Graduation date: 1976

Thesis (Ph. D.)--University of Hawaii at Manoa, 1995. / Includes bibliographical references (leaves 95-107). / Microfiche. / x, 107 leaves, bound ill. (some col.) 29 cm

published_or_final_version / Botany / Master / Master of Science

Pest status of the rice stem-borers, Diopsis longicornis and D. apicalis was not well known in the Republic of Guinee. / In the present study, adult and immature populations of both species were monitored under various local cultural practices, i.e., planting methods (direct and transplanted), different planting dates and seasons (wet and dry). As previously observed in other West African countries, D. apicalis did occasional damage to rice in Guinee. However, contrary to findings elsewhere, D. longicornis was not an important pest of Guinean rice, infesting 4% of stems over the five seasons studied. / Regulators affecting population size and behaviour of D. longicornis were determined, focusing on factors controlling the fly's quiescent period in aggregation sites during the dry season, and the insect's movement to and from these refugia. Availability of cultivated and wild rice was found to interrupt or prevent quiescence of D. longicornis. Abiotic factors, (relative humidity, rainfall and photoperiod) influenced time of dispersal of D. longicornis.

Made available in DSpace on 2015-08-20T17:10:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-03-30. Added 1 bitstream(s) on 2015-08-20T17:27:02Z : No. of bitstreams: 1 000843759.pdf: 1198801 bytes, checksum: a7d728ac692d7c1e17e88074d6859d76 (MD5) / O complexo de manchas da bainha do arroz engloba três doenças causadas por diferentes espécies de Rhizoctonia: a queima-da-bainha (causada R. solani AG-1 IA), a mancha agregada da bainha (R. oryzae-sativae) e a mancha da bainha (R. oryzae). Distinguir os agentes causais é um passo crítico para manejá-los eficazmente. Em levantamento recente efetuado em cinco áreas de cultivo de arroz no Vale do Paraíba, Brasil, e nos Llanos na Colômbia, R. oryzae-sativae, o patógeno da mancha agregada da bainha, foi a espécie predominante em ambos os países. Neste estudo, nosso principal objetivo foi determinar a estrutura genética das populações de R. oryzae- sativae do arroz no agroecossistema da região do Vale do Paraíba e nos Llanos Colombianos. Inferiu-se sobre o fluxo gênico entre populações do patógeno, dentro e entre os países, e sobre o modo reprodutivo predominante. Nosso segundo objetivo foi determinar o potencial de duas populações brasileiras de R. oryzae-sativae em adaptar-se a espécies forrageiras do gênero Urochloa. Uma vez que essas espécies de forrageiras são cultivadas em áreas adjacentes ou em rotação com arroz, podem estar exercendo elevada pressão de seleção sobre as populações de R. oryzae- sativae. Análises da estrutura genética de populações foram baseadas na genotipagem de isolados de quatro populações do patógeno usando cinco marcadores microssatélites. Populações próximas e distantes apresentaram indícios de fluxo gênico. Evidências de reprodução sexuada nas populações do patógeno e a baixa fração clonal, indicaram a predominância de um sistema reprodutivo recombinante. É provável que basidiósporos desempenhem papel mais importante no ciclo da doença do que se supunha anteriormente. Isolados das duas populações brasileiras de R. oryzae-sativae foram patogênicos e apresentaram variação na agressividade à Urochloa spp., porém com baixos índices de herdabilidade,... / The rice sheath-blight complex comprises three diseases caused by different Rhizoctonia species: sheath blight (caused by R. solani AG-1 IA), aggregated sheath spot (R. oryzae-sativae), and sheath spots (R. oryzae). To be able to distinguish among the causal agents is a critical step in order to manage them effectively. In a recent survey in five rice cropping areas from the Paraíba Valley region, Brazil, and from the Llanos in Colombia, R. oryzae-sativae (the aggregated sheath spot pathogen) was the predominant species on both countries. In this study, our primary objective was to determine the genetic structure of populations of R. oryzae-sativae from rice paddy fields sampled from the Paraiba Valley and the Colombian Llanos. We inferred about gene flow among populations within and between countries and the pathogen's main reproductive mode. The second objective was to infer the potential of the two brazilian populations of R. oryzae-sativae to adapt and become pathogen of forage pastures of the genus Urochloa. Once these forage species are intensively cropped in adjacent areas or under rotation with rice, they might be exerting strong selection pressure on R. oryzae-sativae populations. Population