Orientador: Sandra Helena Unêda-Trevisoli / Coorientador: Ignácio José de Godoy / Coorientador: Marcos Doniseti Michelotto / Banca: Ivana Marino Bárbaro Torneli / Banca: Gustavo Vitti Môro / Resumo: O amendoim (Arachis hypogaea L.) é uma cultura oleaginosa de grande importância para o agronegócio brasileiro. Um dos principais fatores que afetam sua produção é a incidência de pragas, com destaque para o tripes-do-prateamento, Enneothrips flavens, Moulton, 1941 (Thysanoptera: Thripidae). Têm-se sugerido que genes que condicionam a resistência genética a esta praga, podem ser encontrados em outras espécies do gênero Arachis L. Entretanto, a utilização de espécies silvestres no melhoramento, torna-se dificultada por barreiras de esterilidade, sendo a maioria devido às diferenças de constituição do genoma e de ploidia. Para contornar essa incompatibilidade, sugeriu-se a obtenção de anfidiploides, resultantes do cruzamento de espécies diploides, seguido da duplicação de seus cromossomos, para então cruzá-los com o amendoim cultivado. Mediante o exposto, este trabalho teve como objetivos estudar o potencial de resistência ao tripes-do-prateamento em populações segregantes iniciais do cruzamento envolvendo a cultivar comercial IAC 503 e o anfidiploide sintético (A. magna x A. cardenasii)4x, monitorar os caracteres indicadores de proximidade agronômica dos segregantes interespecíficos com genótipos da espécie cultivada, bem como a seleção de genótipos superiores por meio de análises uni e multivariadas. Os experimentos foram conduzidos no esquema de blocos aumentados de Federer com testemunhas intercalares em duas gerações: F3, conduzida no ano agrícola de 2013/14 e F4, conduzida... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The peanut (Arachis hypogaea L.) is an oilseed crop of great importance for Brazilian agribusiness. One of the main factors affecting its production is pests incidence, mainly thrips, Enneothrips flavens, Moulton, 1941 (Thysanoptera: Thripidae). There have suggested that genetic resistance to this pest can be found in other species of the genus Arachis L. However, the use of wild species in breeding was hampered by sterility barriers, mostly due to differences in the genome constitution and ploidy. To work around this incompatibility, it was suggested obtaining amphidiploid, resulting from the crossing of diploid species, followed by duplication its chromosomes, and then cross them with cultivated peanut. Through the above, this study aimed to study the potential for resistance to thrips in early segregating populations crossing involving commercial cultivar IAC 503 and synthetic amphidiploid (A. magna x A. cardenasii) 4x, monitor the agronomic traits proximity indicators of interspecific segregating with cultivated species, as well as the selection of superior genotypes using univariate and multivariate analyses. The experiments were conducted on the Federer augmented blocks with additional checks in two generations: F3, conducted in the agricultural year of 2013/14 and F4, conducted in 2014/15, under natural insect infestation. The thrips resistance was evaluated by its infestation, and the symptoms of injuries caused by insects. It was also evaluated, some production compo... (Complete abstract click electronic access below) / Mestre

The occurrence of Boron (B) toxicity in Australian soils is recognised as a limiting factor for cereal productivity. A number of loci conferring tolerance to B toxicity have been identified in barley and chromosomally mapped. However, a lack of knowledge relating to the physiological and molecular events that occur under B toxicity and the molecular basis for B stress tolerance has been a bottleneck in harnessing available genetic diversity in barley and wheat. The recent advances in functional genomics provided an opportunity to examine B stress in barley in more detail. The aim of this project was to analyse genes differentially expressed under B stress in tolerant and intolerant barley to identify candidate genes involved in B toxicity tolerance. Two experimental approaches, Suppression Subtractive Hybridization (SSH) and microarray were adopted. Firstly, SSH was performed to examine gene expression in roots of selected tolerant and intolerant doubled haploid lines from a Clipper (B intolerant) X Sahara 3771 (B tolerant) mapping population, grown under moderate B stress. The SSH experiment aimed to investigate the early transcriptional response of B tolerant barley lines to B stress in order to identify the basis for B toxicity tolerance in roots. Differential screening of the subtracted library generated from B treated plants identified a total of 111 non-redundant clones up-regulated in bulked tolerant lines. On the other hand 94 clones were differentially expressed under non-treated conditions. Among the clones identified from subtracted library generated from B treated plants, metabolism was the largest functional category, representing 21% of the clones. The largest functional category in the subtracted library generated from non treated plants was cellular