Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The deterioration of harvested sugarcane as a result of bacterial growth causes major losses of sucrose and a build-up of exopolysaccharides (EPS). Polysaccharides present during production increase the massecuite viscosity, which negatively influences evaporation and crystallisation. In this study 38 culturable EPSproducing bacteria were isolated from milled sugarcane. Analysis of the EPS showed the ubiquitous presence of glucose, however, 14 polysaccharides also contained mannose, fructose or galactose. In vitro treatment using Chaetomium erraticum dextranase to evaluate is effectiveness indicated that 37 of the EPS were hydrolysed to some extent. There were 21 polysaccharides that were only partially digested. The capacity of the isolates to produce EPS on different sugars indicated a correlation between sucrose and polysaccharide formation in 37 isolates. The results indicate there are more species involved in EPS production than previously thought as well as the presence of non-dextran polysaccharides. / AFRIKAANSE OPSOMMING: Bakteriële groei veroorsaak ‘n afname in gehalte, sukrose en ‘n verhoging in die hoeveelheid van eksternepolisakkeriede (EPS). Die verhoogde konsentrasie van polysakkariede gedurende die verwerkingsprosses veroorsaak ‘n verhoging in “massecuite” viskositeit. Hierdie verskynsel het ‘n nadelige uitwerking op die verdamping en kristalvorming van die produk. In gemaalde skuikerriet was 38 groeibare EPS-produserende bakterieë geisoleer. Die geanaliseerde EPS van hierdie bogenoemde bakterieë was daar in almal glukose teenwoordig. In 14 van hulle was mannose, fruktose en galaktose ook gevind. Die in vitro effektiwieteit van Chaetomium erraticum dekstranase op die EPS het gewys dat 37 het tot ‘n mate gehidroliseer maar 21 was net gedeeltelik verteer. As gevolg van die bo-genoemde resultate was daar gevind dat sukrose was ‘n noodsaaklike subtraat vir EPS produksie in die geisoleerde bakterieë. In hierdie studie was bevestig ‘n groter verskiedenheid EPS-produserende bakterieë gevind was en dat hulle assosiasie aan sukierriet prossering meer kompleks is as wat vooreen gedink was.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Plant diseases are among the major causes of food insecurity. In South Africa the wheat fungal diseases including stem rust caused by Puccinia graminis f. sp. tritici, leaf rust caused by P. triticina and stripe rust caused by P. striiformis f. sp. tritici are the most important. Genetic resistance is a viable way of protecting wheat crops against the wheat rusts, especially cultivars carrying multiple genes that confer durable resistance. In order to breed for multi-gene resistance an effective breeding strategy that allows for selecting multiple resistance genes and other desirable traits needs to be devised. The aim of this study was to identify a number of genotypes with combinations of different rust resistance genes, good grain yield and end-use quality out of an existing pre-breeding population and thereby identify superior parents. In order to achieve the stated aim the following objectives have been identified: identify wheat lines through marker-assisted selection (MAS) carrying the gene complexes, Sr31/Lr26/Yr9, Lr24/Sr24, Lr37/Sr38/Yr17, Lr34/Yr18 and Sr2; to develop inbred lines to evaluate selected lines under field trials. From the initial subset of 64 lines, 60 were chosen and advanced to the doubled haploid (DH) phase and seed multiplication. The 60 lines either carried one or more of the three rust resistance gene complexes. The genes that were the most prominent were Sr31/Lr26/Yr9 and Lr24/Sr24. The selected lines were incorporated into a DH seed multiplication phase. After 4 cycles of seed increases and preliminary field evaluation during multiplication, 15 lines were chosen and subjected to multi-location field trails. The extensive multi-location field trails carried out in this study aided in identifying genotypes from the 15 MS-MARS lines with good adaptability and stability in regards to yield and baking quality. An important observation was that the molecular markers employed to indentify quality loci correlated well with the genes encoding the HMW-GS 5, 10 and 12 as observed with the Agilent© 2100 Bioanalyzer. In future studies the lines which performed the best could be re-introduced into the existing MSMARS pre-breeding programme of the Stellenbosch University’s Plant Breeding Laboratory (SUPBL). The frequencies of desired alleles could be increased in this manner. Since the majority of these characteristics are influenced by quantitatively inherited alleles, using these lines as recurrent parents will increase the frequencies of these alleles in the existing SU-PBL pre-breeding population. / AFRIKAANSE OPSOMMING: Plantsiektes is van die belangrikste oorsake van voedselonsekerheid ter wêreld. In Suid-Afrika is die roesswamme van die belangrikste plantsiektes wat koring produksie beïnvloed. Hierdie siektes sluit in, stamroes wat veroorsaak word deur Puccinia graminis f. sp. tritici, blaarroes wat veroorsaak word deur P. triticina en streeproes wat veroorsaak word deur P. striiformis f. sp. tritici. Genetiese weerstand is ‘n uitstekende manier om koring te beskerm teen hierdie swamsiektes. Weerstand wat gebasseer is op veelvuldige weerstandsgene is veral ‘n goeie middel om genetieseweerstand op ‘n volhoubare basis in koringteling toe te pas. Om veelvuldige weerstandsgene in koringkultivars in te teel word ‘n effektiewe telingstrategie benodig. Die doel van die studie was om genotipes te identifiseer met kombinasies van veelvuldige weerstandsgene vir roes, sowel as goeie