structure analyses were based on genotyping fungal isolates from four populations of the pathogen using five microsatellites markers. Gene flow was detected among geographically close and distant populations. Evidences of sexual reproduction and low clonal fraction found in the populations, indicated the predominance of a mixed reproductive system. It is plausible that basidiospores play a more important role on the disease cycle than previously thought. Isolates from the two brazilian populations of R. oryzae-sativae were pathogenic and varied on aggressiveness to Urochloa spp. However, low levels of heritability for aggressiveness were detected, indicating a yet limited adaptation to Urochloa spp

Orientador: Paulo Cezar Ceresini / Banca: Antonio de Goes / Banca: Daniel Augusto Schurt / Resumo: O complexo de manchas da bainha do arroz engloba três doenças causadas por diferentes espécies de Rhizoctonia: a queima-da-bainha (causada R. solani AG-1 IA), a mancha agregada da bainha (R. oryzae-sativae) e a mancha da bainha (R. oryzae). Distinguir os agentes causais é um passo crítico para manejá-los eficazmente. Em levantamento recente efetuado em cinco áreas de cultivo de arroz no Vale do Paraíba, Brasil, e nos Llanos na Colômbia, R. oryzae-sativae, o patógeno da mancha agregada da bainha, foi a espécie predominante em ambos os países. Neste estudo, nosso principal objetivo foi determinar a estrutura genética das populações de R. oryzae- sativae do arroz no agroecossistema da região do Vale do Paraíba e nos Llanos Colombianos. Inferiu-se sobre o fluxo gênico entre populações do patógeno, dentro e entre os países, e sobre o modo reprodutivo predominante. Nosso segundo objetivo foi determinar o potencial de duas populações brasileiras de R. oryzae-sativae em adaptar-se a espécies forrageiras do gênero Urochloa. Uma vez que essas espécies de forrageiras são cultivadas em áreas adjacentes ou em rotação com arroz, podem estar exercendo elevada pressão de seleção sobre as populações de R. oryzae- sativae. Análises da estrutura genética de populações foram baseadas na genotipagem de isolados de quatro populações do patógeno usando cinco marcadores microssatélites. Populações próximas e distantes apresentaram indícios de fluxo gênico. Evidências de reprodução sexuada nas populações do patógeno e a baixa fração clonal, indicaram a predominância de um sistema reprodutivo recombinante. É provável que basidiósporos desempenhem papel mais importante no ciclo da doença do que se supunha anteriormente. Isolados das duas populações brasileiras de R. oryzae-sativae foram patogênicos e apresentaram variação na agressividade à Urochloa spp., porém com baixos índices de herdabilidade,... / Abstract: The rice sheath-blight complex comprises three diseases caused by different Rhizoctonia species: sheath blight (caused by R. solani AG-1 IA), aggregated sheath spot (R. oryzae-sativae), and sheath spots (R. oryzae). To be able to distinguish among the causal agents is a critical step in order to manage them effectively. In a recent survey in five rice cropping areas from the Paraíba Valley region, Brazil, and from the Llanos in Colombia, R. oryzae-sativae (the aggregated sheath spot pathogen) was the predominant species on both countries. In this study, our primary objective was to determine the genetic structure of populations of R. oryzae-sativae from rice paddy fields sampled from the Paraiba Valley and the Colombian Llanos. We inferred about gene flow among populations within and between countries and the pathogen's main reproductive mode. The second objective was to infer the potential of the two brazilian populations of R. oryzae-sativae to adapt and become pathogen of forage pastures of the genus Urochloa. Once these forage species are intensively cropped in adjacent areas or under rotation with rice, they might be exerting strong selection pressure on R. oryzae-sativae populations. Population structure analyses were based on genotyping fungal isolates from four populations of the pathogen using five microsatellites markers. Gene flow was detected among geographically close and distant populations. Evidences of sexual reproduction and low clonal fraction found in the populations, indicated the predominance of a mixed reproductive system. It is plausible that basidiospores play a more important role on the disease cycle than previously thought. Isolates from the two brazilian populations of R. oryzae-sativae were pathogenic and varied on aggressiveness to Urochloa spp. However, low levels of heritability for aggressiveness were detected, indicating a yet limited adaptation to Urochloa spp / Mestre

No description available.

