This research was conducted to enhance utilization of the Liberty herbicide resistance transgene in rice. Non-lethal methods to determine the sensitivity of transgenic rice plants to hygromycin B and Liberty were developed, tested and used in this research. Four homozygous transformed plants were selected to make reciprocal crosses with their non-transformed parent cultivars Taipei 309 and Nipponbare. Their resistances to Liberty and hygromycin B were controlled by the closely linked single dominant genes bar and hpt. Some non-resistant phenotypes in the F2 populations were due to gene silencing. The bar gene in some of these plants were allelic and some were non-allelic. When seven independently transformed homozygous transgenic plants with bar and hygromycin genes from Taipei 309 and Nipponbare were crossed reciprocally, progeny evaluations showed five allelic locations among the seven transgenic plants. Twenty additional homozygous transgenic plants from independent transformation events were crossed reciprocally with the previous seven transgenic plants. Evaluation of F1, F2, and F3 populations showed that some of the genes were allelic, but most of them were non-allelic with two or more pairs of genes being expressed. The functional foreign gene (bar) appeared to be restrictively inserted into the rice genome in some cases and was not randomly inserted and expressed. Three to five repeated backcrosses were made using transgenic plants as the donor and current cultivars as the recurrent parents. The results from selected progeny rows, and two-years of yield tests with selected lines, indicated that the target bar gene could be transferred to lines similar to commercial cultivars from homozygous transformants in 4-5 years of backcrossing, giving lines similar to the recurrent parents based on phenotype and yield potential. Liberty herbicide has antibiotic characteristics and suppressed growth of several rice fungal pathogens and Burkholderia glumae in in vitro tests. Liberty had a short residual activity against Rhizoctonia solani in field tests, but single applications of Liberty after disease development had started in the field significantly reduced sheath blight ratings and yield loss. Control of sheath blight by Liberty was equal to or better than that given by the registered fungicide Quadris.

Sugarcane (inter-specific hybrids of Saccharum) is grown largely under long-term monoculture production in Louisiana. This can lead to a complex problem termed "yield decline" that results in poor root health and reduced productive capacity of sugarcane. This problem has been documented to be a limiting factor for sugarcane production in diverse regions, including Louisiana, Hawaii, Jamaica, and Australia. Previous work showed that biological factors affect root health and contribute to yield decline. The objectives of this study were to increase our understanding of microbial communities in sugarcane soils, to determine if there are differences in microbial communities associated with sugarcane roots in soil with and without a sugarcane cropping history, and to provide information on possible changes in the microbial communities resulting from monoculture that may contribute to yield decline. <p> To achieve these objectives, two approaches were used for comparing culturable organisms in soil microbial communities from soil with and without a sugarcane cropping history, and methods were adapted to reliably obtain DNA from soil microbial communities for molecular comparisons. In one approach, colonies grown on different types of culture media were quantified and characterized. In the other approach, sole carbon source utilization profiles (SCSUP) of soil communities grown in Biolog(tm) GN2 microplates were compared. Comparisons of the numbers and types of microorganisms that grew on various culture media demonstrated that differences exist between microbial communities associated with sugarcane roots in Louisiana soils with and without a recent sugarcane cropping history. The differences in community functional diversity detected by SCSUP supported the differences found in types of microorganisms isolated on selective media. The SCSUP results showed that differences in community functional diversity exist between sites in soils with a long-term sugarcane cropping history in common. <p> Methods for DNA extraction and polymerase chain reaction (PCR) amplification were optimized for sugarcane soil microbial community samples from Louisiana. This will allow molecular characterization of sugarcane rhizosphere microbial communities in the future.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009. / Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3241. Adviser: Henry T. Wilkinson. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Thesis (M.S.)--Oklahoma State University, 2009. / Vita. Includes bibliographical references.

Thesis (M.S.)--Texas A & M University, 2003. / "Major Subject: Plant Pathology." Title from author supplied metadata (automated record created on Apr. 30, 2004.). Vita. Abstract. Includes bibliographical references.

Thesis (Ph. D.)--Texas A & M University, 2003. / "Major Subject: Plant Pathology." Title from author supplied metadata. Includes bibliographical references.