eienskappe belangrik vir graanopbrengs en bakkwaliteit. Lyne is geïdentifiseer uit ‘n bestaande voortelingspopulasie van Stellenbosch Universiteit se Planteteelt Laboratorium (SU-PTL) wat geteel was met spesifiek weerstand en opbrengs potensiaal in gedagte. Om die doel van die studie te bereik is sekere doelwitte daar gestel. Hierdie doelwitte sluit in om lyne uit die populasie te selekteer deur middel van merker bemiddelde seleksie (MBS) vir gene naamlik Sr31/Lr26/Yr9, Lr24/Sr24, Lr37/Sr38/Yr17, Lr34/Yr18 en Sr2; om die geselekteerde lyne suiwertelend te maak; sowel as om die suiwertelende lyne in veld proewe in te sluit. Van die oorspronklike stel van 64 lyne, is 60 gekies vir verdere studie. Deur middel van die verdubbelde haploïed (VH) tegniek is die lyne suiwertelend gemaak. Die 60 lyne het een of meer van die geselekteerde gene bevat. Die mees prominente gene was die twee geen komplekse Sr31/Lr26/Yr9 en Lr24/Sr24. Na vier siklusse van saadvermeerdering en voorloppige seleksies is 15 lyne ingesluit by ‘n multi-omgewing veldproef. Hierdie uitgebreide multi-omgewing veldproewe het gehelp om individue uit die 15 lyne te identifiseer wat oor goeie aanpasbaarheid en stabiliteit beskik met betrekking tot opbrengs en bak kwaliteit. Die molekulêre merkers gebruik om die gene verantwoordelik vir die kodering van HMGGS 5, 10 en 12 op te spoor het goed gekorreleer met die HMG-GS bande bepaal met behulp van die Agilent© 2100 Bioanalyzer. Toekomstige studies kan moontlik insluit die gebruik van die lyne wat geïdentifiseer was met goeie kenmerke in die bestaande MS-MARS teelprogram van die SU-PTL. Die frekwensies van die verlangde allele kan op hierdie manier in die populasie verhoog word.

O cultivo de trigo (Triticum aestivum L.) tem grande importância no sistema agrícola da região sul, sendo responsável por cerca de 95% da produção de trigo no Brasil. Nesses estados, a variabilidade climática é muito expressiva, fazendo com que os cultivares respondam de maneira diferenciada nos diversos ambientes de cultivo, ocasionando muitas vezes diminuição da produção, produtividade e afetando a qualidade tecnológica de trigo, durante a permanência da cultura na lavoura. Logo para que um cultivar tenha sucesso este deve apresentar estabilidade e elevada produtividade além de qualidade superior, uma vez que a aptidão tecnológica representa uma oportunidade de agregar valor de mercado ao trigo, principalmente em face do mercado internacional e do setor industrial. Baseado nisso, este trabalho teve por objetivos investigar, através de revisão de literatura, quais fatores pré-colheita afetam a qualidade tecnológica do trigo; comparar diferentes métodos (paramétricos e não paramétricos) de adaptabilidade e estabilidade, na seleção de cultivares mais estáveis e responsivos às condições de ambiente e; verificar a influência de variáveis metereológicas sobre a qualidade tecnológica. Conclui-se que os fatores genéticos, meteorológicos e de manejo são determinantes para a obtenção da qualidade desejada. Neste sentido, a adequada escolha do cultivar, o conhecimento das limitações climáticas da região de cultivo e da fertilidade do solo e a execução dos tratos culturais recomendados pela pesquisa, podem contribuir substancialmente para a obtenção das características físicas, químicas e biológicas que conferem qualidade à farinha de trigo e aos produtos que dela derivam. Também, foi possível observar que os métodos de Lin e Binns (1988) e de Eberhart e Russel (1966) foram mais informativos na identificação de cultivares de trigo mais produtivos, adaptados e estáveis, quando comparados aos métodos de ecovalência e de Cruz et al. (1989). Com relação à influência das variáveis meteorológicas sobre a qualidade tecnológica do trigo, observou-se que a precipitação pluvial, a temperatura máxima, a temperatura mínima e a radiação solar promoveram acréscimos e, também, em alguns casos, limitaram a expressão da qualidade tecnológica dos cultivares de trigo avaliados no estado do Paraná. As estimativas de associação entre os parâmetros de qualidade tecnológica e variáveis meteorológicas foram diferentes entre os locais avaliados, tanto no sentido, quanto na magnitude da associação. Desta forma, conclui-se que, através da escolha adequada do cultivar (adaptado, estável e com o potencial genético de qualidade desejado), da execução das práticas de manejo essenciais (fertilidade do solo, rotação de culturas e controle de plantas daninhas, pragas e doenças) e do conhecimento dos períodos em que as condições meteorológicas são mais prejudiciais, nos diferentes locais de cultivo, é possível maximizar tanto a qualidade tecnológica, quanto a produtividade, do trigo no estado do Paraná. / Wheat (Triticum aestivum L.) growing has great importance in the agricultural system of the southern region of Brazil, and is responsible for about 95% of the country’s wheat yield. Climatic variability is very expressive in the southern states. Wheat cultivars therefore respond differently in the various environments where they are grown, and this is often the cause of decreased production and productivity, affecting the technological quality of wheat during the period when the crop remains in the field. Consequently, for a wheat cultivar to be successful it must be stable, provide high productivity, and have superior quality, since technological aptitude represents an opportunity for added market value, especially in face of the international market and the industrial sector. Based on that, this study aimed to investigate, by means of a literature review, which preharvest factors affect the technological quality of wheat; compare different adaptability and stability