLP and one microsatellite. The map covered 1290 cM, representing 89% of the estimated genome size. The paternal map for individual Gil24 was 633 cM, consisting of eight linkage groups. Genetic architecture of quantitative traits was examined with putative QTL identified for height, DBH and stem straightness; one was highly significant (p<0.01), three significant (0.01<p<0.05) and 13 suggestive (p<0.10). Significant QTL each accounted for 7-11% of the phenotypic variance with a high allele substitution effect (0.63-0.81). These QTL were likely to be associated with genes of moderate effect. The suggestive QTL each accounted for 3-6% of the phenotypic variance with an allele substitution effect of 0.40-0.63. Three genomic regions contributed to the expression of multiple traits at multiple ages. Stable QTL had decreasing phenotypic effects with increasing age. The population genetic survey characterised low levels of allelic diversity across the geographic range. Three broad regions were characterised; Papua New Guinea, Cape York and northern Queensland to NSW. There was limited differentiation between provenances within these regions, and high diversity within provenances. Limited genetic differentiation between provenances seems to be the result of genetic stability due to long overlapping generations, limited founder effects and a very low mutation rate. The latter may also contribute the low heterozygosity. Limited marker polymorphism and limited differentiation between provenances within broad regions are common features in A. cunninghamii. Therefore careful parental selection and alternative experimental approaches will be required before undertaking further analysis of quantitative traits.

Evolutionary life history theory predicts that tradeoffs among fitness-related phenotypes will occur as a result of resource limitations and/or physiological constraints. Such tradeoffs are defined as the cost(s) incurred on one component of fitness (e.g., reproduction) by the increased expression of another fitness-related trait (e.g., longevity). Only recently have researchers begun to investigate the mechanistic bases of life history tradeoffs. A recent proposal is that reactive oxygen species (ROS) have a central role in shaping life history traits and tradeoffs. Research on disparate animal taxa has highlighted strong correlations between oxidative stress resistance and fitness-related life history traits, for example. Here, I use the model organism Caenorhabditis elegans to test several hypotheses concerning the effects of ROS on life history traits and the manifestation of life history tradeoffs. Additionally, I use heat stress and an alternate food source to explore the responses of life history traits to other forms of physiological stress. Relative fitness and other traits related to reproduction were found to be affected in mostly negative ways by increasing oxidative insult. Lifespan was surprisingly unaffected by oxidative stress, but was modified by temperature. In vivo ROS levels as measured by fluorescent microscopy reveal a tradeoff between antioxidant production and reproduction in this species.

No description available.

Lignin is a significant recalcitrant in the conversion of plant biomass to bioethanol. Cinnamyl alcohol dehydrogenase (CAD) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the pathway of lignin monomer biosynthesis. Brown midrib mutants in Zea mays and Sorghum bicolor with impaired CAD or COMT activity have attracted considerable agronomic interest for their altered lignin composition and improved digestibility. We identified candidate genes encoding CAD and COMT enzymes in the grass model species Brachypodium distachyon and developed transgenic plants overexpressing artificial microRNA designed to silence BdCAD1 or BdCOMT4. Both transgenes caused altered flowering time and stem count and weight. Downregulation of BdCAD1 caused a leaf brown midrib phenotype, the first time this phenotype has been observed in a C3 plant. While acetyl bromide soluble lignin measurements were equivalent in BdCAD1-silenced and wildtype plants, histochemical staining and thioacidolysis indicated a decrease in lignin syringyl units and reduced syringyl/guaiacyl ratio in the transgenic plants. BdCOMT4-downregulated plants exhibited a decrease in total lignin content, a significant reduction of guaiacyl lignin, and a modest reduction of syringyl lignin. Ethanol yield by microbial fermentation was enhanced in both BdCAD1- and BdCOMT4-downregulated plants. These results have elucidated two key genes in the lignin biosynthetic pathway in B. distachyon that, when perturbed, may result in greater biomass yield and bioconversion efficiency.

