by Graham Neil Thomas. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1995. / Includes bibliographical references (leaves 167-191). / Abstract --- p.i / Contents --- p.iii / List of tables --- p.viii / List of figures --- p.x / Abbreviations --- p.xi / Acknowledgements --- p.xiii / Chapter Chapter 1 - --- Introduction / Chapter 1.1 --- Introduction to the genus rotavirus --- p.1 / Chapter 1.2 --- General characteristics of rotavirus --- p.3 / Chapter 1.3 --- Clinical and epidemiological characteristics of rotaviral infections --- p.4 / Chapter 1.3.1 --- Clinical features of rotavirus infection --- p.4 / Chapter 1.3.2 --- Nosocomial rotavirus infection --- p.4 / Chapter 1.3.3 --- Morbidity and Mortality of rotavirus diarrhoea --- p.5 / Chapter 1.3.3.1 --- Seasonal distribution of rotavirus in temperate regions … --- p.5 / Chapter 1.3.3.2 --- Rotavirus infections in developing countries --- p.6 / Chapter 1.3.3.3 --- Rotavirus infections in developed countries --- p.6 / Chapter 1.3.4 --- Host Resistance to rotavirus infection --- p.7 / Chapter 1.3.5 --- Pathogenesis --- p.9 / Chapter 1.4 --- Vaccine development in rotavirus prevention --- p.10 / Chapter 1.4.1 --- Attenuated HRV as candidate vaccine strains --- p.11 / Chapter 1.4.2 --- Animal RV candidate vaccine strains (Jennerian approach)..… --- p.11 / Chapter 1.4.3 --- Intra- and interspecies reassortants vaccine strains --- p.12 / Chapter 1.4.4 --- Passive immunisation --- p.13 / Chapter 1.5 --- Laboratory diagnosis of rotavirus infections --- p.14 / Chapter 1.5.1 --- Detection of rotavirus --- p.14 / Chapter 1.5.2 --- Negative stain electron microscopy (EM) --- p.15 / Chapter 1.5.3 --- Immunological assays for the detection of rotavirus antigens --- p.15 / Chapter 1.5.4 --- Polyacrylamide gel electrophoresis (PAGE) of RV RNA --- p.16 / Chapter 1.5.5 --- Nucleic acid probe hybridisation assays --- p.17 / Chapter 1.6 --- Antigenic classification of rotaviruses --- p.17 / Chapter 1.6.1 --- Rotavirus groups --- p.17 / Chapter 1.6.2 --- Rotavirus subgroups --- p.18 / Chapter 1.6.3 --- Rotavirus serotypes --- p.19 / Chapter 1.6.4 --- Rotavirus genogroups --- p.21 / Chapter 1.7 --- Molecular biology of rotavirus --- p.21 / Chapter 1.7.1 --- Rotavirus genomic organisation --- p.21 / Chapter 1.7.2 --- Gene coding assignments --- p.22 / Chapter 1.7.3 --- Genome and protein structure of rotavirus VP7 --- p.22 / Chapter 1.8 --- Reverse transcriptase-Polymerase chain reaction (RT-PCR) for the genotyping of rotavirus --- p.32 / Chapter 1.8.1 --- Prevention of contamination in RT-PCR --- p.34 / Chapter 1.9 --- Objectives of the study --- p.36 / Chapter Chapter 2 - --- Methods / Chapter 2.1 --- Collection of specimens --- p.38 / Chapter 2.2 --- Standard rotavirus strains --- p.38 / Chapter 2.3 --- Tissue culture techniques --- p.39 / Chapter 2.3.1 --- Growth of MA104 cell line --- p.39 / Chapter 2.3.2 --- Subculturing of MA104 cell line --- p.40 / Chapter 2.3.3 --- Virus propagation and isolation --- p.40 / Chapter 2.3.4 --- Harvesting and purification of viral particles --- p.41 / Chapter 2.4 --- Rotavirus electropherotyping by PAGE --- p.42 / Chapter 2.4.1 --- RNA extraction --- p.42 / Chapter 2.4.2 --- Polyacrylamide gel electrophoresis (PAGE) --- p.43 / Chapter 2.4.3 --- Silver staining of RNA in polyacrylamide gels --- p.43 / Chapter 2.5 --- Enzyme immunoassays in rotavirus typing --- p.44 / Chapter 2.5.1 --- Preparation of monoclonal antibodies (mAb) from hybridoma cell lines --- p.44 / Chapter 2.5.1.1 --- Growth of hybridoma cell lines --- p.44 / Chapter 2.5.1.2 --- Preparation of the ascitic fluid - monoclonal Abs --- p.45 / Chapter 2.5.2 --- Confirmation of mAb activity by immunofluorescence (IF)..