methods (both parametric and non-parametric) in the selection of cultivars more stable and responsive to environmental conditions; and determine the influence of weather variables on wheat technological quality. It was concluded that genetic, weather, and management factors are crucial in obtaining the desired quality. In this respect, the selection of an adequate cultivar, knowledge about the climatic limitations of the wheat-growing region and soil fertility, and accomplishing the management practices recommended by research can substantially contribute toward obtaining the physical, chemical, and biological characteristics that lend quality to flour and flour-based products. In addition, the Lin and Binns (1988) and Eberhart and Russel (1966) methods were more informative in the identification of more productive, adapted and stable wheat cultivars, as compared to the ecovalence and Cruz et al. (1989) methods. As to the influence of weather variables on wheat technological quality, it was observed that precipitation, maximum temperature, minimum temperature, and solar radiation provided increases and, in some cases, limited the technological quality expression of wheat cultivars evaluated in the State of Paraná. The estimates of associations between technological quality parameters and weather variables were different among the localities evaluated, both in the meaning and the magnitude of the association. It is thus concluded that by adequately choosing a cultivar (adapted, stable, and with the desired genetic potential for quality), performing essential management practices (soil fertility, crop rotation, and control of weeds, pests, and diseases), and knowing the periods when weather conditions are more detrimental in the various cultivation localities, both the technological quality and the productivity of wheat can be maximized in the State of Paraná.

A podridão parda, causada pelo fungo Monilinia fructicola (Wint.) Honey, é a principal doença das fruteiras de caroço (Prunus spp.) uma vez que pode ser encontrada em praticamente todos os pomares, causando severas perdas aos fruticultores. Os principais sintomas dessa doença são a queima das flores, cancros e lesões nos ramos e podridões nos frutos. Assim, os prejuízos econômicos da podridão parda podem ocorrer desde a floração, estendendo-se até as fases de pré e pós-colheita dos frutos. Este trabalho teve por objetivos (i) testar a reação de diversos genótipos de pessegueiro á podridão parda, identificando-se os resistentes e/ou com tolerância à podridão parda em flores; (ii) identificar possíveis fontes de resistência e/ou tolerância a essa doença em frutos; e (iii) identificar os mecanismos de resistências associados as características físicas, químicas e bioquímicas em frutos de pessegueiro; iv) identificar genótipos com características bioquímicas superiores; v) estudar a divergência genética dos genótipos de pessegueiro. O trabalho foi realizado no Laboratório de Fitossanidade, da Universidade Tecnológica Federal do Paraná – Campi Dois Vizinhos e Pato Branco nos ciclos produtivos 2009/2010 e 2010/2011. Os genótipos analisados pertencem coleção de pessegueiro implantado na área experimental da UTFPR, no município de Pato Branco, PR. Foram testados 5 e 16 genótipos no primeiro e no segundo ciclo, respectivamente, quanto à reação á podridão parda nas flores. Quanto à reação da doença nos frutos foram testados 26 e 29 genótipos de pessegueiro nos ciclos produtivos 2009/2010 e 2010/2011, respectivamente. Os testes da reação dos genótipos a doença para ambos os órgãos (flores e frutos) foram realizados avaliando-se a incidência nas flores e a incidência e severidade nos frutos após a inoculação do patógeno. Os frutos foram avaliados quanto às características físico-químicas e bioquímicas, sendo estudadas as possíveis correlações entre as variáveis epidemiológicas e de qualidade dos mesmos. Os genótipos foram caracterizados quanto aos componentes bioquímicos. Também se estudou a divergência genética entre os genótipos tanto pelas variáveis epidemiológicas quanto pelas características bioquímicas. Pelos resultados obtidos, houve diferentes níveis de respostas quanto à suscetibilidade a podridão parda em flores, sendo que os genótipos „Cascata 1070‟ e „Cascata 1055‟ foram os que apresentaram menor suscetibilidade a mesma, tendo assim potencial de uso em pomares ou como genitores em futuros programas de melhoramento. Frutos dos genótipos „Tropic Beauty‟, „Cascata 962‟, „Conserva 1187‟, „Kampai‟, „Cascata 1063‟, „Tropic Snow‟ e „Rubimel‟ foram os que apresentaram menor incidência e severidade a podridão parda nos ciclos produtivos 2009/2010 e 2010/2011, indicando-as como tolerantes a doença. Não houve correlação entre a incidência de podridão parda nas flores e incidência e severidade da doença nos frutos. Houve correlação entre o teor de SST, pH, açúcares redutores e totais, teor de aminoácido e a enzima FAL para respostas dos frutos quanto à podridão parda. / The brown rot caused by the fungus Monilinia fructicola (Wint.) Honey, is the main disease in stone fruit trees (Prunus spp.). It can be found in almost all fruit orchards, causing severe losses to fruit growers. The main symptoms of this disease are the blossom blight, twig cankers and necrosis and, fruits rot. Thus, the economic losses of brown rot may occur since flowering, extending to the pre-and post-harvest fruit phases. The aim of this study were (i) to test the brown rot reaction of different peach genotypes, identifying the resistant or tolerant ones to brown rot on flowers, (ii) to identify resistance and/or tolerance sources to this fruit disease and (iii) to identify