Cannabis sativa L. (hemp) develops plants with either male or female flowers, and growers of hemp greatly prefer female flowers which bear the glandular trichomes that contain cannabinoids. Feminized (all female) seeds are highly desired, which are produced by crossing a female plant with a masculinized female plant. Masculinization is achieved through the inhibition of ethylene and/or addition of gibberellins before flower initiation in female plants. The hemp industry uses silver thiosulfate (STS) to masculinize hemp, but spraying silver poses environmental concerns. This study compared STS to three other ethylene-inhibiting agents: aminoethoxyvinylglycine (AVG), cobalt nitrate (CBN), and 1-methylcyclopropene (1-MCP). Treatments of STS and CBN also included gibberellic acid as a synergist. Plants treated with STS exhibited superior masculinization and pollen dispersal compared to plants treated with AVG, CBN or 1-MCP. Only plants treated with STS or AVG produced pollen in sufficient quantities for collection. This pollen was assayed for germination potential initially and after storage for up to five weeks at 22.2, 7.2, or 1.1°C. Pollen from plants treated with AVG remained viable for four weeks at 1.1°C, whereas STS-treated plants produced pollen that was viable for three weeks at 1.1°C. Due to phytotoxicity problems with AVG, STS remains the best treatment to masculinize female hemp plants when breeding for feminized seeds. In a separate study, flower tissues of hemp had considerably higher total cannabinoid concentrations compared to leaf tissues but significantly lower ratios of cannabidivarin (CBDV) to cannabidiol (CBD). To reduce variability, at least 1 g samples of fresh leaf or flower tissue should be extracted with 10 mL of methanol. Rapid throughput testing of cannabinoids as part of a breeding program should use flower tissue, preferably at the time typical of harvest.

Peanut digging timing is difficult to predict due to indeterminate growth and peanut pods maturing underground, resulting in the need to research methods that provide consistent measurements, while reducing time and effort for farmers and researchers. Experiments were conducted to evaluate the accuracy of the Maturity Index 1 and Maturity Index 2 in predicting peanut grade, the accuracy of the North Carolina 2 degree day method in predicting peanut yield, and remote sensing vegetative indices sensitivity equivalence (SEq) to peanut Maturity Index 2 and harvest grade (TSMK) for cultivars IPG-914 and Georgia-06G in Mississippi. Maturity Index 1 and Maturity Index 2 were found to be inaccurate predictions of peanut grade in Mississippi, suggesting a need to examine the contributions of individual color classes in new genotypes to predict grade and yield. The North Carolina 2 degree day method was found to have a moderate to strong relationship with yield, indicating its potential usefulness in determining digging timing. Results also showed red edge indices were more sensitive to changes in pod maturity and grade. Peanut genotype selection is critical for maximizing peanut grade and yield on farm. Experiments were conducted to evaluate 32 genotypes for maturity, grade, and yield. Several early maturing genotypes showed promise for improving yield and grade without reducing quality, particularly 'UF11x23-3-6-1-1', '16-1-2147', '16-1-2142', '14x029-1-5-1-1', and '14x022-1-2-1-2'. The results suggest earlier maturing genotypes may be a solution to the late-season harvest risk of crop loss due to poor digging conditions, rain, and frost, while maintaining similar pod grades and yield to the current market-leading cultivars. The findings of this study contribute to the ongoing effort to optimize digging timing and improve peanut yields in Mississippi, where peanut farmers face the dual challenges of climatic variability and genotype selection. Future research is needed to examine the adaptability of genotypes on differing soil types, management, and climates throughout Mississippi. Overall, this study highlights the need for more effective and accurate methods for determining digging timing in peanut crops, which is crucial for their grade, and yield.