Xue, Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 95-102). / Abstract also in Chinese. / Thesis committe --- p.2 / Statement --- p.3 / Abstract --- p.4 / Acknowledgement --- p.8 / General abbreviations --- p.10 / Abbreviations of chemicals --- p.13 / List of figures --- p.15 / List of tables --- p.16 / Table of contents --- p.17 / Chapter Chapter 1 --- General Introduction / Chapter 1.1 --- Impact of bacterial blight on rice production --- p.25 / Chapter 1.2 --- The plant immune system --- p.25 / Chapter 1.2.1 --- Preformed resistance --- p.25 / Chapter 1.2.2 --- PAMP triggered immunity (PTI) --- p.26 / Chapter 1.2.3 --- Effecter triggered immunity (ETI) --- p.27 / Chapter 1.2.3.1 --- R genes --- p.27 / Chapter 1.2.3.2 --- Hypersensitive responses (HR) --- p.27 / Chapter 1.2.3.3 --- Systemic acquired resistance (SAR) --- p.28 / Chapter 1.2.3.3.1 --- Salicylic acid is required for SAR establishment --- p.28 / Chapter 1.2.3.3.2 --- Involvement of lipid-based molecules in SAR signaling --- p.28 / Chapter 1.2.3.3.3 --- NPR1: the master regulator of SAR --- p.29 / Chapter 1.2.3.3.4 --- Expression of pathogenesis related (PR) genes --- p.29 / Chapter 1.2.4 --- Interaction between SA and JA --- p.29 / Chapter 1.2.5 --- Other important signaling components in plant defense responses --- p.30 / Chapter 1.2.5.1 --- G proteins --- p.30 / Chapter 1.2.5.2 --- G proteins in defense responses --- p.30 / Chapter 1.3 --- OsGAPl is a C2 (protein kinase C conserved region 2) domain harboring GTPase activating protein --- p.32 / Chapter 1.4 --- OsYchFl is a GTPase and an interacting partner of OsGAPl --- p.32 / Chapter 1.5 --- Hypothesis and objectives of this research --- p.33 / Chapter Chapter 2 --- materials and methods / Chapter 2.1 --- Materials --- p.35 / Chapter 2.1.1 --- Chemicals and reagents --- p.39 / Chapter 2.1.2 --- Commercial kits --- p.40 / Chapter 2.1.3 --- Primers used --- p.41 / Chapter 2.1.4 --- Equipment and facilities used: --- p.47 / Chapter 2.1.5 --- "Buffer, solution, gel and medium:" --- p.47 / Chapter 2.2 --- Methods: --- p.51 / Chapter 2.2.1 --- Culture of bacterial strains --- p.51 / Chapter 2.2.2 --- Composition of medium used in this work for cultivating bacterial strains: --- p.51 / Chapter 2.2.3 --- Plant growth and treatment --- p.52 / Chapter 2.2.3.1 --- Surface sterilization of Arabidopsis thaliana seeds --- p.52 / Chapter 2.2.3.2 --- Seed germination and Arabidopsis plant growth --- p.52 / Chapter 2.2.4 --- Generation of transgenic Arabidopsis --- p.53 / Chapter 2.2.4.1 --- Agrobacterium-mediated Arabidopsis transformation --- p.53 / Chapter 2.2.5 --- Pathogen inoculation test --- p.54 / Chapter 2.2.6 --- Molecular cloning --- p.54 / Chapter 2.2.6.1 --- DNA sequencing: --- p.55 / Chapter 2.2.6.2 --- Transformation of E. coli strains: --- p.55 / Chapter 2.2.6.3 --- Transformation of Agrobacteria by electroporation --- p.55 / Chapter 2.2.7 --- DNA and RNA extraction --- p.56 / Chapter 2.2.7.1 --- Plasmid DNA extraction from bacterial cells --- p.56 / Chapter 2.2.7.2 --- Genomic DNA extraction from plant tissues --- p.56 / Chapter 2.2.7.3 --- RNA extraction from plant tissues --- p.56 / Chapter 2.2.8 --- Northern blot --- p.57 / Chapter 2.2.9 --- Subcellular localization studies --- p.58 / Chapter 2.2.9.1 --- Transformation of tobacco BY-2 cells --- p.58 / Chapter 2.2.9.2 --- Maintenance of transgenic tobacco BY-2 cells --- p.59 / Chapter 2.2.9.3 --- Confocal microscopy --- p.59 / Chapter 2.2.9.4 --- Electron