Thesis (Ph. D.)--University of Oregon, 2000. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 80-86).

Au, Chun Hang. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 124-146). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Hui Cheung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 166-172). / Abstracts in English and Chinese. / Abstract --- p.iii / Acknowledgments --- p.vi / Abbreviations --- p.vii / Table of Contents --- p.viii / Table of Figures --- p.xiii / Table of Tables --- p.xviii / Chapter Chapter 1. --- Literature Reviews / Chapter 1.1 --- Functional Genomics and Its Developments --- p.1 / Chapter 1.1.1 --- Introduction --- p.1 / Chapter 1.1.2 --- "Transcriptomics, Proteomics and Metabolomics" --- p.1 / Chapter 1.1.3 --- Gene-perturbing Strategies --- p.3 / Chapter 1.1.4 --- Applications of Functional Genomics --- p.4 / Chapter 1.2 --- Serial Analysis of Gene Expression (SAGE) and Generation of Longer cDNA Fragments from SAGE tags for Gene Identification (GLGI) --- p.6 / Chapter 1.2.1 --- Introduction --- p.6 / Chapter 1.2.2 --- Principles and Methods of SAGE --- p.6 / Chapter 1.2.3 --- Data Analysis --- Bioinformatics --- p.9 / Chapter 1.2.4 --- Applications of SAGE --- p.9 / Chapter 1.2.5 --- Modifications of SAGE --- p.10 / Chapter 1.2.6 --- Principles and Methods of GLGI --- p.11 / Chapter 1.2.7 --- Applications and Improvements of GLGI --- p.14 / Chapter 1.3 --- Transformation --- p.15 / Chapter 1.3.1 --- Introduction --- p.15 / Chapter 1.3.2 --- Different Methods of Transformation --- p.15 / Chapter 1.3.2.1 --- General Transformation Strategy --- p.15 / Chapter 1.3.2.2 --- Polyethylene Glycol (PEG)-mediated Transformation --- p.16 / Chapter 1.3.2.3 --- Restriction Enzyme Mediated Integration (REMI) --- p.16 / Chapter 1.3.2.4 --- Electroporation --- p.17 / Chapter 1.3.2.5 --- Particle Bombardment --- p.17 / Chapter 1.3.3 --- The Future Needs of Transformation --- p.18 / Chapter 1.4 --- RNA Silencing --- p.20 / Chapter 1.4.1 --- Introduction --- p.20 / Chapter 1.4.2 --- Major Components and Principles of RNAi --- p.21 / Chapter 1.4.3 --- Applications of RNA Silencing --- p.23 / Chapter 1.5 --- The Target Organism Lentinula edodes --- p.25 / Chapter 1.5.1 --- Introduction --- p.25 / Chapter 1.5.2 --- The Life Cycle of L. edodes --- p.26 / Chapter 1.5.3 --- Biochemical and Molecular Studies on L. edodes --- p.27 / Chapter 1.5.4 --- Prospectus --- p.29 / Chapter Chapter 2. --- Development of Methods for Studying Gene Function in Lentinula edodes / Chapter 2.1 --- Introduction --- p.30 / Chapter 2.2 --- Materials and Methods --- p.32 / Chapter 2.2.1 --- Cultivation of Lentinula edodes --- p.32 / Chapter 2.2.2 --- Proplast Release and Regeneration --- p.32 / Chapter 2.2.3 --- Preparation of Plasmid DNA --- p.33 / Chapter 2.2.4 --- Selectable Marker …Bialaphos --- p.35 / Chapter 2.2.5 --- Transformation --- p.35 / Chapter 2.2.5.1 --- Electroporation --- p.35 / Chapter 2.2.5.2 --- PEG-mediated Transformation --- p.36 / Chapter 2.3 --- Results --- p.37 / Chapter 2.3.1 --- Cultivation of Lentinula edodes --- p.37 / Chapter 2.3.2 --- Proplast Release and Regeneration --- p.37 / Chapter 2.3.3 --- Preparation of Plasmid DNA --- p.43 / Chapter 2.3.4 --- Selectable Marker--- Bialaphos --- p.43 / Chapter 2.3.5 --- Transformation --- p.46 / Chapter 2.3.5.1 --- Electroporation --- p.46 / Chapter 2.3.5.2 --- PEG-mediated Transformation --- p.46 / Chapter 2.4 --- Discussions and Conclusions --- p.57 / Chapter Chapter 3. --- Identification of Interested Genes in Expression Profile of SAGE using GLGI Method. / Chapter 3.1 --- Introduction --- p.61 / Chapter 3.1.1 --- Results of SAGE Analysis --- p.61 / Chapter 3.1.2 --- Use of GLGI Method for Extension of SAGE Tags --- p.63 / Chapter 3.1.3 --- 5´ة Extension of GLGI (5'GLGI) --- p.65 / Chapter 3.1.3.1 --- Introduction --- p.65 / Chapter 3.1.3.2 --- "Overall strategy of 5, GLGI Method" --- p.67 / Chapter 3.1.3.3 --- Two-Steps PCR Method --- p.69 / Chapter 3.2 --- Generation of Longer cDNA Fragments from SAGE tags for Gene Identification (GLGI) --- p.71 / Chapter 3.2.1 --- Materials and Methods (GLGI Analysis) --- p.71 / Chapter 3.2.1.1 --- Total RNA Extraction --- p.71 / Chapter 3.2.1.2 --- Messenger RNA (mRNA) Extraction --- p.72 / Chapter 3.2.1.3 --- Preparation of 3´ة cDNA for GLGI --- p.73 / Chapter 3.2.1.4 --- NIaIII digestion of double strand cDNA --- p.74 / Chapter 3.2.1.5 --- PCR amplification of the 3'-cDNAs (Optional) --- p.77 / Chapter 3.2.1.6 --- GLGI Amplification of The Target Template --- p.80 / Chapter 3.2.1.7 --- DNA Cloning (Optional) --- p.82 / Chapter 3.2.1.8 --- Sequencing of GLGI PCR products --- p.85 / Chapter 3.2.2 --- 5' Materials and Methods (5' GLGI Analysis) --- p.86 / Chapter 3.2.2.1 --- Preparation of unique antisense primers --- p.86 / Chapter 3.2.2.2 --- 5' extension of GLGI products --- p.87 / Chapter 3.2.2.3 --- DNA Cloning (Optional) --- p.89 / Chapter 3.2.2.4 --- Sequencing of 5' GLGI PCR products --- p.89 / Chapter 3.2.3 --- Results (GLGI Analysis) --- p.90 / Chapter 3.2.3.1 --- Total RNA Extraction --- p.90 / Chapter 3.2.3.2 --- Messenger RNA Extraction --- p.90 / Chapter 3.2.3.3 --- Preparation of 3' cDNA for GLGI --- p.90 / Chapter 3.2.3.4 --- NIaIII digestion of double strand cDNA --- p.94 / Chapter 3.2.3.5 --- GLGI Amplification of The Target Template --- p.94 / Chapter 3.2.3.6 --- Sequencing of GLGI PCR products --- p.103 / Chapter 3.2.4 --- Results (5' GLGI Analysis) --- p.111 / Chapter 3.2.4.1 --- 5' extension of GLGI products --- p.111 / Chapter 3.2.4.2 --- Sequencing of 5´ة GLGI PCR products --- p.116 / Chapter 3.3 --- Discussions and Conclusions --- p.126 / Chapter 3.3.1 --- GLGI amplification of the target template --- p.126 / Chapter 3.3.2 --- 5' extension of GLGI products --- p.129 / Chapter 3.3.3 --- Two-Steps PCR Method --- p.130 / Chapter 3.3.4 --- Sequencing results of GLGI method and 5' GLGI method --- p.131 / Chapter Chapter 4. --- Identification of Unknown EST Using PCR Method With cDNA Library / Chapter 4.1 --- Introduction --- p.134 / Chapter 4.2 --- Materials and Methods --- p.134 / Chapter 4.2.1 --- Extension of 5' end of EST sequence by PCR method --- p.134 / Chapter 4.2.2 --- Purification of PCR products --- p.136 / Chapter 4.2.3 --- Sequencing of Extended EST products --- p.136 / Chapter 4.3 --- Results --- p.137 / Chapter 4.3.1 --- Extension of 5' end of EST sequence by PCR method --- p.137 / Chapter 4.3.2 --- Sequencing of Extended EST products --- p.137 / Chapter 4.4 --- Discussions and Conclusions --- p.147 / Chapter Chapter 5. --- General Discussions --- p.151 / Appendix I --- p.156 / Reference --- p.166