… --- p.46 / Chapter 2.5.2.1 --- Preparation of virus-infected cells --- p.46 / Chapter 2.5.2.2 --- Confirmation of the serotype specificity of the mAb by immunofluorescence microscopy --- p.47 / Chapter 2.5.3 --- Polyclonal hyperimmune antisera against rotavirus --- p.48 / Chapter 2.5.4 --- Immunoglobulin purification --- p.48 / Chapter 2.5.5 --- Monoclonal antibody-based serotyping and subgrouping EIA --- p.49 / Chapter 2.6 --- Reverse transcription-Polymerase Chain Reaction genotyping of rotavirus (RT-PCR) --- p.53 / Chapter 2.6.1 --- Primers used in RT-PCR --- p.53 / Chapter 2.6.1.1 --- Preparation of oligonucleotide primers for RV genotyping --- p.53 / Chapter 2.6.1.2 --- Detachment of the oligonucleotide from the column --- p.54 / Chapter 2.6.1.3 --- Purification of the oligonucleotides --- p.55 / Chapter 2.6.1.4 --- Confirmation of oligonucleotide synthesis --- p.58 / Chapter 2.6.2 --- Preparation of specimens --- p.59 / Chapter 2.6.3 --- Reverse transcription of genomic RNA template and PCR…… --- p.64 / Chapter 2.6.4 --- PCR genotyping using full-length cDNA template --- p.64 / Chapter 2.6.5 --- Product identification --- p.65 / Chapter Chapter 3 - --- Results / Chapter 3.1 --- Epidemiology of rotavirus infections in Hong Kong --- p.70 / Chapter 3.2 --- RT-PCR genotyping of rotavirus --- p.74 / Chapter 3.3 --- Seasonal distribution of rotavirus genotypes --- p.76 / Chapter 3.4 --- Comparison of RT-PCR genotyping of the VP7 gene with mEIA…… --- p.79 / Chapter 3.5 --- Relationship between electropherotyping and genotyping by RT-PCR --- p.91 / Chapter 3.6 --- Atypical rotavirus strains --- p.92 / Chapter 3.7 --- Specimens exhibiting multiple genotype specificities --- p.93 / Chapter 3.8 --- HRV RT-PCR genotype primers --- p.95 / Chapter Chapter 4 - --- Discussion / Chapter 4.1 --- Epidemiology of rotavirus infections in Hong Kong --- p.101 / Chapter 4.2 --- RT-PCR genotyping of rotavirus --- p.103 / Chapter 4.2.1 --- Modifications to methodology --- p.104 / Chapter 4.2.2 --- Rotavirus genotypes --- p.107 / Chapter 4.3 --- Comparison of RT-PCR genotyping with mEIA typing --- p.111 / Chapter 4.4 --- Relationship between electropherotyping and RT-PCR genotyping --- p.113 / Chapter 4.5. --- Rotavirus genotype distribution in Hong Kong --- p.115 / Chapter 4.6 --- Specimens containing atypical rotavirus strains --- p.119 / Chapter 4.7 --- Stool specimens exhibiting multiple rotavirus genotypes identified by RT-PCR --- p.122 / Chapter 4.8 --- Specificity analysis of RT-PCR primers --- p.124 / Chapter 4.8.1 --- 5non-coding region (1-28) - primer BEG9 --- p.125 / Chapter 4.8.2 --- 3non-coding region (1033/6-1062) - primers END9/RVG9. --- p.125 / Chapter 4.8.3 --- Variable region A (165-198) - primer aAT8 (G8) --- p.125 / Chapter 4.8.4 --- Variable region B (309-351) - primer aBT1 (G1) --- p.126 / Chapter 4.8.5 --- Variable region C (408-438) - primer aCT2 (G2) --- p.127 / Chapter 4.8.6 --- Variable region D (477-504) - primer aDT4 (G4) --- p.127 / Chapter 4.8.7 --- Variable region E (672-711) - primer aET3 (G3) --- p.128 / Chapter 4.8.8 --- Variable region F (747-776) - primer aFT9 (G9) --- p.128 / Chapter 4.9 --- Future developments of the study --- p.131 / Appendices / Chapter A1 --- Materials --- p.135 / Chapter A2.1-2.9 --- Distribution of electropherotypes between July 1985 and April 1994 --- p.145 / Chapter A3.1-3.11 --- Individual rotavirus strain electropherotypes --- p.153 / Chapter A4.1-4.8 --- "Comparison of nucleotide sequences for the 3', 5'-non-coding regions and variable regions A to F for the VP7 gene" --- p.158 / Chapter A4.9 --- Rotavirus strains and nucleotide sequence references for the VP7 gene --- p.166 / References