Plant symbiosis with arbuscular mycorrhizal (AM) fungi provides many benefits for plants, including increased nutrient uptake, drought tolerance, and belowground pathogen resistance. In order to have a better understanding of the genetic architecture of mycorrhizal symbiosis, we conducted a genome-wide association study (GWAS) by phenotyping a diversity panel of cultivated sunflower (Helianthus annuus) for root colonization under inoculation with the AM fungus Rhizophagus intraradices. This mapping panel consists of 261 inbred lines that capture approximately 90% of the genetic diversity present in the cultivated sunflower germplasm. Using a mixed linear model approach with a high-density genetic map, we determined regions of the genome that are likely associated with AM colonization in sunflower. Additionally, we used a ‘core 12' set of twelve diverse lines (representing approximately 50% of the genetic diversity in the cultivated germplasm) to assess the effect that inoculation with AM fungi has on dried shoot biomass and macronutrient uptake. Colonization rate among lines in the mapping panel ranged from 0 to 70% and was not correlated with mycorrhizal growth response, shoot P response, or shoot K response among the core 12 lines. Association mapping yielded three SNPs that were significantly associated with AM colonization rate. These SNPs explained 19.0%, 14.4%, and 27.9% of the variance in three different metrics used to measure the degree of root colonization. Three genes of interest identified from the significant regions that contained these SNPs are potentially related to plant defense. Overall, our data suggests that candidate genes involved in plant defense may affect AM colonization rates within cultivated sunflower, and that these genes have a large effect size.

Downy mildew has been a potentially devastating constraint to crop production within the Brassicaceae family worldwide (CABI, 2022) and on the Central Coast of California (Smukler, et al, 2008; Koike, et al. 2007). Downy mildew is a foliar disease, caused by the pathogens in the Hyaloperonospora genus on plants within the Brassicaceae family (Goker, et al, 2009). Downy mildew is a disease that is common in region of the world with Coastal climates that provide humidity and moderate temperatures (Sarahan, et al, 2017). Crops within the Brassicaceae family maintain a predominant role in agricultural systems worldwide (Cartea, et al, 2011) and on the Central Coast of California, in Monterey, San Luis Obispo, Santa Cruz, San Benito, and Ventura Counties (Hidalgo, et al, 2022; Settevendemie, et al, 2022; Sanford, et al, 2022; Griffin, et al, 2022; Chang, et al, 2022; Williams, et al, 2022). The crop production within the Brassicaceae family includes broccoli, cabbage, and cauliflower, and the spring mix production of wild arugula, cultivated arugula, and baby kale. In the first study, an in-lab screening of wild arugula (Diplotaxis tenuifolia) for downy mildew resistance was conducted to identify accessions that contain potential resources of resistance to Hyaloperonospora diplotaxidis. The germplasm of 199 wild arugula accessions was grown out under greenhouse conditions and inoculated with a v single isolate of H. diplotaxidis. A subset of 40 accessions of wild arugula were further inoculated with an additional three isolates of H. diplotaxidis and the ten most resistant accessions were selected for further inoculations. The inoculations of the final subset of ten accessions with the same three isolates were replicated an additional two times. When a factorial ANOVA was conducted to test the interaction between the isolate and accession used, it was found that the impact of the accession on disease incidence was independent from the isolate (P=0.993). Three accessions, 185, 79, and 17 were identified as a potential source of resistance to the isolates utilized in this study, for maintaining a disease incidence below 1%. To compare the results found in the in-lab resistance screening, a field trial was conducted with a subset of wild arugula accessions with diverse reactions to downy mildew. When a regression was conducted comparing the disease incidence under field and lab conditions, the R2 value was found to be 0.37. A second study was conducted to characterize the genetic, morphological, and host range diversity of downy mildew causing pathogens in the Hyaloperonospora genus of hosts in the Brassicaceae family. An isolate collection of approximately 40 isolates of Hyaloperonospora spp. was established and the phylogenetic relationships of these isolates were analyzed by creating two phylogenetic trees using their cox2 mtDNA and ITS rDNA sequences. The H. brassicae and H. diplotaxidis isolates from this study formed separate monophyletic groups in both the cox2 mtDNA and ITS rDNA phylogenetic analyses. When the host range of H. brassicae and H. diplotaxidis were characterized by inoculating a genetically and morphologically diverse set of four host plant species, the H. brassicae and H. diplotaxidis were found to have distinct host ranges. The H. brassicae isolate was found to be parasitic of all B. oleracea morphotypes including broccoli, cabbage, kale, kohlrabi, and ornamental cabbage. The H. diplotaxidis isolate was found to only be parasitic on wild arugula, not cultivated arugula, wild mustard, or any of the B. oleracea morphotypes. The difference between sporangia of H. brassicae and H. diplotaxidis were found to be statistically significant, where the sporangia of H. brassicae were nearly circular and the sporangia of H. diplotaxidis were closer to an oval.