transport, representing 19% of the clones. Based on sequence similarity, about 170 transcripts identified in this experiment were assigned to chromosomal segments (bins) on the three homoeologous genomes of bread wheat. In total, 36 clones from the subtracted library generated from B treated plants were analysed as candidates. Nine were genetically mapped within the region of B tolerance QTL on three chromosomes (2H, 4H and 6H). The genes mapped to 4H and 6H QTL have the highest association with these loci in the Clipper X Sahara 3771 doubled haploid mapping population. A 4H B tolerance QTL candidate gene was identified as a B transporter gene with similarity to the Arabidopsis BOR1 gene. Genes identified to be differentially expressed in the tolerant lines from SSH suggest activation of a diverse defence response in the roots of barley plants under B stress. Data from SSH experiment indicate that cell wall-plasma membrane cytoskeleton continuum constitute the first action site against B toxicity and the influence of toxic B on K+ uptake could be the key initiating factor. In the second approach, the Affymetrix 22K Barley1 GeneChip(TM) was used to investigate B stress adaptation processes in barley. Gene expression was profiled in leaves of Sahara 3771 and Clipper plants grown under various B concentrations. The results show that the two genotypes respond differently to B toxicity. The B intolerance of Clipper is expressed through the induction of a high number of probe sets (2310) even at a low B concentration of 100 µM. In contrast, Sahara 3771 responded to a high B concentration (2000 µM) through the induction of only a few hundred (266) probe sets. In Sahara 3771 no change in the expression level of any probe sets was observed at 100 µM B. Altogether 286 probe sets showed differential expression in Sahara 3771 under three levels of B treatment (500, 1000 and 2000 µM). About 30% of these were down-regulated and about 70% were up-regulated in Sahara 3771 in response to B treatment. Most of the probe sets (59%) up-regulated in Sahara 3771 did not respond to B treatment in Clipper. These genes are either salt stress responsive or related to plant defense and thus could play a key role in protecting barley plants from the toxic effects of B. Two differentially expressed probe sets annotated as B transporters were identified between Sahara 3771 and Clipper under control condition. These two B transporter probe sets did not respond to B treatment but showed opposing expression patterns in the two varieties. One of these probe sets (Contig21126_at) is similar to the B transporter gene isolated from the SSH experiment that maps to the 4H tolerance locus. The map location and expression of this B transporter gene suggest that it could be the borate anion efflux transporter predicted by the proposed efflux model of B tolerance in Sahara 3771 barley. The other B transporter gene (Contig14139_at) showed over expression in Clipper under control condition and could be contributing to high B accumulation in Clipper which needs further investigation. Data from both experiments have indicated that B toxicity triggers oxidative stress and that jasmonate-based signaling plays a key role in B toxicity tolerance. SSH data indicate that Sahara 3771 which evolved in the harsh environment of Africa is more efficient in osmoregulation and ROS scavenging than Clipper. This trait is likely to give Sahara 3771 an edge over Clipper in tolerating toxic the effect of B. In addition to the efflux mechanism, which becomes less efficient with increasing B supply, Sahara 3771 appears to apply a number of other mechanisms for alleviating or withstanding toxic B induced stress to sustain growth. Some of these mechanisms are already known to be used by plants to cope with a number of stresses. / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

Striga, a genus of obligate parasitic weeds in the family Orobanchaceae, has been identified as the most important biological factor limiting agricultural productivity in sub-Saharan Africa. Germination of Striga seeds is triggered by strigolactone root exudates from host plants. Strigolactones also induce hyphal branching in arbuscular mycorrhizal (AM) fungi, which are important for plant uptake of phosphorus in low phosphorus soils. Mechanisms of Striga resistance based on reduced strigolactone production may also convey resistance to AM fungi which would require higher inputs of phosphorus fertilizer to attain optimal crop growth. There is evidence for genetic differences in mycorrhizal responsiveness in other grain crops; therefore it is beneficial for breeders to be aware of these differences when developing Striga-resistant sorghum cultivars. This research aims to determine phosphorus and mycorrhizal responsiveness of sorghum genotypes important for or developed by breeders working on Striga resistance. Phosphorus response curves were determined for twelve sorghum genotypes using pasteurized low phosphorus soil amended to achieve four different phosphorus levels. Simple linear regression was performed on