Genotype by environment interactions (GxE) can form a potential source of inefficiency in animal breeding if selection decisions are made without accounting for their effects. The UK sheep industry covers an assorted range of farming systems and environments, with each flock having a unique and diverse set of resources and management styles. As a result, what may be the best performing genotype in one environment may not necessarily be the best performing genotype in another. This thesis reports on an investigation into the presence of GxE within the UK sheep industry. Pedigree and performance data, available from both hill and terminal sire breeds, were analysed using a number of different methods. When environments were defined as 2 individual hill farms, genetic correlations were estimated between farms, for a range of Scottish Blackface ewe and lamb traits. Those found to be significantly different from 1 (P<0.05), and therefore indicating the presence of GxE, were lamb birth weight and ewe premating weight. Following on from this, fine-scale information obtained by a farmer questionnaire, from 79 different terminal sire flocks was combined with nationally-available climatic data and analysed using principle coordinate analysis and non-hierarchical clustering methods. Three distinct clusters of farm environments were identified, with grazing type, climatic conditions and the use of vitamin/mineral supplements proving to be the most distinguishing factors. The presence of GxE was then investigated by estimating genetic correlations between the clusters identified, using performance data from Charollais lambs, for 21 week old weight (21WT), ultrasound back-fat (UFD) and muscle (UMD) depths. The correlations estimated between clusters 1 and 2, which had the highest number of common Charollais sires used, were all low and significantly different from 1 (P<0.05) suggesting GxE was evident in terms of both scaling and re-ranking. Finally, the relationship between the level of concentrate feed used in each flock, as obtained from the questionnaire, and performance and climatic information available nationally for all flocks was estimated using canonical correlation analysis. This allowed the development of a farm environment scale, applicable to all flocks within the UK, and the use of reaction norm analyses to investigate the presence of GxE. The reaction norm describes the phenotype of an individual animal as a function of the environment. The environment scale developed, using data from Texel flocks only, went from low performance averages and poorer weather conditions to high performance averages and improved weather conditions. The slope of the reaction norm measures the sensitivity of an animal to a change in the environment. For each trait, (21WT, UMD and UFD), evidence of both re-ranking and scaling of sires were observed. A number of “robust” sires, with a low level of environmental sensitivity, were also identified. The findings from these analyses may have implications for future sheep breeding programmes. Providing a suitable “measure of environment” can be agreed, the identification of sires that perform well in specific environments, as well as those who perform consistently across a number of different environments, would be beneficial for farmers. This would potentially remove any unwanted effects of GxE and allow the farmer to select animals best suited to their overall farm environment.

