Soybean mosaic virus (SMV), has been the cause of numerous and often devastating disease epidemics, causing reduction in both the quality and quantity of soybeans worldwide. Two important genes for resistance to SMV are Rsv1 and Rsv4. Alleles at the Rsv1 locus have been shown to control resistance to all but the most virulent strain of SMV. This locus has been mapped previously to the soybean F linkage group. Rsv4 is an SMV resistance locus independent of Rsv1 and confers resistance to all strains of SMV. This locus has not been mapped previously. The purpose of this study is to investigate the two genomic regions that contain these vitally important resistance genes. A population of 281 F2 individuals that had previously been genotyped for reaction to SMV was evaluated in a mapping study which combined bulk segregant analysis with Amplified Fragment Length Polymorphism (AFLP). A Rsv4-linked marker, R4-1, was identified that mapped to soybean linkage group D1b using a reference mapping population. More than 40 markers were mapped in the Rsv4 segregating population including eleven markers surrounding Rsv4. This will provide the necessary framework for the fine mapping of this important genetic locus. Previous work has located Rsv1 to a genomic region containing several important resistance genes including Rps3, Rpg1, and Rpv. An RFLP probe, NBS5, whose sequence closely resembles that of several cloned plant disease resistance genes has been mapped to this chromosomal region. The efficacy of using this sequence to identify potential disease resistance genes was assessed by screening a cDNA library to uncover a candidate disease resistance gene which corresponds to this NBS5 sequence. Two related sequence classes were identified that correspond to NBS5. Interestingly, one class corresponds to a full length gene closely resembling other previously cloned disease resistance genes offering evidence that this NBS5-derived clone is a candidate disease resistance gene. A new marker technique was developed by combining the speed and efficiency of AFLP with DNA sequence information from cloned disease resistance genes. Using this strategy, three new markers tightly linked to Rsv1 were identified. One of these markers, which maps 0.6 cM away from Rsv1, has motifs consistent with other cloned disease resistance genes, providing evidence that this approach is an efficient method for targeting genomic regions where disease resistance genes are located. / Ph. D.

Mapping quantitative trait loci in outbred populations is important since development of inbred lines in livestock species is usually not feasible. Traditional genetic mapping methods, such as Least Squares and Maximum Likelihood, cannot fully accommodate complex pedigree structures, and more sophisticated methods such as Bayesian analysis are very demanding computationally. In this thesis, an alternative approach based on a Residual Maximum Likelihood method for estimation of position and variance of one or two linked QTLs and of additive polygenic and residual variances is presented. The method is based on a mixed linear model including polygenic and random QTL allelic effects. The variance-covariance matrix of QTL allelic effects and its inverse is computed conditional on incomplete information from multiple linked markers. The method is implemented using interval mapping and a derivative-free algorithm, where the required coefficient matrix of the Mixed Model Equations is derived from a Reduced Animal Model. simulation studies based on a granddaughter design with 2000 sons, 20 sires and 9 ancestors were performed to evaluate parameter estimation and power of QTL detection. Daughter Yield Deviations of sons were simulated under three QTL models, a biallelic, a multiallelic (10 alleles), and a normal-effects model. A linkage group of five or nine markers located on the same chromosome was assumed, and genotypes were available on sons, sires and ancestors. Likelihood ratio statistics were used to test for the presence of one or two linked QTLs. Parameters were estimated quite accurately for all three QTL models, showing that the method is robust to the number of alleles at the QTL. The effect of considering or ignoring relationships in the analyses did not have a major impact on parameter estimates but reduced the power of QTL detection. In general, power tended to decrease as the number of sons per sire, QTL contribution to additive genetic variance, or distance between QTLs was reduced. The method allowed for detection of a single QTL explaining 25% of the additive genetic variance, and for detection of two QTLs when jointly they accounted for 50% or 12.5% of the additive genetic variance. Although the REML analysis is an approximate method incorporating an expected covariance matrix of the QTL effects conditional on marker information, it is a computationally less expensive alternative to Bayesian analysis for accounting for the distribution of marker-QTL genotypes given marker and phenotypic information. For the designs studied, parameters were estimated accurately and QTLs mapped with satisfactory power. / Ph. D.