Thesis (M.S.)--Texas A & M University, 2003. / "Major Subject: Plant Pathology." Title from author supplied metadata. Includes bibliographical references.

3 pp. / This publication describes the factors affecting development of downy mildew of lettuce and provides disease management strategies.

In this study, Red clover necrotic mosaic virus (RCNMV) was used to better understand the functions of replication proteins and to identify the terminal promoter element involved in viral replication. RCNMV genome contains two positive-sense, single-stranded RNAs. RNA-1 encodes two proteins essential for viral replication: p27 and p88. p88 is a fusion protein containing p27 at its N terminus and RNA dependent RNA polymerase motifs at its C-terminal domain. The function of p27 is not known. In this work, studies of RNA-1 chimerical clones between a highly infectious clone and a poorly infectious clone and subsequent mutagenesis demonstrated that the N-terminal 14 amino acids of p27 and p88 were required for efficient RNA replication. Sequence analysis indicated that it is possibly involved in membrane interaction. Another important aspect of viral replication is template recognition by the replicase at the 3' promoter. The 3' -29 nucleotides of both RCNMV RNA-1 and RNA-2 can be predicted to form an identical stem-loop structure (SLS). Mutational analysis of the SLS indicated that both the structure and the loop sequence were required for viral replication. Within the 5-nt loop region, three discontinuous nucleotides were identified as critical nucleotides for RNA-replicase interaction. The functional groups in these key nucleotides involved in replicase recognition are predicted. The 3' promoter element of RCNMV not only affects viral RNA replication but also influences transgenic recombination. RCNMV RNA-2 encodes a movement protein (MP) that is required for viral cell-to-cell movement and systemic infection. Transgenic Nicotiana benthamiana plants expressing different versions of MP mRNA neither resisted RCNMV nor complemented RNA-1 infection. However, systemic infection was observed in transgenic lines expressing 5' truncated MP mRNA when only RNA-1 was inoculated. Further analysis showed that the infection was resulted from nonhomologous RNA recombination events between infecting RNA-1 and MP transgene mRNA. A replicase-mediated template switch model of the transgenic recombination was proposed. The presence of the 3' promoter element in the transgene mRNA thus was a major factor determining transgenic recombination frequencies. As predicted from the model, transgene mRNA lacking the 3' promoter element would not be a good donor RNA for transgenic recombination. Consequently, no transgenic recombination was detected in transgenic plants expressing the 3' truncated MP mRNA upon inoculation with RCNMV RNA-1.

Considering the economic importance of asparagus as a crop and the historical association of Fusarium spp. as a principal cause of stand decline of this crop, a study was conducted from 1995-1997 in Southern California and Northern Mexico. The main objectives were to determine the causal agent of asparagus crown rot and the study the etiology of the causal agents which affects asparagus spears in these two important growing regions. Asparagus crowns exhibiting symptoms of crown decay were selected from each of the above production regions and processed in the laboratory. Based on morphological characteristics, F. proliferatum and F. oxysporum were the dominant species isolated from crowns. F. proliferatum produced mono and polyphialides and conidia in long chains. F. oxysporum was distinguished by the production of chlamydospore and conidia not produced in chains. Both species were recovered from marketable spears with an incidence ranged from 20-90%. Pathogenicity test on asparagus seedlings with isolates of F. proliferatum and F. oxysporum obtained from spears were positive. To determine the source of spear infection in commercial asparagus plantings, crowns and spears were collected from two fields in the Imperial Valley of California. Both F. proliferatum and F. oxysporum were recovered from crown tissues and from spears. However, F. proliferatum was the most prevalent species of Fusarium isolated from both spears and crowns. Evaluation of the influence of Fusarium species on quality characters of marketable asparagus was also studied. The quality of marketable spears infected with F. proliferatum and F. oxysporum was found to decrease significantly as the length of storage increased from five to ten days and as temperature of storage was increased from 5 C to 26 C. Since some species of Fusarium are known to produce fumonisins (a mycotoxin), and investigation of the possible presence of fumonisins in commercial asparagus spears was conducted. Spears were obtained from two different geographic regions of Mexico and two in California. Spear samples naturally colonized by Fusarium spp. were analyzed for fumonisin B1, B2 and B3. No detectable levels of fumonisin, regardless of geographic location of samples, were founded.