Avaliou-se o efeito isolado e associado de pós de origem vegetal e de genótipos de feijoeiro sobre o comportamento, biologia e danos de Zabrotes subfasciatus (Boh.) e Acanthoscelides obtectus (Say). Inicialmente, foi avaliado o efeito dos pós obtidos de 18 plantas sobre a atratividade e mortalidade dos adultos, e oviposição. A seguir, foi testado o efeito de 12 genótipos de feijoeiro incluindo materiais melhorados contendo arcelina (Arc1, Arc2, Arc3 e Arc4) e sem essa proteína (IAC Carioca Aruã, IAC Carioca Pyatã, IAC Carioca Akytã, IAC Maravilha, IAC Una, IAC Bico de Ouro, Porrillo 70 e Goiano Precoce) sobre a oviposição (com e sem chance de escolha) e biologia dos insetos. Com base nestes resultados, foram selecionados, para cada espécie de inseto, quatro genótipos (três resistentes e um suscetível) e quatro pós vegetais, para os quais foi avaliado o efeito associado sobre a atratividade e mortalidade dos adultos, preferência para oviposição, biologia e danos causados pelos insetos. Concluiu-se que: a) os pós obtidos da parte aérea de Chenopodium ambrosioides (erva-de-santa-maria), f. (forma) 1 e f.2; de folhas de Eucalyptus citriodora (eucalipto cheiroso), de Mentha pulegium (poejo) e de Ruta graveolens (arruda), e de cascas de frutos de Citrus reticulata (laranja cv. Murcote) são repelentes aos adultos das duas pragas; b) os pós obtidos de folhas de Ocimum basilicum (alfavaca) e de O. minimum (manjericão) são repelentes apenas para Z. subfasciatus, enquanto os pós de cascas de frutos de Citrus sinensis (laranja cv. Pêra) e de frutos de Lafoensia glyptocarpa (mirindiba) apresentam efeito repelente apenas em relação a A. obtectus; c) o pó de folhas de L. glyptocarpa apresenta atratividade a Z. subfasciatus; d) os pós de C. ambrosioides (f.2), M. pulegium, O. basilicum e R. graveolens apresentam efeito altamente tóxico aos adultos de Z. subfasciatus, causando 100% de mortalidade e impedindo a oviposição; e) em relação a A. obtectus, há total mortalidade de adultos e ausência de oviposição, com o uso de pós de C. ambrosioides (f.2) e de folhas de Coriandrum sativum (coentro); f) em teste sem chance de escolha, o genótipo Arc3 é menos ovipositado por Z. subfasciatus que 'IAC Carioca Pyatã' e 'IAC Bico de Ouro', enquanto, em relação a A. obtectus os materiais são igualmente preferidos para oviposição; g) os materiais contendo arcelina (Arc1, 2, 3 e 4) apresentam resistência do tipo não-preferência para alimentação e/ou antibiose a Z. subfasciatus, alongando o período de desenvolvimento (ovo-adulto) e reduzindo o peso dos adultos, a longevidade e a fecundidade; h) em relação a A. obtectus, a resistência do tipo não-preferência para alimentação e/ou antibiose só ocorre com o Arc1, genótipo em que há alongamento do período de desenvolvimento e menor peso dos adultos; i) 'Goiano Precoce' é o material mais adequado ao desenvolvimento dos dois insetos; j) com o emprego associado de pós vegetais e genótipos resistentes de feijoeiro, ocorre apenas efeito aditivo (e não sinérgico) das duas técnicas de controle para ambas as espécies de insetos; k) o peso consumido de grãos de feijão por Z. subfasciatus e A. obtectus não é afetado pelos pós inseticidas; esse peso, entretanto, é menor nos genótipos contendo arcelina para os dois insetos. / It was evaluated the isolated and associated effects of powders from different vegetal and bean genotypes on the behaviour, biology and damage of Zabrotes subfasciatus (Boh.) and Acanthoscelides obtectus (Say). Initially, it was evaluated the effect of powders of 18 plants on the attractivity and mortality of the adults, and oviposition. Then, the effect of 12 bean genotypes was tested including