resistance mechanisms associated with the physical, chemical and biochemical characteristics in peach fruits, iv) to identify superior genotypes for biochemical characteristics; v) to study the genetic divergence of peach genotypes on the UTFPR collection. The work was carried out at Laboratório de Fitossanidade, Universidade Tecnológica Federal do Paraná (UTFPR) – Campi Dois Vizinhos and Pato Branco, in the 2009/2010 and 2010/2011 production cycles. The genotypes analyzed were the peach collection of the UTFPR, in Pato Branco, PR. Five and 16 genotypes were tested in the first and second cycles, respectively, in relation for flowers brown rot reaction. For fruit disease reaction 26 and 29 peach genotypes were tested in the production cycles 2009/2010 and 2010/2011, respectively. The tests aimed to evaluate the flower incidence and the fruits incidence and severity, after pathogen inoculation. The physical-chemical and biochemical fruit characteristic, and were evaluated as well as their relation if any with epidemiological variables. Genotypes were also determined by biochemical fruit characteristics. The genetic divergence among peach genotypes for epidemiological variables and biochemical fruit characteristics was also studied. Different levels of susceptibility to blossom blight were obtained, being the 'Cascata 1070' and 'Cascata 1055' the ones with lowest susceptibility, demonstrating potential for use in orchards or as parents in future breeding programs. The 'Tropic Beauty', 'Cascata 962', 'Conserva 1187', 'Kampai', 'Cascata 1063', 'Tropic Snow' and 'Rubimel' peach genotypes showed the lowest incidence and severity for brown rot in the 2009/2010 and 2010/2011 cycles, which indicates them as disease possible tolerant. There was no correlation between the blossom blight incidence percentage and the brown rot fruit incidence and severity. There were correlation between TSS, pH, reducing sugars, total amino acid content and PAL enzyme for brown rot reaction.

Artemisia annua L. é uma espécie vegetal herbácea nativa da Ásia que possui folhas aromáticas que contém artemisinina, uma lactona sesquiterpênica que tem demonstrado eficácia contra doenças como câncer e malária. Para atender a demanda pela molécula, técnicas de manejo e melhoramento genético podem ser utilizadas para obtenção de genótipos superiores. Os objetivos deste estudo foram: obter genótipos de A. annua de alto rendimento de artemisinina e biomassa por meio da indução de poliploidia utilizando colchicina; analisar a expressão de genes relacionados com as vias de biossíntese em artemisina em plantas sob diferentes níveis nutricionais; realizar um ensaio a campo visando identificar genótipos de alto rendimento para artemisinina e biomassa. A indução de poliploidia foi realizada em sementes de A. annua e na cultivar Artemis (F2) com solução de colchicina 1% nas doses de 0%, 0,05%, 0,1%, 0,15% e 0,2% durante 0, 6, 12,18, 24 e 30 horas, totalizando 25 tratamentos. Para análise da expressão gênica foi utilizada a técnica de RT-PCR semiquantitativa onde os genótipos B23, B24, C23, C32 foram submetidos, em casa de vegetação, a diferentes doses de solução nutritiva, sendo utilizados 25%, 50% e 100% da dose completa (solução de Hoagland), com 3 repetições em delineamento inteiramente casualizado. Para o ensaio a campo, os mesmos genótipos e a cultivar Artemis (F2) foram analisados em delineamento de blocos ao acaso com quatro repetições. Foram realizadas, em todos os experimentos, avaliações agronômicas, fisiológicas e fitoquímicas. Foi constatado efeito da colchicina no teor de artemisinina, sendo o valor máximo 0,60% para a dose de 0,10% sendo que não foi possível afirmar se houve poliploidização. Na avaliação da produção de metabólitos secundários e a expressão dos genes de enzimas envolvidas na síntese de artemisinina dos genótipos de A. annua submetidos a diferentes níveis de nutrição observou-se que a aplicação de doses crescentes de solução nutritiva para plantas de A. annua possibilita incremento linear para produção de biomassa, com relação contrária na produção de artemisinina. Genótipos submetidos à níveis nutrição de 50% apresentam melhor relação para a produção de biomassa e artemisinina e óleo essencial. Os genes ADS1 e CYP71AV aumentam a transcrição em plantas submetidas a níveis de 50% de solução nutritiva. No experimento de seleção de genótipos superiores a campo, foi possível observar que a variedade Artemis (F2) apresentou melhor desempenho em produtividade de biomassa e óleo essencial que os demais genótipos. A maior produção de biomassa para Artemis (F2) justifica o maior rendimento de óleo essencial. Essa variedade possui arquitetura de planta diferenciada das demais, apresentando maior estatura e maior adensamento entre ramos. / Artemisia annua L. is a native herbaceous plant species from Asia that has aromatic leaves containing artemisinin, a sesquiterpene lactone that has shown efficacy against diseases such as cancer and malaria. To meet the demand for the molecule, management techniques and genetic improvement can be used to obtain superior genotypes. The objectives of this study were: to obtain A. annua genotypes with high yield of artemisinin and biomass by inducing polyploidy using colchicine; to analyze the genes expression related to artemisin biosynthesis pathways in plants under different nutritional levels; to perform a field assay to identify high yield genotypes for artemisinin and biomass. The polyploidy induction was tested in A. annua seeds and Artemis F2 variety with colchicine solution in 1% on doses of 0%, 0.05%, 0.1%, 0.15% and 0.2% for 0, 6, 12, 18, 24 and 30 hours, totaling 25 treatments. For gene