Estimated at approximately $43 billion annually, the cultivated soybean Glycine max (L.) Merr., is the second most valuable crop in the United States. Soybeans account for 57% of the world oil-seed production and are utilized as a protein source in products such as animal feed. The value of a soybean crop, measured in seed quality and quantity, is negatively affected by biotic and abiotic stresses. This research is focused on resistance to biotic disease stress in soybean. In particular, we are working on the Phytophthora soja (P. sojae) and Soybean Mosaic Virus (SMV) systems. For each of these diseases, we are working to develop superior soybean germplasm that is resistant to the devastating economic impacts of pathogens. The majority of this research is focused on screening for novel sources of P. sojae resistance with core effectors to identify resistance genes (R-genes) that will be durable under field conditions. Four segregating populations and two recombinant inbred line (RIL) populations have been screened with core effectors. Effector-based screening methods were combined with pathogen-based phenotyping in the form of a mycelium-based trifoliate screening assay. One RIL population has been screened with virulent P. sojae mycelium. Disease phenotyping has generated a preliminary genetic map for resistance in soybean accession PI408132. The identification of novel R-genes will allow for stacking of resistance loci into elite G. max cultivars. The second project covered in this dissertation describes the validation of the SMV resistance gene Rsv3. Utilizing a combination of transient expression and homology modeling; we provide evidence that Glyma14g38533 encodes Rsv3. / Ph. D.

It was suggested that marker and phenotypic information be combined in order to obtain more accurate or earlier genetic evaluations. An improvement in accuracy or time of evaluation due to utilization of marker assisted selection (MAS) increases genetic progress. Fernando and Grossman (1989) suggested including marker information directly into the Animal Model, Best Linear Unbiased Prediction system, but several problems need to be solved before their approach becomes feasible. Other selection indices were suggested but either do not use all the available information or are suitable only for evaluation of the offspring of the sire from which the marker information was established. A selection index combining marker and Animal Model information was developed to allow comparisons involving offspring, grandoffspring and great-grandoffspring of a sire. Marker information was assumed to be a least square estimate of the difference between the average effects of the two quantitative trait loci (QTL) alleles present in a sire (D_p) and the standard error of this estimate (SE(D_p)). Estimates may have been obtained from a daughter or granddaughter design. Comparisons among grandoffspring and great-grandoffspring also require an estimate of the recombination rate (r) between the marker and the QTL. The Animal Model information consists of predicted transmitting ability (PTA) and reliability of PTA. PTA was assumed not to include any marker information. The expected percentage of the gain in accuracy (PGA) due to the inclusion of marker information in the selection indices is affected by the degree of polymorphism at the marker locus. The polymorphism information content (PIC) of a marker locus was computed for the second and third generations and for mates genotyped or not. PGA increased with larger Dos lower SE(D_p), lower r, a smaller number of own and progeny records, and larger PIC. PGA and PIC reduce over generations. Marker information in dairy cattle is likely to be used in generations beyond offspring. Then, only the use of highly polymorphic markers with a large and accurately estimated effect may be economically justified. / Master of Science