materials with arcelin (Arc1, Arc2,Arc3 and Arc4) and without this protein (IAC Carioca Aruã, IAC Carioca Pyatã, IAC Carioca Akytã, IAC Maravilha, IAC Una, IAC Bico de Ouro, Porrillo 70 and Goiano Precoce) on the oviposition (free-choice and no-choice tests) and biology of the insects. Based on these results, four genotypes (three resistant and one susceptible) and four powders were selected for each insect species. It was evaluated the associated effect on the attractivity and mortality of the adults, preference for oviposition, biology and damage caused by the insects. It was concluded that: powders of the aerial part from Chenopodium ambrosioides f. (form) 1 and f.2; leaves from Eucalyptus citriodora, from Mentha pulegium and from Ruta graveolens, and rinds of fruits from Citrus reticulata (cv. Murcote) are repellents to the adults of the two pests; b) powders of leaves from Ocimum basilicum and O. minimum are repellent only for Z. subfasciatus, while powders of rinds of fruits from Citrus sinensis (cv. Pêra) and fruits from Lafoensia glyptocarpa shows repellent effect only on A. obtectus; c) powder of leaves from L. glyptocarpa shows attractivity on Z. subfasciatus; d) powders from C. ambrosioides (f.2), M. pulegium, O. basilicum and R. graveolens show high toxicity on adults of Z. subfasciatus, causing 100% mortality and inhibiting the oviposition; e) in relation to A. obtectus, total mortality of adults and no oviposition is observed with the use of powders from C. ambrosioides (f.2) and leaves from Coriandrum sativum; f) in no-choice test, Arc3 was less oviposited by Z. subfasciatus than IAC Carioca Pyatã and IAC Bico de Ouro, while in relation to A. obtectus the materials are equally preferred for oviposition; g) the materials with arcelin (Arc1, 2, 3 and 4) show non-preference resistance for feeding and/or antibiose to the Z. subfasciatus, prolonging the time for insect development (egg-adult) and reducing the adult weight, longevity and fecundity; h) in relation to A. obtectus, non-preference resistance for feeding and/or antibiose only occurs with Arc1, genotype that prolongs the development period and reduces the adult weight; i) Goiano Precoce is the most suitable material for the development of both insects; j) with the association of vegeta powders and resistant bean genotypes, only additive effect (and not syhngistic) is observed with the two control tactics for both insect species; k) the weight of consumed bean grains for Z. subfasciatus and A. obtectus was not affected by insecticide powders; however the weight, however, was lower in the genotypes with arcelin for both insects.

Objectives: About 2% of the US population suffers from severe malocclusion discrepancies that are beyond the limits of orthodontics alone. This study explores correlations between 3D malocclusion phenotypes and craniofacial development genes. Methods: CBCTs (124) or digital casts (161) of 285 subjects with skeletal Class I (n=60), II (n=143) and III (n=82) malocclusion were digitized with 48 dental landmarks. 3D coordinates were superimposed prior to Principal Component (PC) analyses to identify symmetric (sym) and asymmetric (asym) aspects of shape variation related to malocclusion. PCs explaining 51%-67% of total shape variation were regressed on 200 variants genotyped within 75 genes adjusting for race, gender, age and data source. Results: Significant correlations (p<0.01) were found for sym variation with BMP3, PITX2, MAFB, SNAl3, FGF8, ABCA4-ARHGAP29, FOXL2 and asym variation PAX7, TBX1, LEFTY1, SATB2, SOX2, TP63 and the 400Kb region containing D1S435. Conclusion: Results suggest genetic pathways associated with malocclusion.