expression analysis, a semi-quantitative RT-PCR technique was used, where the B23, B24, C23, C32 genotypes were submitted to different doses of nutrient solution in a greenhouse, using 25%, 50% and 100% of the complete dose (Hoagland's solution), with 3 replicates in a completely randomized design. To the field assay the same genotypes and variety Artemis F2 were tested in randomized block design with four replications. Agronomic, physiological and phytochemical evaluations were performed in all experiments. It has been found colchicine effect on artemisinin content, with maximum 0.60% for 0.10% dose, and it was not possible to confirm if polyploidization occurred. In the assessment of the production of secondary metabolites and the genes expression of enzymes involved in the synthesis of artemisinin from A. annua genotypes submitted to different levels of nutrition, it was observed the application of increasing doses of nutrient solution to A. annua plants allows linear increase for the production of biomass, with a contrary relation in the artemisinin production. Genotypes submitted to nutrition levels of 50% present better relation for the production of biomass, artemisinin and essential oil. The genes ADS1 and CYP71AV increase transcription in plants submitted to 50% levels of nutrient solution. These enzymes are directly involved in the artemisinin biosynthesis pathway. In the experiment of selecting superior genotypes, it was observed the variety Artemis F2 showed better performance in productivity of biomass and essential oil than other genotypes. The increased production of biomass for Artemis F2 justifies the higher oil yield. This variety has a differentiated plant architecture from the others, with greater height and greater density of branches.

O cultivo de trigo (Triticum aestivum L.) tem grande importância no sistema agrícola da região sul, sendo responsável por cerca de 95% da produção de trigo no Brasil. Nesses estados, a variabilidade climática é muito expressiva, fazendo com que os cultivares respondam de maneira diferenciada nos diversos ambientes de cultivo, ocasionando muitas vezes diminuição da produção, produtividade e afetando a qualidade tecnológica de trigo, durante a permanência da cultura na lavoura. Logo para que um cultivar tenha sucesso este deve apresentar estabilidade e elevada produtividade além de qualidade superior, uma vez que a aptidão tecnológica representa uma oportunidade de agregar valor de mercado ao trigo, principalmente em face do mercado internacional e do setor industrial. Baseado nisso, este trabalho teve por objetivos investigar, através de revisão de literatura, quais fatores pré-colheita afetam a qualidade tecnológica do trigo; comparar diferentes métodos (paramétricos e não paramétricos) de adaptabilidade e estabilidade, na seleção de cultivares mais estáveis e responsivos às condições de ambiente e; verificar a influência de variáveis metereológicas sobre a qualidade tecnológica. Conclui-se que os fatores genéticos, meteorológicos e de manejo são determinantes para a obtenção da qualidade desejada. Neste sentido, a adequada escolha do cultivar, o conhecimento das limitações climáticas da região de cultivo e da fertilidade do solo e a execução dos tratos culturais recomendados pela pesquisa, podem contribuir substancialmente para a obtenção das características físicas, químicas e biológicas que conferem qualidade à farinha de trigo e aos produtos que dela derivam. Também, foi possível observar que os métodos de Lin e Binns (1988) e de Eberhart e Russel (1966) foram mais informativos na identificação de cultivares de trigo mais produtivos, adaptados e estáveis, quando comparados aos métodos de ecovalência e de Cruz et al. (1989). Com relação à influência das variáveis meteorológicas sobre a qualidade tecnológica do trigo, observou-se que a precipitação pluvial, a temperatura máxima, a temperatura mínima e a radiação solar promoveram acréscimos e, também, em alguns casos, limitaram a expressão da qualidade tecnológica dos cultivares de trigo avaliados no estado do Paraná. As estimativas de associação entre os parâmetros de qualidade tecnológica e variáveis meteorológicas foram diferentes entre os locais avaliados, tanto no sentido, quanto na magnitude da associação. Desta forma, conclui-se que, através da escolha adequada do cultivar (adaptado, estável e com o potencial genético de qualidade desejado), da execução das práticas de manejo essenciais (fertilidade do solo, rotação de culturas e controle de plantas daninhas, pragas e doenças) e do conhecimento dos períodos em que as condições meteorológicas são mais prejudiciais, nos diferentes locais de cultivo, é possível maximizar tanto a qualidade tecnológica, quanto a produtividade, do trigo no estado do Paraná. / Wheat (Triticum aestivum L.) growing has great importance in the agricultural system of the southern region of Brazil, and is responsible for about 95% of the country’s wheat yield. Climatic variability is very expressive in the southern states. Wheat cultivars therefore respond differently in the various environments where they are grown, and this is often the cause of decreased production and productivity, affecting the technological quality of wheat during the period when the crop remains in the field. Consequently, for a wheat cultivar to be successful it must be stable, provide high productivity, and have superior quality, since technological aptitude represents an opportunity for added market value, especially in face of the international market and the industrial sector. Based on that, this study aimed to investigate, by means of a literature review, which preharvest factors