microscopy --- p.59 / Chapter 2.2.10 --- Bimolecular fluorescence complementation studies (BiFC) --- p.60 / Chapter 2.2.10.1 --- Construct making --- p.61 / Chapter 2.2.10.2 --- Preparation of rice protoplasts --- p.61 / Chapter 2.2.10.3 --- PEG-mediated transfection --- p.62 / Chapter 2.2.10.4 --- Detection of protein-protein interaction --- p.62 / Chapter Chapter 3 --- Results / Chapter 3.1 --- OsGAPl interacts with OsYchFl in vivo --- p.63 / Chapter 3.1.1 --- Construction of vectors for BiFC transient assay in rice protoplasts --- p.64 / Chapter 3.1.2 --- BiFC assay in rice protoplasts revealed in vivo interaction between the OsGAPl and the OsYchFl proteins --- p.66 / Chapter 3.2.1 --- Subcellular localization of OsGAPl --- p.68 / Chapter 3.2.2 --- Localization of OsGAPl and OsYchFl in rice leaves revealed by electron microscopy --- p.70 / Chapter 3.3 --- Functional characterization of OsYchFl / Chapter 3.3.1 --- Characterization of Arabidopsis YchF1 knockdown mutant --- p.75 / Chapter 3.3.2 --- Complementation of AtYchF1 knockdown Arabidopsis --- p.77 / Chapter 3.3.3.1 --- Pathogen inoculation test --- p.80 / Chapter Chapter 4 --- Discussion / Chapter 4.1 --- Significance of the project --- p.85 / Chapter 4.2 --- In vivo interaction between OsGAPl and OsYchFl --- p.86 / Chapter 4.3 --- OsGAPl is located either inside the cytosol or on the plasma membrane in transgenic tobacco BY-2 cells --- p.87 / Chapter 4.4 --- Study of wounding effect on the subcellular localization of OsGAPl and OsYchFl at whole plant level by EM --- p.88 / Chapter 4.5 --- OsYchFl functions as a negative regulator of defense responses in A.thaliana --- p.90 / Chapter 4.6 --- Conclusion --- p.92 / References --- p.95 / Appendix --- p.103

Typescript. / Thesis (Ph. D.)--University of Hawaii at Manoa, 1983. / Bibliography: leaves [459]-474. / Microfiche. / xxiv, 474 leaves, bound ill. (some col.), maps 29 cm

The African Rice Gall Midge (AfRGM), Orseolia oryzivora Harris and Gagné (Diptera: Cecidomyiidae), is an endemic rice pest found throughout Africa. The failure of most other control methods imposes the need to use crop resistance. This study was initiated: (1) to develop an accurate method for assessing damage caused by AfRGM; (2) to determine AfRGM resistance genes’ modes of action, the heritability estimates of their resistance to AfRGM and the behavioural pattern of progenies with resistance to AfRGM attack; (3) to reveal convergent evolution of same or similar resistance gene(s) in geographically distinct landraces, or divergent evolution of genotypes carrying the same gene, by analysing the genetic diversity among five AfRGM parental lines; (4) to build a core sample of progenies to be used as a reduced mapping population, largely reflecting the entire genome of the whole population, after an estimate of the heritability of 15 agro-morphological descriptors and; (5) determine Simple Sequence Repeat (SSR) markers flanking genes or quantitative trait loci (QTLs) linked to resistance to AfRGM. A method of accurately assessing damage caused by AfRGM was determined by comparing four methods of assessment including the International Rice Research Institute’s (IRRI) Standard Evaluation System (SES) for rice and three methods based on resistance index (RI) assessments differing in the computing of the percentage of tillers with galls on a resistant check variety. The RI-based assessment (RI-BA) methods consistently provided a better evaluation of AfRGM damage