The flavour or fragrance of Basmati rice is associated with the presence of 2-acetyl-1- pyrroline. This work shows that a gene with homology to betaine aldehyde dehydrogenase (BAD) has significant polymorphisms in the coding region of fragrant genotypes relative to non fragrant genotypes. Accumulation of 2-acetyl-1-pyrroline in fragrant rice genotypes may be explained by the presence of mutations resulting in loss of function of the fgr gene product. The fgr gene corresponds to the gene encoding BAD2 in rice while BAD1 is encoded by a gene on chromosome 4. Development of an allele specific amplification (ASA) based around the deletion in the gene encoding BAD2 allows, perfect, simple and low cost discrimination between fragrant and non-fragrant rice varieties and identifies homozygous fragrant, homozygous non-fragrant and heterozygous non-fragrant individuals in a population segregating for fragrance. The cDNAs transcribed from rice chromosomes 4 and 8, each encoding an enzyme with homology to betaine aldehyde dehydrogenase were cloned and expressed in E. coli. The enzyme responsible for fragrance, encoded from chromosome 8, had optimum activity at pH 10, showed low affinity towards betaine aldehyde (bet-ald) with Km value of approximately 63ìM but a higher affinity towards -aminobutyraldehyde (GABald) with a Km value of approximately 9ìM. The enzyme encoded from chromosome 4 had optimum activity at pH 9.5 and showed generally lower affinity towards most substrates compared to the enzyme encoded from chromosome 8, substrate specificities suggest that the enzymes have higher specificity to aminoaldehydes and as such both should be renamed as an aminoaldehyde dehydrogenase (AAD). The inactivation of AAD2 (BAD2) in fragrant rice varieties likely leads to accumulation of its main substrate GABald which then cyclises to 1-pyrroline the immediate precursor of 2AP.

Butternut (Juglans cinerea L.), a lesser-known relative of black walnut (Juglans nigra L.), is a native tree species beneficial for wildlife, valuable for timber, and part of the great diversity of species in the eastern forests of North America. Populations of butternut are being devastated by butternut canker disease, caused by the fungus Sirococcus clavigignenti-juglandacearum (V.M.G. Nair, Kostichka, & Kuntz), which is thought to be introduced to North America. The disease causes multiple branch and stem cankers that eventually girdle trees. Small population sizes, lack of sprouting, and shade intolerance exacerbates the disease and results in permanent losses of butternut across the native range. Fortunately, healthy, canker-free butternut trees have been found proximal to diseased trees, indicating that a breeding approach could be a feasible strategy for producing and reintroducing resistant butternuts. A successful restoration program will require an understanding of genetic variation in open-pollinated seedlings, genetic basis of disease resistance, seedling establishment procedures, site requirements, and a greater understanding of disease development over time. This dissertation is divided into six parts, with the overall goal of insight into butternut ecology and management techniques which could be used to guide restoration decisions for this important species. The first two parts are an introduction and a literature review. In the third section, butternut seedlings were propagated in nursery progeny plantings to determine the genetic and phenotypic variability among one-year-old seedlings in a controlled environment. Part four outlines the disease development of butternut seedlings across progeny in resistance screening plantings at various locations. Part five aims at aiding restoration techniques by determining the impact of phenotypic and genetic variables on establishment success across various planting sites with different silvicultural treatments. Part six describes the dynamics of a large population of healthy and diseased butternut trees including disease development across temporal scales. The information gained from this research will be directly used in gene conservation strategies, the construction of disease resistant breeding orchards, and in determining appropriate restoration techniques.