root and shoot dry weight data. Results indicate variability in phosphorus responsiveness within Striga resistant and susceptible genotypes. Seven of these genotypes were selected for continued research, which analyzed responsiveness to phosphorous and differences in mycorrhizal responsiveness in relation to reported mechanisms of Striga resistance. Treatments included three levels of phosphorus amendments and the addition of Funneliformis mosseae inoculum. All genotypes were strongly responsive to P amendment when grown without AM fungi and showed a decrease in responsiveness to P when inoculated with F. mosseae. Trends for all genotypes indicate a greater uptake of P, Zn, and Mg by mycorrhizal plants as compared to nonmycorrhizal plants. All seven genotypes were responsive to mycorrhizae, with a significant increase in biomass for all genotypes, especially at the lowest phosphorus level. The responsiveness to the mycorrhizal fungus does not appear to be directly related to the susceptibility of genotypes to the parasitic weed Striga. / Graduation date: 2012

Cotoneaster is an ornamental shrub valued for showy flowers, berries and architecture as well as the ability tolerate adverse conditions under which other taxa fail. Cotoneaster is a highly diverse genus of over 400 species, of which few are available in the US nursery trade. Some species commercially available have been identified as potentially invasive in the state of Oregon and also are susceptible to the bacterial disease fire blight. Cotoneaster selections with reduced fertility and disease resistance would be desirable characteristics for low input landscape plants. A goal of my research was to characterize Cotoneaster spp. to provide information for the rationale planning and development of novel clones to meet these horticultural goals. In the first study, genome sizes were estimated using flow cytometery and ploidy levels were inferred using holoploid genome size. Observed differences in monoploid genome sizes translate to a difference in chromosome size. Differences in chromosome size may present a reproductive barrier when they are large. This may pose a challenge in wide crosses, but may be utilized to achieve sterility in the F1 interspecific hybrid population. Differences in genome size are not related to taxonomic ordering, so wide inter sectional and inter subgeneric crosses may be possible. In the second study, susceptibility of Cotoneaster to fire blight was measured on plants inoculated with Erwinia amylovora strain Ea153. In greenhouse assays conducted over two years, plants were inoculated by cutting leaves with scissors infested with the pathogen. Some species were 'highly susceptible' to fire blight where plants were killed to the ground, and others were rated 'highly resistant' and no lesions were observed. Seventeen accessions were rated as resistant to fire blight This research provides the first report of ploidy, genome sizes, and susceptibility of species of Cotoneaster to fire blight. Collectively this research provides a toolbox for a breeder to tackle the challenge of creating disease resistant cultivars with reduced fertility. / Graduation date: 2013

Victoria blight, caused by fungus Cochliobolus victoriae, is a disease originally described on oats and recapitulated on Arabidopsis. Victoria blight is used as a model plant disease that conforms to an inverse gene-for-gene interaction. C. victoriae virulence is dependent upon its production of victorin, a host-specific toxin that induces programmed cell death in sensitive plants. In oats, victorin sensitivity and disease susceptibility is conferred by the Vb gene, which is genetically inseparable from the Pc-2 crown rust resistance gene. In Arabidopsis, victorin sensitivity and disease susceptibility is conferred by the LOCUS ORCHESTRATING VICTORIN EFFECTS 1 (LOV1) gene which encodes a NB-LRR protein, a type of protein commonly associated with disease resistance. LOV1-mediated cell death occurs when victorin binds Thioredoxin-h5 (TRX-h5) and LOV1 appears to "guards" TRX-h5. Together, these results suggest C. victoriae causes disease by inducing a resistance response. The work presented here aimed to determine if the response mediated by LOV1 is functionally related to a resistance response. We genetically characterized the response mediated by LOV1 with virus-induced gene silencing. We determined SUPPRESSOR OF THE G2 ALLELE OF SKP1 (SGT1), a gene required for the function of many resistance genes, is required for victorin sensitivity and involved in LOV1 protein accumulation. We screened a normalized library and identified six genes that suppressed victorin-mediated cell death and cell death induced by expression of the RESISTANCE TO PERONOSPORA PARASITICA PROTEIN 8 (RPP8) resistance gene: a mitochondrial phosphate transporter, glycolate oxidase, glutamine synthetase, glyceraldehyde 3-phosphate dehydrogenase and the P- and T-protein of the glycine decarboxylase complex. Silencing the latter four also inhibited cell death induced by the expression of an autoactive form of the resistance