affect the technological quality of wheat; compare different adaptability and stability methods (both parametric and non-parametric) in the selection of cultivars more stable and responsive to environmental conditions; and determine the influence of weather variables on wheat technological quality. It was concluded that genetic, weather, and management factors are crucial in obtaining the desired quality. In this respect, the selection of an adequate cultivar, knowledge about the climatic limitations of the wheat-growing region and soil fertility, and accomplishing the management practices recommended by research can substantially contribute toward obtaining the physical, chemical, and biological characteristics that lend quality to flour and flour-based products. In addition, the Lin and Binns (1988) and Eberhart and Russel (1966) methods were more informative in the identification of more productive, adapted and stable wheat cultivars, as compared to the ecovalence and Cruz et al. (1989) methods. As to the influence of weather variables on wheat technological quality, it was observed that precipitation, maximum temperature, minimum temperature, and solar radiation provided increases and, in some cases, limited the technological quality expression of wheat cultivars evaluated in the State of Paraná. The estimates of associations between technological quality parameters and weather variables were different among the localities evaluated, both in the meaning and the magnitude of the association. It is thus concluded that by adequately choosing a cultivar (adapted, stable, and with the desired genetic potential for quality), performing essential management practices (soil fertility, crop rotation, and control of weeds, pests, and diseases), and knowing the periods when weather conditions are more detrimental in the various cultivation localities, both the technological quality and the productivity of wheat can be maximized in the State of Paraná.

A podridão parda, causada pelo fungo Monilinia fructicola (Wint.) Honey, é a principal doença das fruteiras de caroço (Prunus spp.) uma vez que pode ser encontrada em praticamente todos os pomares, causando severas perdas aos fruticultores. Os principais sintomas dessa doença são a queima das flores, cancros e lesões nos ramos e podridões nos frutos. Assim, os prejuízos econômicos da podridão parda podem ocorrer desde a floração, estendendo-se até as fases de pré e pós-colheita dos frutos. Este trabalho teve por objetivos (i) testar a reação de diversos genótipos de pessegueiro á podridão parda, identificando-se os resistentes e/ou com tolerância à podridão parda em flores; (ii) identificar possíveis fontes de resistência e/ou tolerância a essa doença em frutos; e (iii) identificar os mecanismos de resistências associados as características físicas, químicas e bioquímicas em frutos de pessegueiro; iv) identificar genótipos com características bioquímicas superiores; v) estudar a divergência genética dos genótipos de pessegueiro. O trabalho foi realizado no Laboratório de Fitossanidade, da Universidade Tecnológica Federal do Paraná – Campi Dois Vizinhos e Pato Branco nos ciclos produtivos 2009/2010 e 2010/2011. Os genótipos analisados pertencem coleção de pessegueiro implantado na área experimental da UTFPR, no município de Pato Branco, PR. Foram testados 5 e 16 genótipos no primeiro e no segundo ciclo, respectivamente, quanto à reação á podridão parda nas flores. Quanto à reação da doença nos frutos foram testados 26 e 29 genótipos de pessegueiro nos ciclos produtivos 2009/2010 e 2010/2011, respectivamente. Os testes da reação dos genótipos a doença para ambos os órgãos (flores e frutos) foram realizados avaliando-se a incidência nas flores e a incidência e severidade nos frutos após a inoculação do patógeno. Os frutos foram avaliados quanto às características físico-químicas e bioquímicas, sendo estudadas as possíveis correlações entre as variáveis epidemiológicas e de qualidade dos mesmos. Os genótipos foram caracterizados quanto aos componentes bioquímicos. Também se estudou a divergência genética entre os genótipos tanto pelas variáveis epidemiológicas quanto pelas características bioquímicas. Pelos resultados obtidos, houve diferentes níveis de respostas quanto à suscetibilidade a podridão parda em flores, sendo que os genótipos „Cascata 1070‟ e „Cascata 1055‟ foram os que apresentaram menor suscetibilidade a mesma, tendo assim potencial de uso em pomares ou como genitores em futuros programas de melhoramento. Frutos dos genótipos „Tropic Beauty‟, „Cascata 962‟, „Conserva 1187‟, „Kampai‟, „Cascata 1063‟, „Tropic Snow‟ e „Rubimel‟ foram os que apresentaram menor incidência e severidade a podridão parda nos ciclos produtivos 2009/2010 e 2010/2011, indicando-as como tolerantes a doença. Não houve correlação entre a incidência de podridão parda nas flores e incidência e severidade da doença nos frutos. Houve correlação entre o teor de SST, pH, açúcares redutores e totais, teor de aminoácido e a enzima FAL para respostas dos frutos quanto à podridão parda. / The brown rot caused by the fungus Monilinia fructicola (Wint.) Honey, is the main disease in stone fruit trees (Prunus spp.). It can be found in almost all fruit orchards, causing severe losses to fruit growers. The main symptoms of this disease are the blossom blight, twig cankers and necrosis and, fruits rot. Thus, the economic losses of brown rot may occur since flowering, extending to the pre-and post-harvest fruit phases. The aim of this study were (i) to test the brown rot reaction of different peach genotypes, identifying the resistant or tolerant ones to brown rot on flowers, (ii) to identify