WRKY transcription factors (TFs) belong to a large family of regulatory proteins in plants that modulate many plant processes. Extensive studies have been conducted on WRKY-mediated defense response in Arabidopsis thaliana and many crop species. This study aims to investigate the potential roles and contributions of WRKY TFs regulation in improving defense response in the resynthesized Arabidopsis allotetraploids (Arabidopsis suecica) from two related autotetraploid progenitors, Arabidopsis thaliana (At4) and Arabidopsis arenosa (Aa). Upon infection by Pseudomonas syringae (Pst), the allotetraploids has showed enhanced resistance against the pathogen when compared to the parents. Rapid induction of WRKY18, WRKY40, WRKY38, WRKY53, WRKY6; MAP kinase pathway related genes, WRKY33, PAD3; SA-pathway related genes, ICS1, EDS1, PBS3, MYB31; was evident in response to Pst and salicylic acid treatment in the allotetraploids. Cleaved amplified polymorphic sequences analysis further revealed that the AtWRKY18, AaWRKY40, AtWRKY33, and AtWRKY60 alleles expressed at higher levels when compared to their respective homoeologs in the allotetraploids, suggesting potential altered protein-protein interaction networks in the hybrids. Therefore, a split-luciferase complementation assay was used to characterize and quantify protein-protein interaction among these homoeologous WRKYs in the allotetraploids. Results showed that preferential protein-protein interactions exist for the cis-interacting AtWRKY18/AtWRKY18 homodimer or trans-interacting AtWRKY18/AaWRKY40 heterodimer when compared to the respective interacting complexes. In addition, differential affinities of WRKY18 and WRKY40 homo- and hetero- dimers toward the W-boxes at the WRKY60 promoter were observed. In the allotetraploids, PR1 expression was repressed under basal state when compared to the progenitors. Although PR1 is expressed at a higher level in A. thaliana, its expression fold change was higher and faster in the all otetraploids upon salicylic acid treatment. Transient expression of WRKY18 or WRKY40 homodimer in various combinations induced differential expression of PR1 gene in their respective wrky18 and wrky40 Arabidopsis thaliana mutants. In contrast, similar PR1 induction by homodimer in various combinations was observed when they were transiently expressed in the allotetraploids. In addition, transgenic AtWRKY18 overexpression plant displayed enhanced disease resistance against Pst when compared to AaWRKY18 overexpression lines. Such enhanced disease resistance was found to associate with the higher expression of PR1 and PR2 in AtWRKY18 transgenic lines. Moreover, differential Pst-induced expression of the direct targets (ICS1, EDS1 and PBS3) of WRKY18 in the Arabidopsis AtWRKY18 and AaWRKY18 overexpressors supported a biological difference between the At and Aa homodimers in mediating the targets regulation, thus contributing to the difference in disease responses. Overall, our findings suggested that the rapid differential alleles expression and altered protein-protein or protein-DNA interactions of WRKY transcription factors could contribute to the improved defense in the allotetraploids, providing a molecular basis of for heterotic phenotype development in hybrids.

A number of major crop species, such as allohexaploid wheat and autotetraploid potato are polyploid. Potato is the fourth most important crop in terms of production and has become an important food source in many countries. Therefore, the molecular analysis was directed towards investigating ways to develop markers to assist the potato breeding process; for example breeding for powdery scab disease resistance, and tolerance to cold induced sweetening. Polyploids have more possible genotypes per population, allele dosage effects and increased marker complexity compared to diploids. Potato is also outcrossing and therefore highly heterozygous. Various methods for detecting marker-trait associations including, linkage, quantitative trait locus (QTL) and association mapping were studied and protocols developed. A mapping population was produced and a number of traits were measured including powdery scab resistance. Powdery scab disease assays were carried out over six seasons and markers associated with disease resistance were identified. Markers associated with resistance to powdery scab were identified on chromosomes I, IV, V, VI, VIII and IX using analysis of variance (ANOVA). Linkage maps were produced for each parent of the population and QTL associated with resistance and susceptibility to disease were identified using interval mapping, which revealed QTL on chromosomes II, V, VII , VIII, IX and an unanchored linkage group. QTL were detected across years on regions of chromosomes VIII and IX. These QTL results had some overlap with the marker-trait associations that were identified using ANOVA analysis. Another marker identification technique was tested, known as association or linkage disequilibrium mapping. Alleles of candidate genes were tested for association with cold-induced sweetening using a germplasm collection. The alleles identified as important were of the apoplastic invertase and UGPase genes and a unique interaction between alleles of the apoplastic invertase and apoplastic invertase inhibitor was also detected. This thesis describes the first study into the genetics of powdery scab resistance and the markers identified as associated with resistance will be validated for use in a marker-assisted selection (MAS) programme. The tools and resources developed as part of this thesis are vital to the potato breeding programme that requires the identification of associated molecular markers.