<p dir="ltr"><a href="" target="_blank">Shoot architecture in plants refers to the spatial layout of the above-ground organs, which develops through complicated networks of genetic and environmental interactions. Modification of shoot architecture has been a major driver of yield increases in many crop species, but knowledge of the genetic control of shoot architectural traits in soybeans remains incomplete. Chapter 1 provides an overview of soybean shoot architecture traits, encompassing stem growth habit, plant height, branch number, branch angle, petiole angle, leaf size, and leaf shape. The review not only delves into the genetic basis of these traits but also underscores their importance, identifies knowledge gaps, and outlines avenues for future research leveraging cutting-edge technologies in gene editing, phenomics, and genomics. Chapter 2 describes the identification and mapping of a novel locus modulating semideterminate and indeterminate stem growth habits, <i>dt3</i>, on chromosome 10. Allelic and haplotypic analysis of the USDA soybean germplasm collection was conducted to find semideterminate soybean accessions which did not carry known stem termination alleles at the <i>dt1</i> and <i>Dt2 </i>loci. Mapping populations were developed by crossing several of these accessions to indeterminate cultivars, and initial mapping revealed a region on chromosome 10 common to all populations. <i>dt3</i> is a recessive mutation resulting in semideterminate growth habits, and this locus displays a unique pattern of inheritance compared with known stem growth habit genes in soybean or other plant species. Chapter 3 describes the identification of <i>Dt4</i>, a novel semideterminacy allele of <i>FT5a</i> originating from wild soybean. <i>Dt4</i> was identified by quantitative trait locus (QTL) mapping using a population developed by crossing LD00-3309, an indeterminate cultivar with a semideterminate recombinant inbred line (RIL1890) originating from a cross between wild and domesticated soybean. A combination of fine mapping and candidate gene expression analysis pinpointed the allele of the floral inducer <i>FT5a</i> in RIL1890 as <i>Dt4 </i>for semideterminacy. Intriguingly, when the <i>Dt4 </i>allele was transformed into LD00-3309, it resulted in not only semideterminate stem growth habit but also narrowed leaf shape. Chapter 4 describes the identification and mapping of <i>GmBa1</i>, a novel locus specifying soybean branch angle, in which wide branch angle is completely dominant over narrow branch angle. This locus was identified in two distinct biparental mapping populations. The findings described in this dissertation deepen our understanding of genetic mechanisms underlying shoot architecture traits and provide a valuable resource for breeders looking to modify these traits for soybean improvement.</a></p>

Thesis (PhD)--Stellenbosch University, 2004. / ENGLISH ABSTRACT: Progressive familial heart block I (PFHBI) is an inherited autosomal dominant cardiac conduction disorder which segregates in a large South African (SA) pedigree, two smaller SA families and a Lebanese family. It specifically affects conduction in the ventricles and is of unknown cause. Clinically, PFHBI is detected on electrocardiogram (ECG) by evidence of bundle-branch disease, i.e., as right bundle branch block, left anterior or posterior hemiblock, or complete heart block with broad QRS complexes. The PFHBI-causative gene was mapped to a lOcM region on chromosome 19ql3.3 using linkage analysis, and the locus was subsequently reduced to 7cM by genetic fine mapping. The present study involved a multi-strategy approach to search for the PFHBI gene. The objectives were the further reduction of the PFHBI locus by genetic fine mapping using published and novel markers, searching for short gene transcripts from publicly available databases and the generation of an integrated map of the locus to which genes were mapped. Prioritised genes were screened for PFHBI-causing mutations and, in addition, the PFHBI locus was searched for the presence of a G protein-encoding gene (PI 15- RhoGEF), a connexin (Cx) gene and any genes containing a CTG repeat expansion motif, since these genes are plausible PFHBI candidate genes. Genotyping and fine genetic mapping using known and novel polymorphic dinucleotide (CA)n and novel