Doctor of Philosophy / Cystic fibrosis (CF) is the most common inherited lethal disorder among Caucasian populations. Chronic pulmonary infections, particularly from Pseudomonas aeruginosa, are the major determinant of the morbidity and mortality of people with CF. It is generally accepted that people with CF acquire this pathogen independently from their surrounding environment, and that individual CF patients carry unique strains different from others. The spread of this pathogen from patient to patient is thought to be rare and occurs particularly among closely contacted cases such as CF siblings. However, over the past decade, there have been several reports of an emergence of clonal P. aeruginosa strains commonly found infecting a number of CF patients. One such report is from the CF paediatric clinic at the Royal Children’s Hospital in Melbourne in which more than half of the patients were infected with a single strain or clone, subsequently called Australian epidemic strain 1 or AES-1. A preliminary survey showed that AES-1 had spread extensively along the Australian eastern seaboard among CF patients attending other CF centres in Melbourne, Sydney and Brisbane, including adult patients at the Royal Prince Alfred Hospital (RPAH), Sydney. Another clonal strain, subsequently called AES-2, was identified in both CF adults and children at the Prince Charles Hospital and the Royal Children’s Hospital, in Brisbane. The total extent of prevalence of the AES-1 and AES-2 strains at the RPAH as well as the clinical status of patients who carried these strains was unknown. Moreover, the pathogenicity of these two clonal strains had not been investigated. The studies presented in this thesis investigated the prevalence of these clonal strains among CF patients attending the adult CF clinic at RPAH, Sydney by using pulsed-field gel electrophoresis. Overall, 50% of 112 patients with P. aeruginosa were found to be infected with clonal strains. The AES-1 and AES-2 strains were identified in 38% and 5% of the patients respectively. Two new clonal strains, called Sydney-1 and Sydney-2, were also identified. Patients with clonal strains had a significant increase in their number of exacerbations and hospitalisation days, and tended to have lower pulmonary functions when compared to patients infected with non-clonal strains. By using a variety of bioassays to examine the pathogenicity of the clonal and non-clonal strains, it was found that both AES-1 and AES-2 produced more virulence factors and were more resistant to antibiotics when compared to the non-clonal strains. AES-1 and AES-2 were associated with increased production of proteases, including elastase, alkaline protease and protease IV. Overall the results presented in this thesis suggest that there may be a link between virulence and transmissibility of this pathogen. The studies presented in this thesis also compared the biofilm forming capacities of the AES-1 and non-clonal isolates. AES-1 was shown to have greater biofilm-forming capacity than the non-clonal strains, when they were grown on a glass surface, suggesting a possible association between clonality and biofilm formation. A model for the study of bacteria grown in conditions similar to CF sputum was also developed. P. aeruginosa grown in this model was found to develop into clumps which may be comparable to the biofilm structure in the CF lung. This model was shown to be beneficial for transcriptomic and proteomic studies which are underway within the research group. AES-1 was also found to have phenotypic variations between isolates. By applying the amplified fragment length polymorphism technique, more subtypes of this clone were revealed. However, these detected subtypes did not correlate with the different phenotypes, suggesting minor mutations such as single point polymorphisms may be responsible for the phenotypic diversity within the clone. The final part of this thesis was devoted to examining the safety of a novel CF treatment: hypertonic saline (HS) inhalation. HS was shown to increase airway mucociliary clearance, while increased osmolarity associated with the use of HS was also shown to have an inhibitory effect on the formation of biofilms. Findings in this study proved that there was no evidence of strain selection in patients who received the long-term treatment with HS. The study also demonstrated that AES-1 was significantly more persistent in the CF lung than the non-clonal strains. The present thesis not only defines the clonal strains of P. aeruginosa and their implications for infected patients, but also provides a general understanding into the pathogenesis of both clonal and non-clonal strains infecting CF lungs.