than the SES, regardless of the trial size. Within RI-BA methods, RI-BA2 was always more accurate than RI-BA1 and RI-BA3 when the plot was large. RI-BA2 and RI-BA3 were equally accurate when the plot size was small, and they provided better estimates than RI-BA1. When the plot was of medium size, RI-BA2 was more accurate than RI-BA3; RI-BA3 also surpassed RI-BA1. Overall, the best method of assessing AfRGM damage was RI-BA2, regardless of the plot size. Five rice populations including F1, F2 and F3 generations involving ITA306, a susceptible variety of Oryza sativa subsp. indica, and four varieties having different reactions against AfRGM were used to determine the genetic basis of resistance and estimate the heritability of resistance to AfRGM. All the F1s were susceptible, suggesting recessive gene inheritance. The F2 generations’ segregation pattern of 1R:15S in both ITA306-TOS14519 and ITA306-TOG7106 crosses as well as the segregation of 1R:8Seg:7S in ITA306-TOS7106 F3 families indicated that the AfRGM resistance expression being studied is governed by two genes. The deviation of the segregation patterns of crosses involving ITA306 and the tolerant parental lines from Mendelian segregation ratios suggests that the tolerance to AfRGM shown by BW348-1 and Cisadane is under complex mechanisms of control rather than under simple genetic control. The narrow-sense heritability estimates of resistance to AfRGM were low in populations involving tolerant varieties and were high in populations involving resistant varieties. They ranged from 0.086 in the ITA306-Cisadane population, to 0.4 in the ITA306-TOG7106 population. Conversely, the broad-sense heritability estimates ranged from 0.23 (ITA306-Cisadane) to 0.63 (ITA306-TOS14519). The behavioural patterns of progenies against AfRGM attack were evaluated for 532, 413 and 479 F2 progenies from ITA306-BW348-1, ITA306-Cisadane and ITA306-TOS14519 crosses, respectively, in addition to 90 BC1F2 progenies from the ITA306 and TOG7106 cross. One F3 generation of 649 families from a cross between ITA306 and TOS14519 was also tested. Four types of behavioural pattern categories were observed: (1) progenies were more resistant than the resistant check entry at 45 DAT and 70 DAT; (2) progenies were more resistant at 45 DAT and became susceptible at 70 DAT; (3) progenies were susceptible at both 45 DAT and 70 DAT; (4) progenies were susceptible at 45 DAT but reverted to resistant at 70 DAT. The first three categories were the most frequently observed and occurred in all cross combinations. The last category was observed only for a few progenies from the ITA306-TOS14519 F2 and F3 generations and, surprisingly, many from the ITA306 and BW348-1 cross. Heritability estimates were calculated for 15 major traits in an F3 population in order to predict the genetic gain associated with each trait, together with the resistance to AfRGM and to estimate the influence of the environment on phenotypic values. Broad-sense heritability (H2) estimates were high for the penultimate leaf length (PLL) - 0.99, penultimate leaf width (PLW) – 1.0, flag leaf length (FLL) - 0.99, flag leaf width (FLW) – 1.0, ligule length (LigL) - 0.99, tillering ability (Til) - 0.99, number of days to booting (DB) - 0.95, number of days to first heading (DFH) - 0.96, number of days to heading (DH) - 0.89, number of days to maturity (DM) - 0.98, culm length (CL) - 0.99, plant height (PH) - 0.99, panicle length (PanL) - 0.95, secondary branching (SB) - 0.95 and the thousand grains weight (TGW) - 0.71. Conversely, narrow-sense heritability estimates were very low (nearly 0) in PLL, FLL, Lig, DB, DFH, DM and SB or low (at most 0.267) in PLW, FLW, DH and PH, with a high value of 0.727 for TGW. Inheritance of the traits studied was therefore under non-additive gene effects rather than additive genetic effects and can therefore be improved using pedigree breeding schemes along with breeding for AfRGM resistance. Fine genetic evaluation of five AfRGM parental lines was studied in terms of polymorphisms using 303 SSR primers covering the rice genome. Of the 178 polymorphic primers identified, 60 were highly polymorphic and informative. The number of alleles amplified by these primers ranged from one to five for a total of 1,041 alleles. The polymorphism rate was globally high, ranging from 45.2% to 66.8%. The mean of the polymorphism information content (PIC) was 0.553. Factorial analysis, based on the allelic diversity, demarcated the parental lines into Oryza glaberrima Steud, Oryza sativa subsp. japonica and O. sativa subsp. indica groups, while a cluster analysis distinguished them into four groups: AfRGM resistant, susceptible, moderately resistant and tolerant. BW348-1 and Cisadane showed the least diversity, despite their distant geographical origins. TOS14519 and TOG7106 showed more divergence to ITA306 despite their common West African origin. This variability amongst the genotypes tested is the result of farmer-based selection for AfRGM resistance rather than direct breeding efforts through breeder intervention. A method of selecting individuals for a mapping population, based on a core sample, was developed in order to speed up the mapping procedure. A diversity study amongst F2 and F3 generations involving 15 quantitative and 26 qualitative agro-morphological characters was carried out and led to the dropping of seven non-discriminant descriptors. The diversity index (H) was calculated for each remaining character and the discriminant descriptors were selected based on a diversity index threshold value above 0.4. Four descriptors of H values less than 0.35 were therefore dropped. The sizing of the core collection of 64 individuals and the selection of these individuals were done using MSTRAT version 4.1 package in redundancy mode, a construction run of 100 times with an iteration number of 500. The core sample was similar to the whole population for clustering pattern, minimum and maximum quantitative values and diversity index, while mean values and coefficient of variation distinguished them. The core sample, which represents 10% of the whole population, also revealed the same phenotypic variation and the same genotypic segregation according to two SSR markers. It can therefore efficiently reflect the whole population as a mapping population. Finally, a study was undertaken to identify flanking markers to the gene/QTL involved in the resistance against AfRGM using bulked segregant analysis (BSA). A polymorphism study between ITA306 and TOS14519 displayed 145 polymorphic SSR markers, which were used to screen the bulks that originated from the two tails, and depicted only two SSRs as candidate markers linked to gall midge resistance. These markers included RM317 and RM17303 which displayed strong significance after an analysis of variance using an F test, meaning that they were segregating with the resistant alleles. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.