gene PTO, and reduced PTO-mediated resistance to Pseudomonas syringae pv. tabaci. These results provide evidence that victorin-mediated cell death is functionally similar to a resistance response, further supporting the hypothesis that a resistance response is exploited by C. victoriae for pathogenesis in Victoria blight. Resistance function of LOV1 was evaluated by observing Pseudomonas syringae pv. tomato virulence upon LOV1 activation. The LOV1 response pathway in Arabidopsis was adapted to activate upon infection with Pseudomonas syringae pv. tomato expressing the type III-dependent effector protein AvrRpt2, a well-characterized protease. We developed a construct to express a beta-glucuronidase (GUS) and TRX-h5 fusion protein separated by an AvrRpt2 proteolytic cleavage site, in which GUS sterically inhibits TRX-h5 function in LOV1-mediated cell death. The fusion is cleaved upon infection by P. syringae pv. tomato expressing avrRpt2, thereby leading to TRX-h5-mediated activation of LOV1 in the presence of victorin. However, when this strain was inoculated with victorin into transgenic LOV1 trx-h5 plants expressing the GUS/TRX-h5 fusion protein, no decrease in pathogen virulence was observed. Technical shortcomings likely prevented observable LOV1 resistance function. ��� / Graduation date: 2013 / Access restricted to the OSU Community at author's request from Oct. 9, 2012 - Oct. 9, 2013

[No abstract available] / xi, 176 leaves : ill. (chiefly col.) ; 29 cm

Progress in tree biotechnology initially trailed behind agricultural crops due to their long life cycle, difficult tissue culture and regeneration protocols, and their abundance in natural forests. However, rapid global deforestation rates, together with an increased world demand for pulp, paper and timber products, have prompted scientific and commercial focus to improve genetic timber stocks. South Africa, a tree-poor country (where indigenous forests are protected), has relied almost solely on exotic plantations to meet its demand for timber. A pioneer study investigating the feasibility of using direct (biolistic) and indirect (Agrobacterium-mediated) methods for gene transfer was undertaken in Pinus patula Schiede et Deppe, a Mexican softwood and a forerunner for saw timber, pulpwood and paper in the South African forest industries. The aim of the transformation methods was to impart herbicide resistance to the trees. This was achieved via the introduction of a bar-GUS pAHC25 cassette under the control of the ubiquitin promoter. To provide target material for transformation, two in vitro micropropagation pathways were used: somatic embryogenesis and organogenesis. Both embryonal suspensor masses (ESM) and somatic embryos at various stages of development were initially used as target explants for the biolistic study using an established in vitro protocol. A stepwise selection was implemented in order to allow transformed (particularly bombarded) cultures the opportunity to regenerate under selection pressure using MSG3 maintenance medium supplemented with BASTA® herbicide at 1 mg l ¯¹ followed by 3 mg l¯¹ active ingredient at the next subculture. Biolistic transgene delivery was more efficient when sorbitol was included in the pre-bombardment medium enabling use of higher vacuum and shooting pressures, without lowering the regeneration potential of ESM significantly. Bombarded material from two genotypes (Lines 2 and 3) was regenerated to produce mature somatic embryos using an optimized regeneration regimen. The indirect study with Agrobacterium tumefaciens (LBA4404), transformed with the pAHC25 vector via triparental mating or heat shock, used a variety of target tissues including: mature somatic embryos, ESM and mature zygotic embryos (MZE's) - a novel in vitro system for P. patula. The Agrobacterium-mediated method resulted in optimized decontamination conditions using a combination of liquid MSG3 (or sterile dH₂O for mature embryos) supplemented with 500 mg l ¯¹ cefotaxime, with rotation, and sterile 65 mm Whatman No. 3 filter paper stacks, which avoided excess filtering and stress to transformation material. Further efforts to aid regeneration during the indirect study included L-proline post-transformation, though no mature somatic embryos were regenerated at the conclusion of the Agrobacterium-mediated study. Recovery of transformed ESM in both studies was best during the active growth phase 4-6 d after subculture. Regeneration with good somatic embryo potential was an exigent aspect in both transformation studies. Expression of positive histochemical GUS activity in all transformed material was confirmed by polymerase chain reaction (PCR) analysis indicating that Pinus patula tissue was amenable to transformation. A new bar PCR regime was implemented in P. patula. In the biolistic study, a higher transformation efficiency of bar amplicons (53%) than GUS amplicons (45%) was observed, reflecting their non-linked status on the pAHC25 transformation vector. This is the first report of biolistic transformation of P. patula that will allow for the production of transgenic ESM. The production of transgenic P. patula holds great promise for commercial development in the South African forestry industry. The application of transgenic trees in the timber industry is numerous but the aims most relevant to P. patula include wood modification and disease resistance to pathogens like pitch canker fungus. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