This study investigates geographic patterns of genetic variation in aspen spring phenology to understanding how tree population adapts to climatically risk environments. These finding suggest rules to guide seed transfer between regions. I use a classical common garden experiment to reveal genetic differences among populations from western Canada and Minnesota, and present a novel method to seamlessly map the heatsum required for remotely sensed green-up. Both approaches reveal two major geographic patterns: northern and high elevation aspen populations break bud earlier than sources from the boreal plains, and late budbreak is strongly associated with the driest winter and spring environments. This suggests selection pressures for late budbreak due to both frost and drought risks in early spring, and we therefore caution against transfer of seed to drought regions of the boreal plains. Although such transfers have been shown to increase plantation productivity in short-term tests, non-local planting material may be susceptible to exceptional spring droughts. / Forest Biology and Management

The most intriguing problems in genetics epidemiology are to predict genetic disease susceptibility and to associate single nucleotide polymorphisms (SNPs) with diseases. In such these studies, it is necessary to resolve the ambiguities in genetic data. The primary obstacle for ambiguity resolution is that the physical methods for separating two haplotypes from an individual genotype (phasing) are too expensive. Although computational haplotype inference is a well-explored problem, high error rates continue to deteriorate association accuracy. Secondly, it is essential to use a small subset of informative SNPs (tag SNPs) accurately representing the rest of the SNPs (tagging). Tagging can achieve budget savings by genotyping only a limited number of SNPs and computationally inferring all other SNPs. Recent successes in high throughput genotyping technologies drastically increase the length of available SNP sequences. This elevates importance of informative SNP selection for compaction of huge genetic data in order to make feasible fine genotype analysis. Finally, even if complete and accurate data is available, it is unclear if common statistical methods can determine the susceptibility of complex diseases. The dissertation explores above computational problems with a variety of methods, including linear algebra, graph theory, linear programming, and greedy methods. The contributions include (1)significant speed-up of popular phasing tools without compromising their quality, (2)stat-of-the-art tagging tools applied to disease association, and (3)graph-based method for disease tagging and predicting disease susceptibility.

This study focuses how the MLR-tagging for statistical covering, i.e. either maximizing average R2 for certain number of requested tags or minimizing number of tags such that for any non-tag SNP there exists a highly correlated (squared correlation R2 > 0.8) tag SNP. We compare with tagger, a software for selecting tags in hapMap project. MLR-tagging needs less number of tags than tagger in all 6 cases of the given test sets except 2. Meanwhile, Biologists can detect or collect data only from a small set. So, this will bring a problem for scientists that the estimates accuracy of tag SNPs when constructing the complete human haplotype map. This study investigates how the MLR-tagging for statistically coverage performs under unbias study. The experiment results shows MLR-tagging still select small amount of SNPs very well even without observing the entire SNP in the sample.