resistance and/or tolerance sources to this fruit disease and (iii) to identify resistance mechanisms associated with the physical, chemical and biochemical characteristics in peach fruits, iv) to identify superior genotypes for biochemical characteristics; v) to study the genetic divergence of peach genotypes on the UTFPR collection. The work was carried out at Laboratório de Fitossanidade, Universidade Tecnológica Federal do Paraná (UTFPR) – Campi Dois Vizinhos and Pato Branco, in the 2009/2010 and 2010/2011 production cycles. The genotypes analyzed were the peach collection of the UTFPR, in Pato Branco, PR. Five and 16 genotypes were tested in the first and second cycles, respectively, in relation for flowers brown rot reaction. For fruit disease reaction 26 and 29 peach genotypes were tested in the production cycles 2009/2010 and 2010/2011, respectively. The tests aimed to evaluate the flower incidence and the fruits incidence and severity, after pathogen inoculation. The physical-chemical and biochemical fruit characteristic, and were evaluated as well as their relation if any with epidemiological variables. Genotypes were also determined by biochemical fruit characteristics. The genetic divergence among peach genotypes for epidemiological variables and biochemical fruit characteristics was also studied. Different levels of susceptibility to blossom blight were obtained, being the 'Cascata 1070' and 'Cascata 1055' the ones with lowest susceptibility, demonstrating potential for use in orchards or as parents in future breeding programs. The 'Tropic Beauty', 'Cascata 962', 'Conserva 1187', 'Kampai', 'Cascata 1063', 'Tropic Snow' and 'Rubimel' peach genotypes showed the lowest incidence and severity for brown rot in the 2009/2010 and 2010/2011 cycles, which indicates them as disease possible tolerant. There was no correlation between the blossom blight incidence percentage and the brown rot fruit incidence and severity. There were correlation between TSS, pH, reducing sugars, total amino acid content and PAL enzyme for brown rot reaction.

Submitted in fulfillment of the requirements of the Master of Information and Communications Technology degree in Information Technology, Durban University of Technology, Durban, South Africa, 2017. / This dissertation reports on the original study that undertakes the development of a frugal information system to support subsistence farmers through the use of the Agricultural Production Systems Simulator (APSIM) as a support tool to assist them in optimal strategic decisions making. The field of agriculture is vast and in-depth and a number of critical factors like soil type, rainfall and temperature are involved that farmers have to take into account. Farmers persistently face the challenges of increasing and sustaining yields to meet with the populaces demand with often limited resources, which makes strategic decisions on what to plant, when to plant, where to plant and how to plant in a particular season imperative. The way in which this study attempts to solve this agricultural decision making problem is with the use of the APSIM. This technology platform provides an advanced simulation of agricultural systems that can enable subsistence farmers to simulate a number of variables ranging from plant types, soil, climate and even management interactions. This research presents a frugal web-based crop planning decision support system that subsistence farmers can take advantage with the use of the APSIM. The APSIM platform was used to run simulations for various regions with the results containing the expected level of success along with other useful information for a specified crop in the vicinity, using state of the art software platforms and tools ranging from Google Maps application programming interfaces, Microsoft’s model view controller framework, JavaScript and others. The validity of this system was tested through a number of design science methods including structural testing and illustrative scenarios, show capability of the information system. The results obtained from this evaluation show a small but powerful tool that has the capability of servicing a multitude of farmers with crop management decisions. / M

<p>Plant microbiomes are increasingly recognized for their potential to help plants with critical functions such as nutrient acquisition. Nitrogen is the most limiting nutrient in agriculture and growers apply substantial amounts to meet crop needs. Only 50% of N fertilizers are generally taken up by plants and the rest is subject to loss which negatively affects environmental quality. Organic fertilizers such as cover crops and animal manure can help reduce this loss, though these materials must mineralize via microbial mediated processes before they are available for plant uptake, which makes managing fertility using these sources difficult. Some plants can scavenge nutrients from organic materials by stimulating positive priming processes in soil. Carrot (<i>Daucus carota.