Maize (Zea mays L.) streak virus disease (MSD) is the most important virus disease in Africa but farmers are unaware of its status. A project was initiated to assess the current status of MSD and to breed for its resistance. Four populations comprised of two BC1F1 and two F2 progenies developed by backcrossing and selfing the F1 progenies of two crosses between a donor line (CMl 202) and two susceptible lines (CMl 321 and CMl 384) were developed. Conventional and molecular marker assisted selection (MAS) methods were used to screen for resistance to MSD in each of the four populations. To facilitate unbiased comparison, separate screening nurseries were established for MAS and conventional screening. The objectives of the study were five-fold; 1) to assess the status of MSD in Uganda and understand farmers' preferences and varietal selection criteria for maize using a participatory rural appraisal (PRA), 2) to screen for MSD resistance in early generations of segregating maize populations using conventional method, 3) to screen for resistance to MSD using SSR marker assisted selection , 4) to compare the effectiveness of marker assisted selection and conventional methods for selection for resistance to MSD, and 5) to compare costs associated with MAS and conventional selection methods. Results of PRA showed that unreliable rainfall and insect pests were the dominant constraints to maize productivity in Uganda. Diseases were ranked fifth among the production constraints . Maize streak virus disease was considered the most important disease constraint. Farmers showed common preference for high yielding and early maturing cultivars. However, farmers had other special preferences which were diverse and included large, white and high test density kernels for marketing, and sweet taste, particularly for home consumption. Farmers' research priorities included tolerance to drought, resistance to insect pests and diseases, sweetness, prolificacy, resistance to lodging, and drooping leaves because theyt cover the soil fast and prevent weed growth. Conventional screening for resistance to MSD showed that backcross and selfing populations segregated in 1:1 and 3:1 Mendelian ratios confirming the presence of one major gene with simple inheritance . Severity and incidence of disease were positively correlated suggesting a non-reference by the insects. In the selfing populations, the presence of complete esistance against MSD was suggested because frequency distribution patterns were highly skewed in favour of resistance. There was a decrease in disease severities with selection from BC1F1 to BC2F1 and from F2 to F3 generations indicating that high response to selection was achieved. On the other hand, one marker, umc1917, consistently polymorphic and eo-dominant was selected and used in MAS protocol. Results showed that the observed outcomes fitted the expected ratio of 1:2:1 for a F2 population and 1:1 for a BC1F1 population (X2 not significant). Evaluation of F3 and BC2F1 progeny selected using markers showed low disease severity suggesting that marker assisted selection was effective. However, the study showed that the presence of the O'Tl, was not consistent with symptom expression in the field. Evaluation of lines in three-way crosses identified ten potential lines that were high yielding, highly resistant to MSD and stable across three locations. Both MAS and conventional selection were equally effective in identifying high yielding lines although resistance was higher under MAS. Costs of MAS and conventional method varied depending on the units for comparison. The total costs of conventional method were higher than that of MAS in both first and second selection cycles. Comparing costs per row for conventional and costs per plant or data point for MAS showed that conventional selection was 2.4 times more expensive than costs per sample for MAS. However, costs per plant for MAS were 6.6 times higher than for conventional selection. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2006