tetranucleotide (A3G)n repeat markers across the PFHBI locus were performed. Publicly available databases, such as LLNL (Livermore, USA), and GENEMAP (NCBI) were searched for ESTs which, in turn, were extended using clustering programmes, such as UNIGENE (NCBI) and STACK (SANBI), and the resulting consensus sequences were subsequently BLAST-searched against the protein databases. Using the available data, an integrated physical and genetic map of the PFHBI locus was generated and, as the HGP progressed, a number of novel genes were placed thereon. Subsequently, genes were prioritised on the basis of position, function and expression profile. Genetic fine mapping reduced the PFHBI locus from 7cM to 4cM. The EST approach yielded 38 ESTs, of which 24 ESTs matched proteins, such as activating transcription factor 5 (ATF5), actin-binding protein (KPTN) and zinc finger protein 473 (ZFP473) (May 2003). All the map data generated experimentally and computationally were placed on the PFHBI map. The PI 15-RhoGEF was excluded as a PFHBI candidate gene and although homologous sequences to connexin 37 (Cx37) was located on both chromosome 19 radiation hybrid clones (RHG12 and ORIM-7), it was not identified on the DNA clones spanning the PFHBI locus. No evidence of an expansion of a CTG repeat motif sequence in PFHBI-affected individuals was found. Five highly prioritised candidate genes, namely, 5CZ2-associated X protein (BAX), potassium voltage-gated channel Shaker-related subfamily member 7 (KCNA7’), potassium inwardly-rectifying channel, subfamily J, member 14 (KIR2.4), lin-7 homolog B {LIN-7B) and glycogen synthase 1 (GSYI) were selected for mutation screening. No disease associated mutations were identified in the exonic and flanking intronic regions of these genes. In summary, this study reduced the PFHBI locus substantially and generated a detailed map of the region. A number of attractive candidate genes were excluded from causing PFHBI; however, several plausible candidate genes are still present at this gene-rich locus and remain to be screened. Identifying the PFHBI-causative gene and associated mutation will provide a platform for further studies to understand the pathophysiology, not only of PFHBI, but also of other more commonly occurring conduction disturbances. / AFRIKAANSE OPSOMMING: Progressiewe familiele hartblok I (PFHBI) is ‘n autosomaal dominant oorerflike kardiale geleidingstoomis wat in ‘n groot Suid-Afrikaanse (SA) familie, twee kleiner SA families en ‘n Lebanese familie segregeer. Dit affekteer hoofsaaklik die geleiding in die ventrikels en die oorsaak daarvan is onbekend. Klinies word PFHBI op elektrokardiogram (EKG) geidentifiseer as a bondeltak-siekte, naamlik, as regter bondeltakblok, linker anterior of posterior hemiblok, of volledige hartblok met wye QRS komplekse. Die PFHBI-veroorsakende geen is voorheen deur koppelingsanalise tot ‘n lOcM gebied op chromosoom 19ql3.3 gekarteer, en daaropvolgens is die lokus verklein tot 7cM deur genetiese fyn kartering. Die huidige studie behels ‘n veelvuldige-strategie benadering in die soektog na die PFHBI geen. Die doel van die studie was die verdere verkleining van die PFHBI lokus deur gebruik te maak van beide gepubliseerde en nuwe genetiese merkers, die identifisering van kort geentranskripte (ESTs) uit publieke databanke en die generasie van ‘n geintegreerde kaart van die lokus. Geprioritiseerde gene is geanaliseer vir die PFHBI-veroorsakende mutasie en, daarby, is die PFHBI lokus deursoek vir die teenwoordigheid van ‘n G proteien-enkodeeringsgeen (PIJ5-RhoGEF), ‘n konneksien (Kx) geen en enige gene wat ‘n uitgebreide CTG-herhalingsmotief bevat, aangesien hierdie gene as sterk PFHBI kandidaatgene geag is. Genotipering en fynkartering deur die gebruik van bekende asook nuwe polimorfiese dinukleotied- [(CA)n] en nuwe tertranukleotied- [(A3G)n] herhalingsmerkers wat die PFHBI lokus oorbrug, is uitgevoer. Publieke databanke, soos LLNL (Livermore, USA), en GENEMAP (NCBI) is ondersoek vir ESTs wat vervolgens verleng is deur gebruik te maak van groeperende programme soos UNIGENE (NCBI) en STACK (SANBI) en die gevolglike konsensus volgordes is daama met behulp van BLAST geanaliseer teen die protei'endatabanke. Die bekomde data is vervolgens gebruik om ‘n geintegreerde fisiese en genetiese kaart van die PFHBI lokus te produseer en, soos die mens genoomprojek gevorder het, is nuwe gene daarop geplaas. Daarna is gene geprioritiseer vir mutasie analise gebaseer op posisie, funksie en uitdrukkingsprofiele. Genetiese fynkartering het die PFHBI lokus van 7cM tot 4cM verklein. Die EST benadering het 38 ESTs gei'dentifiseer, waarvan 24 ESTs proteien gelyke gehad het, bv aktiverende transkripsie faktor 5 (ATF5), aktien-verbindingsprotei'en (KPTN) en sink-vingerproteien 473 (ZFP473) (Mei 2003). A1 die karterings data wat eksperimenteel en rekenaar-gewys gegenereer is, is op die PFHBI kaart geposisioneer. Die P115-RhoGEF is uitgeskakel as ‘n PFHBI kandidaatgeen en alhoewel ’n volgorde met homologie aan konneksien37 (Kx37) gevind is op albei chromosoom 19 radiasiehibried klone (RGH12 and ORIM-7), is dit nie gei'dentifiseer in die DNS klone wat die PFHBI lokus oorbrug nie. Geen bewyse van uitbreiding van CTG herhalingsmotiewe is gevind in PFHBIaangetasde persone nie. Vyf hoogs-geprioritiseerde kandidaat gene, naamlik, BCL2-geassosieerde X proteien (BAX), kalium spanningsbeheerde kanaal, subfamilie J, lid 14 (KIR2.4), lin-7 homoloog B (LIN-7b) en glikogeen sintase 1 (GYS1), is geselekteer vir mutasie-analise. Geen siekteveroorsakende mutasie is egter gei'dentifiseer in die eksoniese of die naasliggende introniese gebiede van hierdie gene nie. Ter opsomming, hierdie studie het die PFHBI lokus verklein en het ‘n omvattende kaart van die gebied gegenereer. Verskillende kandidaat gene is uitgesluit as die oorsaak van PFHBI, alhoewel daar nog heelwat goeie kandidaat gene in hierdie geen-ryke lokus is wat geanaliseer behoort te word. Die identifiseering van die PFHBI-veroorsakende mutasie sal ‘n platform bied vir verdere studies om die patofisiologie van nie alleen PFHBI nie, maar ook meer algemene geleidingstoomisse, te verstaan.

Diabetic retinopathy is an ischemic retinal neovascular disease causing vision loss among adults. The studies presented involve the design and testing of a gene therapy vector to inhibit retinal revascularization, similar to that found in diabetic retinopathy. Gene therapy has proven to be an effective method to introduce therapeutic proteins to treat retinal diseases. Targeting a specific cell type and expression of therapeutic proteins according to the tissue microenvironment should have an advantage over traditional gene therapy by avoiding unwanted transgene expression. Hypoxia plays a significant role in the pathophysiology of many retinal ischemic diseases. Retinal Mèuller cells provide structural and functional support to retinal neurons, as well as playing a significant role in retinal neovascularization. Targeting Mèuller cells may be an effective strategy to prevent retinal neovascularization under pathological conditions. ... The hypoxia regulated, glial specific vector successfully reduced the abnormal neovascularization in the periphery by 93% and reduced the central vasobliterated area by 90%. A substantial amount of exogenous endostatin was produced in the retinas of P17 OIR mice. A significant increase in human endostatin protein and reduced vascular endothelial growth factor (VEGF) were identified by Western blot and ELISA, respectively. These findings suggest hypoxia-regulated, glial cell-specific scAAV mediated gene expression may be useful to prevent blindness found in devastating retinal diseases involving neovascularization. / by Manas Ranjan Biswal. / Thesis (Ph.D.)--Florida Atlantic University, 2012. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