Post-harvest seedcoat darkening is a major problem in many pulses, including common bean (</i>Phaseolus vulgaris</i> L.). In some bean market classes, such as pinto, beans that have a darkened seedcoat are discounted in the market place as it is assumed that the beans are old and will be hard-to-cook (HTC). Pinto genotypes that darken more slowly than conventional pinto beans would be more desirable and have been identified in the bean breeding program at the University of Saskatchewan. <p>To study the slow-darkening trait, a quick, reliable, and inexpensive screening method that would not affect seed germination would be beneficial. Three potential protocols to accelerate seedcoat darkening were examined. The greenhouse protocol was conducted in the greenhouse by placing the bean seeds in polybags with a 1 cm2 piece of moistened felt. For the UV light protocol, bean seeds were placed 10 cm below an UV lamp which had a wavelength of 254 nm. For the cabinet protocol, bean seeds were placed in a cabinet set at 30¢ªC, 80% relative humidity, and full fluorescent lights. Color measurements were taken routinely using a Hunter Lab colorimeter. All three methods were successful in distinguishing darkening beans from slow-darkening beans although the UV light protocol was considered to be superior to the greenhouse and cabinet protocol as the UV light protocol was quick, consistent over years, and the most economical. Unlike the greenhouse and the cabinet protocols, the UV light protocol did not affect seed germination following accelerated darkening. <p>The stability of the slow-darkening trait was further investigated in genotype by environment (g x e) studies across different indoor and outdoor environments. In the g x e study across different field environments, it was found that prior to accelerated seedcoat darkening the g x e interaction was significant. Following accelerated seedcoat darkening, environment and genotype were both significant and g x e was not. The slow-darkening genotypes had lighter seedcoats than the darkening genotypes and those field sites that had more favorable weather had lighter seedcoats. For the g x e study across indoor and outdoor environments, when the genotypes were split into either slow-darkening or darkening, the g x e interaction was not significant and the slow-darkening genotypes had lighter seedcoats. <p>Genetic control of the slow darkening trait was determined. For crosses between slow-darkening genotypes and CDC Pintium, the F2 populations segregated 3 darkening : 1 slow-darkening with distinct bimodal distribution. This indicated that seedcoat darkening was controlled by a single gene and darkening was dominant over slow-darkening. For both slow-darkening by slow-darkening crosses, the F2 populations¡¯ L* values were unimodal, normal distributions, indicating there may be modifying genes for the slow-darkening trait.

Post-harvest seedcoat darkening is a major problem in many pulses, including common bean (</i>Phaseolus vulgaris</i> L.). In some bean market classes, such as pinto, beans that have a darkened seedcoat are discounted in the market place as it is assumed that the beans are old and will be hard-to-cook (HTC). Pinto genotypes that darken more slowly than conventional pinto beans would be more desirable and have been identified in the bean breeding program at the University of Saskatchewan. <p>To study the slow-darkening trait, a quick, reliable, and inexpensive screening method that would not affect seed germination would be beneficial. Three potential protocols to accelerate seedcoat darkening were examined. The greenhouse protocol was conducted in the greenhouse by placing the bean seeds in polybags with a 1 cm2 piece of moistened felt. For the UV light protocol, bean seeds were placed 10 cm below an UV lamp which had a wavelength of 254 nm. For the cabinet protocol, bean seeds were placed in a cabinet set at 30¢ªC, 80% relative humidity, and full fluorescent lights. Color measurements were taken routinely using a Hunter Lab colorimeter. All three methods were successful in distinguishing darkening beans from slow-darkening beans although the UV light protocol was considered to be superior to the greenhouse and cabinet protocol as the UV light protocol was quick, consistent over years, and the most economical. Unlike the greenhouse and the cabinet protocols, the UV light protocol did not affect seed germination following accelerated darkening. <p>The stability of the slow-darkening trait was further investigated in genotype by environment (g x e) studies across different indoor and outdoor environments. In the g x e study across different field environments, it was found that prior to accelerated seedcoat darkening the g x e interaction was significant. Following accelerated seedcoat darkening, environment and genotype were both significant and g x e was not. The slow-darkening genotypes had lighter seedcoats than the darkening genotypes and those field sites that had more favorable weather had lighter seedcoats. For the g x e study across indoor and outdoor environments, when the genotypes were split into either slow-darkening or darkening, the g x e interaction was not significant and the slow-darkening genotypes had lighter seedcoats. <p>Genetic control of the slow darkening trait was determined. For crosses between slow-darkening genotypes and CDC Pintium, the F2 populations segregated 3 darkening : 1 slow-darkening with distinct bimodal distribution. This indicated that seedcoat darkening was controlled by a single gene and darkening was dominant over slow-darkening. For both slow-darkening by slow-darkening crosses, the F2 populations¡¯ L* values were unimodal, normal distributions, indicating there may be modifying genes for the slow-darkening trait.