Making quality and winterhardiness in barley are "ultimate" phenotypes composed of component, quantitatively inherited traits. A 69-point genome map of the seven chromosomes of barley was used, in conjunction with multi-environment phenotypes for grain yield and malting quality, to determine the chromosome locations of quantitative trait loci (QTLs). A combined analysis of the two environments identified QTLs that were both common and unique to each environment. Dispersed QTLs with positive relationships provide ready targets for marker-assisted selection. Overlapping QTLs for agronomic and making quality QTLs with favorable alleles contributed by alternate parents will require further, higher resolution mapping to determine if negative relationships are due to linkage or pleiotropy. There is preliminary evidence for orthologous agronomic trait and malting QTLs in barley. This QTL analysis will hopefully assist in the rapid development of winter making varieties that will maximize the profitability of Oregon barley production. / Graduation date: 1994

published_or_final_version / abstract / toc / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Meeting future demands of food security will require enhanced rice production that is more environmentally sustainable. To achieve this it is important to know the genetic and molecular mechanism controlling the root traits. High throughput phenotyping which can keep pace with genotyping is needed, but for many researchers this needs to be cheap as well as meaningful. Here a very simple, low cost and reliable method of assessing root depth of seedling using a layer of diuron-soaked filter paper buried 25 cm deep in a soil-filled box has been developed which is suitable for screening of hundreds of accessions. The assumption is that deep-rooting plants die quicker. This method was then used to screen five established rice panels. Deep rooted cultivars were screened from a panel of an aus panel from IRRI and a panel of Brazilian and Japanese cultivars by using this method. Root QTLs were detected by using bi-parental mapping population and GWA study was performed in two panels, the rice diversity panel (RDP-1) and Bengal Assam Association Population. Assessing 139 RILs from Bala x Azucena bi-parental population revealed heritability of 55% for herbicide symptoms where eleven QTLs were detected, many of which were co-localised with previously reported root QTLs in this population. A GWA study was performed using RDP1) of 356 accessions with 44k SNP markers. Analysis revealed 17% of phenotypic variation of herbicide score was attributable to rice sub-population where the aus showed the deepest rooting systems. A number of QTLs have been identified and a number of positional candidate gene lists were produced. A further 298 cultivars from Bengal and Assam were screened and GWA was performed using 2 M SNP database available from sequencing. ANOVA revealed 37% variation for herbicide score explained by genotype. Soil-filled rhizotron were used to assess 12 of these cultivars, revealing strong xx correlations between deep root traits and herbicide score, confirming the reliability of this method. GWA revealed a number of significant SNPs associated with the traits in this population. Finally a set of mutant gene (LOC_Os09g31478, LOC_Os05g40330, LOC_Os11g34140) which are functional candidate gene for root growth QTLs were studied. Here hydroponic phenotypic screening approach were used to identify the T-DNA mutant lines. However, no convincing mutants were revealed. The herbicide screening method has been shown to be a quick and robust system for the assessment of deep rooting rice plants in soil. This method can now be used for screening large number of cultivars and the identification of QTLs and candidate genes.

Thesis (Ph.D.)--Montana State University--Bozeman, 2006. / Typescript. Chairperson, Graduate Committee: Janice Bowman. Includes bibliographical references.

No description available.

No description available.

DNA markers tightly-linked to nuclear fertility restorer genes for cytoplasmic male sterility (CMS) are valuable tools for breeders and researchers working with these genes. Two different targeting approaches were used to identify markers linked to the Rfp1 restorer gene for the pol CMS of canola (Brassica napus L.): nearly isogenic line (NIL) comparison and bulked segregant analysis. These methods were equally efficient in identifying markers linked to Rfp1; combining them allowed a targeting efficiency of 100% to be achieved. The efficiency of bulked segregant analysis was found to be limited by the inadvertent occurrence of shared homozygosity at specific chromosomal regions in the bulks, in contrast with the efficiency of NIL comparison which was limited by the occurrence of residual DNA from the donor cultivar at scattered sites around the genome of the NILs. Eleven DNA markers linked to the Rfp1 gene were identified, one of which perfectly co-segregates with Rfp1. The linkage group on which Rfp1 is localized contains 17 DNA markers. Two restorer genes of the pol CMS, Rfp1 and Rfp2, and a Rfn restorer gene of the nap CMS were found to be at least tightly linked to one another and may all reside at the same locus. A fourth restorer gene, the Rfo restorer for the ogu CMS, was, however, found to be unlinked to the other restorer genes. Different restorer genes for the nap CMS were found in the lines 'Westar-Rf and 'Karat'. A linkage map of the B. napus genome containing 146 markers organized into 23 linkage groups covering a total length of 850.2 cM was constructed from a BC$ sb1$ population. This map contains 63 loci previously localized on the B. napus genome through analysis of an F$ sb2$ population. Comparative analysis indicates that the total length of the BC$ sb1$-derived map is smaller than that of the F$ sb2$-derived map, which suggests that a reduction in recombination frequency is occurring in male gametes. The preferential use of two or three probe-