Wild barley (Hordeum vulgare subsp. spontaneum) could be a source of useful genes for improving cultivated barley. The useful genes present in Hordeum vulgare subsp. spontaneum may be new alleles at described loci, or these may be entirely new genes in the sense that there is limited allelic variation at these loci in the cultivated germplasm pool. This research was directed at gene discovery in wild barley and involved two steps: (i) characterization of diversity using genetic markers and (ii) development and characterization of novel germplasm for gene discovery. Simple Sequence Repeats (SSRs) of known map location were used to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine the informativeness and utility of SSRs in differentiating and classifying the three sets of barley germplasm. Crop progenitors had the highest number of alleles per SSR locus, followed by mapping population parents and elite breeding lines. The cluster analysis indicated a high level of diversity within the crop progenitor accessions and within the mapping population parents. It revealed a much lower level of diversity within the elite breeding germplasm. A set of Recombinant Chromosome Substitution Lines (RCSLs) representing introgressions of Hordeum vulgare subsp. spontaneum genome in to a cultivated barley background were developed using the Advanced Backcross strategy. An accession of Hordeum vulgare subsp. spontaneum was the donor parent and the variety "Harrington" was the recurrent parent. The RCSLs were developed via two backcrosses to the recurrent parent followed by six generations of selfing. The genomic architecture of the RCSLs was determined by molecular marker fingerprinting with SSRs. The consequences of introgressions of Hordeum vulgare subsp. spontaneum genome segments into the recurrent parent were assessed in terms of inflorescence yield components, malting quality traits, and domestication-related traits. Hordeum spontaneum subsp. spontaneum, despite its overall inferior phenotype, contributed favorable alleles for some characters of agronomic performance. In other cases, the introgressions caused a disruption of the Harrington phenotype, a "reverse genetics" approach to gene discovery. / Graduation date: 2003

Characterization of the determinants of economically important phenotypes showing complex inheritance should lead to more effective use of genetic resources. This study was conducted to determine the number, genome location and effects of QTLs determining malting quality and agronomic traits in the two North American barley quality standards. Using a doubled haploid population of 140 lines from the cross of Harrington x Morex, agronomic phenotype and malting quality data sets from nine and eight environments, respectively, and a 107-marker linkage map, QTL analyses were performed using simple interval mapping and simplified composite interval mapping procedures. Thirty five QTLs were associated either across environments or in individual environments, with five grain and agronomic traits (yield, kernel plumpness, test weight, heading date and plant height). Thirteen QTLs were associated with five malting quality traits (grain protein percentage, soluble/total protein ratio, ��-amylase activity, diastatic power and malt extract percentage). QTLs for multiple traits were coincident. The loci controlling inflorescence type [vrsl on chromosome 2 (2H) and int-c on chromosome 4 (4H)] were coincident with QTLs affecting all traits except heading date and malt extract percentage. The largest effect QTLs -for yield, kernel plumpness test weight, plant height grain protein percentage, S/T ratio, and diastatic power- were coincident with the vrsl locus. QTL analyses were conducted separately for each sub-population (six-rowed and two-rowed). Ten new QTLs were detected in the sub-populations. There were significant interactions between the vrsl and int-c loci for plant height, grain protein percentage, and SIT protein ratio. Positive transgressive segregants were found for all agronomic traits. They were more prevalent in the six-rowed sub-population, indicating that more favorable alleles were fixed in the two-rowed parent. Results suggest that this mating of two parents representing different germplasm groups caused a disruption in the balance of traits involved in malting quality, which resulted in no progeny carrying all favorable alleles and therefore surpassing the quality of either parent. This study describes some of the genetic determinants of agronomic and malting quality traits in a two-rowed x six-rowed cross and it is a first step toward the further characterization and manipulation of these determinants. / Graduation date: 2001