Coronaviruses are a diverse group of large, single-stranded RNA virus that cause respiratory and enteric diseases in mammalian and avian species. Phylogenetic analysis shows that SARS-CoV is an unique branch of coronavirus showing no close relationship to other groups of coronaviruses. The genome size of SARS-CoV is about 30 kilobase and the genome, like other coronaviruses, is composed of replicase (rep), spike (S), envelope (E), membrane (M) and nucleocapsid (N) and 8 additional unknown open reading frames (ORFs) (ORF 3a, ORF 3b, ORF 6, ORF 7a, ORF 7b, ORF8a, ORF 8b and ORF 9b). The 3a gene, the largest unknown ORF, encodes a viral protein which is predicted to be a transmembrane protein. In this study, we showed that the 3a protein was expressed in SARS patients' lung and intestinal tissues, and it is localized to the endoplasmic reticulum (ER) in 3a-transfected monkey kidney Vero E6 cells. Results from experiments including chromatin condensation, DNA fragmentation and antibody microarray suggest that the 3a protein may trigger apoptosis through a caspase-8-dependent pathway and possibly a PKR-mediated FADD-caspase-8 pathway. Our data show that over-expression of the SARS-CoV protein can induce apoptosis in vitro. / Severe acute respiratory syndrome (SARS), an atypical form of pneumonia, is first recognized in Guangdong Province, China in November 2002 and later spread to Hong Kong in mid February 2003. It is believed that the etiological agent of SARS is a previously unknown coronavirus - SARS-CoV. Over 8,400 cases and 789 deaths were reported to World Health Organization (WHO) from over 28 countries around the world including Hong Kong. Up to now, there are still no efficient antiviral drugs to treat the disease, and the detailed pathology of SARS-CoV infection and the host response to the viral infection are still unknown. During the epidemic, we have done complete genome sequencing for five SARS-CoV isolates and we postulate that at least two SARS-CoV strains with distinct etiological origins exist in the environment during the epidemic. / Law Tit-wan Patrick. / "Aug 2005." / Adviser: Stephen K. W. Tsui. / Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3594. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 156-172). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract in English and Chinese. / School code: 1307.

by Peter, Wei Gong Chang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 103-124). / ACKNOWLEDGEMENTS --- p.i / ABSTRACT --- p.ii / TABLE OF CONTENTS --- p.iv / ABBREVIATIONS --- p.viii / Chapter CHAPTER 1 --- INTRODUCTION / Chapter 1.1 --- General introduction --- p.1 / Chapter 1.2 --- Human genome project --- p.5 / Chapter 1.3 --- Human adult heart cDNA library --- p.7 / Chapter 1.4 --- Human fetal heart cDNA library --- p.8 / Chapter 1.5 --- Sequencing of a human heart cDNA clone --- p.9 / Chapter 1.6 --- Knowledge of the role of selenium --- p.13 / Chapter 1.7 --- Mouse 56kDa selenium binding protein and acetaminophen-binding protein --- p.16 / Chapter CHAPTER 2 --- MATERIALS AND METHODS / Chapter 2.1 --- Plating out the cDNA library --- p.20 / Chapter 2.1.1 --- "Mediums, buffers and solutions" --- p.20 / Chapter 2.1.2 --- Bacteriophage clones preparation --- p.21 / Chapter 2.2 --- cDNA clone amplification by PCR --- p.23 / Chapter 2.3 --- Cycle sequencing of PCR products --- p.25 / Chapter 2.3.1 --- "Media, buffers and solutions" --- p.25 / Chapter 2.3.2 --- Preparation of sequencing reaction --- p.25 / Chapter 2.4 --- Gel electrophoresis using an automated A.L.F sequencer --- p.27 / Chapter 2.5 --- DNA sequence analysis --- p.29 / Chapter 2.6 --- Preparation of competent E. coli for transformation --- p.30 / Chapter 2.7 --- Transformation of plasmid into competent E. coll --- p.31 / Chapter 2.8 --- Mini-preparation of plasmid DNA --- p.32 / Chapter 2.9 --- Large scale plasmid DNA preparation by QIAGEN --- p.34 / Chapter 2.10 --- Cloning the human 56 kDa selenium binding protein (hSP56) into the pAED4 vector --- p.36 / Chapter 2.10.1 --- Bacterial strains and vector --- p.36 / Chapter 2.10.2 --- "Media, buffers and solutions" --- p.38 / Chapter 2.10.3 --- Primers design and PCR --- p.42 / Chapter 2.10.4 --- Purification of PCR products by Geneclean --- p.43 / Chapter 2.10.5 --- Restriction digestion of purified PCR product and pAED4 --- p.44 / Chapter 2.10.6 --- Ligation and transformation of hSP56 --- p.45 / Chapter 2.10.7 --- Screening and purification ofpAED4hSP56. --- p.47 / Chapter 2.11 --- Expression of hsp56 --- p.50 / Chapter 2.11.1 --- Induction of hSP56 expression --- p.50 / Chapter 2.11.2 --- SDS-PAGE and protein detection --- p.51 / Chapter 2.12 --- Northern hybriddization of hSP56 --- p.53 / Chapter 2.12.1 --- Animals & human tissue --- p.53 / Chapter 2.12.2 --- "Mediums, buffers and solutions" --- p.53 / Chapter 2.12.3 --- Preparation of total RNA --- p.56 / Chapter 2.12.4 --- Formaldehyde agarose gel electrophoresis --- p.57 / Chapter 2.12.5 --- Preparation of radioactive probe --- p.58 / Chapter 2.12.6 --- RNA transfer and Northern hybridization --- p.59 / Chapter 2.13 --- Chromosomal mapping of the hSP56 gene --- p.62 / Chapter CHAPTER 3 --- RESULTS / Chapter 3.1 --- The sequencing results of 553 cDNA clones --- p.63 / Chapter 3.2 --- Catalogues of genes expressed --- p.65 / Chapter 3.3 --- Sequence analysis of hSP56 --- p.71 / Chapter 3.4 --- Northern hybridization of hSP56 --- p.84 / Chapter 3.5 --- Cloning of hSP56 into pAED4 --- p.87 / Chapter 3.6 --- Expression of the hSP56 in E. coli --- p.89 / Chapter 3.7 --- Chromosomal mapping of the hSP56 gene --- p.92 / Chapter CHAPTER 4 --- DISCUSSION / Chapter 4.1 --- General discussion --- p.94 / Chapter 4.2 --- The possible roles of hSP56 and mSP56 --- p.101 / Chapter 4.3 --- Future prospects --- p.102 / REFERENCES --- p.103 / APPENDIX 1 --- p.125 / APPENDIX.2 --- p.127

[Truncated abstract] Narrow-leaf lupin (Lupinus angustifolius L.) was first recorded as having been introduced into Germany during the mid-19th century for use as green manuring and as fodder crops. However, it was not until post World-War I that there was any serious attempt to domesticate the species. Since that time several key domestication genes have been incorporated to enable the species to be grown as a crop over a range of climates, harvested as a bulk commodity and, the seed used for both animal and human consumption. However, the recent domestication of this species has seen a rather limited use of wild germplasm largely as a result of the difficulty in retaining these key domestication genes. To make the task of retaining these genes manageable, it was decided to resort to molecular technology. A mapping population of F8 derived recombinant inbred lines (RILs) has previously been established by the Department of Agriculture and Food, Western Australia, from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin. The parents together with 89 RILs (of a population of 115) were subjected to DNA fingerprinting using microsatelliteanchored fragment length polymorphism (MFLP) to rapidly generate DNA markers for construction of a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 8 or more markers. ... Five pairs of QTLs were found to be involved in epistasis, 2 of these having an effect on early vigour and another 3 influencing the time to opening of the first florets. Variation explained for each trait ranged from 28% for seed size, to 88% for days to flowering. We showed that it was possible to use this data to predict genotypes of superior progeny for these traits under Mediterranean conditions. QTL regions were compared on a second published linkage map and regions of conserved synteny with the model legume Medicago truncatula high-lighted. The work presented in this thesis demonstrates the importance of tight linkage between markers and genes of interest. It is especially important when dealing with genetically diverse material as found in the wild. One of the main problems faced by molecular scientists is the phenomenon known as linkage disequilibrium in marker populations caused by either small population size or 4 insufficient opportunity for recombination. This frequently results in the development of markers with little or no application outside of the population in which it was developed. Although the relatively small size of the population used in this study exposes it to such constraints, in this case excellent and valuable results were achieved in developing useful markers to at least 3 of the domestication traits within a relatively short time period of less then 4 years.