</i> L) is known as an N scavenging crop, making it an ideal model crop to study these interactions. In a greenhouse trial, soils were amended with an isotopically labeled corn residue to track N movement, and planted with one of five carrot genotypes expected to differ in nitrogen use efficiency (NUE). Changes in soil b-glucosidase activity, ammonium (NH₄⁺-N) and nitrate (NO₃^--N) concentrations, soil bacterial community composition, weight and carbon and N concentrations, and total δ¹⁵N of above and below ground carrot biomass were determined. Results indicate that there are genetic differences in the ability of carrots to promote priming under N limited conditions, which could be exploited to enhance NUE in carrots. Soil microbial communities differed between genotypes, indicating that some of these microbes could play a role in the differential N scavenging responses observed, and/or contribute to other important functions such as resistance to pests. Endophytic microbes residing inside carrot taproots also have potential to contribute to NUE and other benefits, but are notoriously difficult to isolate and culture. New next generation sequencing technologies have revolutionized the study of microbiomes, though using these tools to study bacterial endophytes in plants is still difficult due to co-amplification of plant organelles. Consequently, a second study was conducted to determine if subjecting carrot tissues to hollow fiber microfiltration followed by enzymatic digestion could enhance recovery and amplification of bacterial endophytes. Carrot taproot digests were subject to amplification using a standard V3-V4 16S primer set, as well as two alternative (blocking and mismatch) primer sets that have prevented amplification of plastids/mitochondria in other plant species. Results indicate that the microfiltration/digestion procedure can increase the number of bacterial endophyte OTUs assigned and could be further optimized for use in carrots. The blocking and mismatch primer sets were not as effective in blocking co-amplification of plant products as they are in other studies, possibly due to the presence of a high number of chromoplasts in carrot tissues. Taxonomic assignment of bacterial endophytes differed significantly between the primer sets, indicating that multiple primer sets may be needed to fully characterize these communities in carrots. The enzymatic digestion procedure could artificially inflate certain taxa, which could be helpful if targeting specific taxa. These studies demonstrate that carrots are intimately connected with microbes residing in the soil and within their taproots, and further exploration of these plant-soil-microbial relationships could enhance the yield and sustainability of carrot production systems.</p>

Precise engineering of genomes holds great promise to advance our understanding of gene function and biotechnological applications. DNA double strand breaks are repaired via imprecise non-homologous end joining repair or via precise homology-directed repair processes. Therefore, we could harness the DSBs to engineer the genomes with a variety of genetic outcomes and with singlebase- level precision. The major barrier for genome engineering was the generation of site-specific DNA DSBs. Programmable DNA enzymes capable of making a complete and site-specific cut in the genome do not exist in nature. However, these enzymes can be made in in vitro as chimeric fusions of two modules, a DNA binding module and a DNA cleaving module. The DNA cleaving module can be programmed to bind to any user-defined sequence and the DNA cleaving module would generate DSBs in the target sequence. These enzymes called molecular scissors include zinc finger nucleases (ZFNs) and transcriptional activator like effector nucleases (TALENs). The programmability of these enzymes depends on protein engineering for DNA binding specificity which may be complicated, recourse intensive and suffer from reproducibility issues. Recently, clustered regularly interspaced palindromic repeats (CRISPR)/ CRISPR associated endonuclease 9 (Cas9) an adaptive immune system of bacterial and archaeal species has been developed for genome engineering applications. CRISPR/Cas9 is an RNA-guided DNA endonuclease and can be reprogrammed through the engineering of single guide RNA molecule (sgRNA). CRISPR/Cas9 activity has been shown across eukaryotic species including plants. Although the engineering of CRISPR/Cas9 is quite predictable and reproducible, there are many technological challenges and improvements that need to be made to achieve robust, specific, and efficient plant genome engineering. Here in this thesis, I developed a number of technologies to improve specificity, delivery and expression and heritability of CRISRP/Cas9-modification in planta. Moreover, I used these technologies to answer basic questions to understand the molecular underpinning of the interplay between splicing and abiotic stress. To improve Cas9 specificity, I designed and constructed a chimeric fusion between catalytically dead Cas9 (dCas9) and FOKI catalytic DNA cleaving domain (dCas9.FoKI). This synthetic chimeric fusion enzyme improved Cas9 specificity which enable precision genome engineering. Delivery of genome engineering reagents into plant cells is quite challenging, I developed a virus-based system to deliver sgRNAs into plants which facilitates plant genome engineering and could bypass the need for tissue culture in engineering plant genomes. To improve the expression of the CRISPR/Cas9 machinery in plant species, I developed a meiotically-driven expression of CRISPR/Cas9 which improved genome editing and heritability of editing in seed progeny, thereby facilitating robust genome engineering applications. To understand the molecular basis of the interplay between splicing stress and abiotic stress, I used the CRISPR/Cas9 machinery to engineer components of the U2snRNP complex coupled which chemical genomics to understand the splicing stress regulation in response to abiotic stress conditions. Finally, I harnessed the technological improvements and developments I have achieved with CRISPR/Cas9 system to develop a directed evolution platform for targeted trait engineering which expands and accelerates trait discovery and engineering of plant species resilient to climate change conditions.