The discovery of the Arabidopsis ttg1 mutant almost three decades ago provided a unique opportunity for the study of how several cell fates and organ identity pathways are co-regulated. Besides showing a lack of flavonoid based pigments, the pleiotropic ttg1 mutant is also deficient for the development of several epidermal characters including plant hair cells (trichomes), the non-hair cells of the root and the mucilage-secreting cells of the seed coat epidermis. Ectopic expression of the maize R bHLH transcriptional regulator of the flavonoid pigment pathway could completely suppress all the ttg1 mutant phenotypes, providing the first clue to the nature of the control mechanisms governing TTG1-dependent traits. Because it was established that a bHLH and a Myb protein are required for the regulation of anthocyanin pigment production in several plant species and an Arabidopsis Myb gene was necessary for trichome initiation, the existence of bHLH and Myb proteins that would regulate all the TTG1-dependent developmental pathways was hypothesized. This study works towards the elucidation of the transcriptional control mechanisms that regulate the TTG1-dependent developmental pathways. The identification and characterization of a key regulator, EGL3, uncovered the redundant nature of bHLH proteins operating under the TTG1 regulatory umbrella. As a result, bHLH regulators were assigned to all TTG1-dependent epidermal cell fate pathways and new roles for previously identified bHLH proteins were revealed. Roles suggested in the literature for Arabidopsis Myb factors suspected of regulating the flavonoid pigment pathway were at odds with findings from other plant models. Analysis of Myb loss-of-function RNAi lines and TTG1:GR and GL3:GR fusion lines presented here provides a clarified understanding of the regulation of anthocyanin biosynthesis by the Myb/bHLH/WDrepeat complex in Arabidopsis. Missing from the combinatorial complex model is the Myb component controlling the differentiation of the seed coat epidermis. Work presented here characterizes Myb5 as the primary Myb regulator of this differentiation pathway and defines a new role for TT2 as partially redundant with Myb5 for testa epidermis development. Myb5 also plays a minor role in trichome development and PA biosynthesis. Thus pleiotropy among the TTG1-dependent Myb regulators previously unobserved is first noted here. A more complete Myb/bHLH combinatorial transcription factor network model for the regulation of the TTG1-dependent pathways is proposed based on the results of work presented in this dissertation. / text

Nuclear DNA content of the amphidiploid, G. hirsutum, and two closely related diploid species, G. herbaceum var. africanum and G. raimondii, was ascertained by the reassociation kinetics of 250 nucleotide DNA fragments. Between diploid species the difference in chromosome size is attributed largely to variation in repetitive sequences, where there has been a change in both frequency and complexity. The evolution of single-copy DNA sequences by cross hybridizations among species reveals: (1) a high degree of sequence conservation between diploid species, showing 78% duplex formation under standard criterion and 6% sequence mismatch upon thermal denaturation; and (2) greater than 95% duplex formation between the diploid species and the amphidiploid with less than 1% single-copy sequence mismatch. The latter findings are consistent with an early Pleistocene origin for the tetraploid cottons.

No description available.

Self-fertilization requires less energetic expenditures than cross-fertilization and benefits from a 50% advantage in its rate of gene transmission. Yet, no plant species is known that reproduces exclusively via self-fertilization, as all appear to maintain a certain outcrossing rate. I test the hypothesis that, under specific circumstances, cross-fertilization provides short-term advantages over self-fertilization in Corydalis sempervirens, a self-compatible winter annual. / Some fitness components of selfed and crossed progeny were compared under different experimental conditions. Crossed progeny derived short-term advantages from both their higher mean individual heterozygosity and their greater genotypic diversity. Overall, they had higher mean fitnesses than selfed individuals (heterosis), especially in favorable environments. Crossed progeny also displayed greater constancy of yield under increasing densities. In all test-environments, the few individuals with highest fitness resulted from outcrossing. However, as a group, crossed offspring did not have higher fitness values than selfed offspring and not all crosses generated progeny with equally high fitness. The fittest individuals were produced in crosses between parents which shared an intermediate number of common ancestors.

Recent scientific support for the involvement of genetic locus interaction in quantitative trait variation and the widespread use of quantitative trait locus (QTL) mapping has resulted in the need to examine those aspects concurrently. Computer software was written to simulate interacting quantitative trait loci (QTLs) in plant populations. Using this software, interacting QTLs were simulated to examine effects of epistasis on the detection of QTLs and the quality of QTL parameter estimates. Simulations involved doubled haploid populations exhibiting two non-epistatic traits and seven epistatic traits, each trait at four levels of heritability. Detection efficiency of QTL main and interaction effects decreased with decreasing heritability. At a given level of broad-sense heritability, traits differed with respect to the relative quality of main-effect detection and interaction-effect detection. Main-effect detection was notably poor for one epistatic locus that has a relatively small additive effect. Position estimates were accurate but their precision deteriorated with decreasing heritability. The quality of QTL effect estimates declined consistently with decreasing heritability, and loss in the accuracy was associated with losses in power of detection.

Thesis (Ph. D.)--Rutgers University, 2007. / "Graduate Program in Plant Biology." Includes bibliographical references.