In Southern Africa and Mozambique, tropical lowland accounts for 22% and 65%, respectively, of area under maize production, but grain yield is compromised by downy mildew disease (DM, which is caused by Peronosclerospora sorghi (Weston and Uppal) Shaw), and lack of appropriate varieties, especially hybrids. Among other factors, productivity can be enhanced by deploying DM resistant hybrids, which are higher yielding than open pollinated varieties. Development of a viable hybrid-breeding programme requires knowledge of genetic effects governing yield and DM resistance in inbreds, and effective germplasm management requires heterotic groups and heterotic patterns to be established. In addition, knowledge of farmer-preferred traits is required. Currently, such information is not available to the hybrid-breeding programme in Mozambique. The objectives of this study were, therefore; i) to identify farmers’ preferred variety traits and major production constraints, ii) to determine combining ability effects of inbred maize S4 lines for grain yield and DM resistance, iii) to determine heterotic groups and heterotic patterns among the elite inbred maize lines, and iv) to investigate gene effects governing resistance to DM in breeding source inbred maize lines from the breeding programme in Mozambique. During 2007/08, 142 households were involved in a survey conducted in three districts representing two maize agro-ecological zones in Mozambique. Formal surveys and informal farmer-participatory methods were employed and data subjected to analysis in the SPSS computer programme. Results indicated that there was a low utilization of improved varieties, especially hybrids, with grain yield estimated at 0.7 t ha-1. Farmers were aware of the major production constraints and could discriminate constraints according to their importance for their respective communities. For the lowland environment, farmers identified downy mildew, drought, and cutworm and stem borer damage as the main constraints. In contrast, for the high altitude environments, they ranked ear rot, seed and fertilizer availability, turcicum leaf blight, grey leaf spot diseases and low soil fertility among the major constraints limiting productivity. The most important variety selection criteria were grain yield, short growth cycle, white and flint grain with stress tolerance to drought, low soil fertility, diseases, and grain weevils. These afore mentioned traits, would be priority for the breeding programmes for the lowland and mid altitude environments in Mozambique. To determine combining ability for downy mildew resistance, heterotic groups and heterotic patterns, two testers (open-pollinated varieties) ZM523 (Z) and Suwan-1 (S), were crossed with 18 lines to generate 36 top crosses for evaluation. Crosses were evaluated at two sites under DM. Preponderance of GCA effects indicated that additive gene effects were more important than non-additive gene effects in governing both grain yield and downy mildew resistance in the new maize lines. Based on specific combining ability (SCA) data, lines for yield were classified into two heterotic groups, S and Z; whereas based on heterosis data, lines were fitted into three heterotic groups (S, Z and SZ). Further heterotic patterns and gene action for yield were determined by subjecting nine inbred lines and the two testers, S and Z, to an 11 x 11 diallel-mating scheme. The diallel crosses, three hybrid checks and the two testers were evaluated in six environments in Mozambique. Results revealed that non-additive gene effects were predominant for yield components. In addition, high levels of heterosis for yield was observed and three heterotic groups identified (Z, S and S/Z), and five exceptional heterotic patterns among the inbred elite maize lines were observed. Topcrosses with yield levels comparable to single cross hybrids were also identified, and these would be advanced in the testing programme with potential for deployment as alternative cheaper and sustainable technology to conventional hybrids for the poor farming communities in Mozambique. To determine gene effects for downy mildew resistance in potential breeding lines, two maize populations were derived from crosses between downy mildew susceptible line LP67, and resistant lines DRAC and Suwan-L1. To generate F2 and backcross progenies (BCP1 and BCP2), F1 progenies were self-pollinated and simultaneously crossed to both inbred parents (P1 and P2). All the six generations (P1, P2, F1, F2, BCP1, and BCP2) of the populations were evaluated at two sites under downy mildew infection. A generation mean analysis was performed in SAS. It was revealed that downy mildew resistance was influenced by genes with additive and dominance effects, plus different types of epistatic effects such as additive x additive, and dominance x dominance. Overall results indicated that genes with predominantly non-additive effects controlled resistance in DRAC, whereas resistance in Suwan-L1 was largely influenced by additive gene effects. These findings have serious implications on the effective use of these downy mildew resistance sources in breeding programmes that aim to generate varieties with downy mildew resistance. Overall, results suggested that inbreeding and selection within heterotic groups, followed by hybridization between inbreds within and across heterotic groups would be effective to generate new hybrids. The breeding programme will consider development of conventional hybrids, such as single crosses and three way crosses, and top crosses. Implications of the findings of the study and recommendations are discussed. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010.

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.