Orientador: Marcelo Menossi Teixeira, Andrea Akemi Hoshino / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-21T05:45:50Z (GMT). No. of bitstreams: 1 Souza_CesarBuenode_D.pdf: 2755272 bytes, checksum: 945d7a45c10893c9a58603f1e04813ef (MD5) Previous issue date: 2012 / Resumo: O Brasil é o maior produtor mundial de cana-de-açúcar e no cenário atual, em que o aumento na busca por energia renovável é visível, o aumento na produtividade da cana é de extremo interesse para o setor sucroalcooleiro. Estresses abióticos influenciam grandemente a produtividade de espécies como a cana e, sendo assim, estudos relacionados com a tentativa de diminuir esse impacto na produtividade são de grande importância. A seca é o estresse ambiental que mais causa prejuízos ao agronegócio e por esse motivo é muito desejável que se desenvolvam novas variedades de cana-de-açúcar que sejam mais tolerantes a esses estresses e com isso o setor sucroalcooleiro será largamente beneficiado. A transgenia é uma das ferramentas utilizadas na produção de novos cultivares comerciais com características agronômicas interessantes e, para o seu sucesso, a identificação de genes com potencial para melhorar essas características faz-se necessária. Sendo assim, o maior objetivo desse trabalho foi a avaliação do potencial biotecnológico de seis genes de cana-de-açúcar que são modulados por seca. Os genes aqui estudados tiveram seu perfil de resposta a seca anteriormente avaliado por microarranjos de DNA e foram selecionados como candidatos para a produção de um novo cultivar de cana-de-açúcar que seja mais tolerante a estresses abióticos. Esses genes foram analisados em plantas transgênicas de tabaco, cana-de-açúcar e/ou Brachypodium. A superexpressão de dois genes de cana em tabaco conferiu maior tolerância a seca e salinidade das plantas transgênicas quando comparadas às selvagens e a proteção de seus usos na produção de plantas tolerantes a estresses abióticos foi solicitada. Há evidências de que um terceiro gene de cana conferira tolerância ao estresse oxidativo em plantas transgências de cana. Além disso, outros três genes de cana foram inseridos em Brachypodium, mas os eventos gerados ainda não foram avaliados. Com o trabalho desevolvido foi, portanto, possível gerar plantas transgênicas tolerantes a estresses abióticos e com isso é possível concluir que a seleção de genes candidatos para melhorias de características agronômicas de interesse através de microarranjos é algo que deve ser explorado e pode-se concluir, ainda, que alguns dos genes analisados estão envolvidos na resposta a seca e/ou aos estresses ambientais em geral / Abstract: Brasil is the largest producer of sugarcane in the world and the seeking for renewable energy is currently visible what makes the increase of sugarcane productivity highly desirable. Abiotic stresses greatly influence the productivity of species such sugarcane. Therefore, studies related to the reduction of these impacts on productivity are highly important. Drought is the environmental stress that causes more damage to agribusiness and because of it the development of new cultivars with higher tolerance to abiotic stresses is desirable since the sugar and ethanol sector will be largely benefited. Transgenic plants production is one of the tools that have been used in the development of new cultivars with interesting agronomic traits and for its success identifying genes that can improve these characteristics is necessary. Thus, the main objective of this study was evaluating the biotechnological potential of six drought-modulated genes from sugarcane. The genes studied here have their drought response profile previously showed by microarray and were selected as candidates for the production of a new sugarcane cultivar with higher tolerance to abiotic stresses. These genes were analyzed in transgenic tobacco, sugarcane and/or Brachypodium plants. The overexpression of two sugarcane genes in tobacco conferred higher drought and salinity tolerance in tobacco plants compared to wild-type and the protection of their uses in the production of plants with higher tolerance to abiotic stress was requested. There are evidences that a third sugarcane gene confers tolerance to oxidative stress in transgenic sugarcane. Furthermore, three other genes were inserted in Brachypodium but these transgenic events were not yet analyzed. With this work was possible to produce transgenic plants that are tolerant to abiotic stresses what let us to conclude that the selection of candidate genes to improve agronomic traits by microarrays is useful and that some of the analyzed genes are involved into drought and/or abiotic stresses in general responses / Doutorado / Genetica Vegetal e Melhoramento / Mestre em Genética e Biologia Molecular

Common bean is a major dietary component in several countries, but its productivity is negatively affected by abiotic stresses. Dissecting candidate genes involved in abiotic stress tolerance is a paramount step toward the improvement of common bean performance under such constraints. Thereby, this thesis presents a systematic analysis of the DEHYDRATION RESPONSIVE ELEMENT-BINDING (DREB) gene subfamily, which encompasses genes that regulate several processes during stress responses, but with limited information for common bean. First, a series of in silico analyses with sequences retrieved from the P. vulgaris genome on Phytozome supported the categorization of 54 putative PvDREB genes distributed within six phylogenetic subgroups (A-1 to A-6), along the 11 chromosomes. Second, we cloned four novel PvDREB genes and determined their inducibility-factors, including the dehydration-, salinity- and cold-inducible genes PvDREB1F and PvDREB5A, and the dehydration- and cold-inducible genes PvDREB2A and PvDREB6B. Afterwards, nucleotide polymorphisms were searched through Sanger sequencing along those genes, revealing a high number of single nucleotide polymorphisms within PvDREB6B by the comparison of Mesoamerican and Andean genotypes. The nomenclature of PvDREB6B is discussed in details. Furthermore, we used the BARCBean6K_3 SNP platform to identify and genotype the closest SNP to each one of the 54 PvDREB genes. We selected PvDREB6B for a broader study encompassing a collection of wild common bean accessions of Mesoamerican origin. The population structure of the wild beans was accessed using sequence polymorphisms of PvDREB6B. The genetic clusters were partially associated with variation in latitude, altitude, precipitation and temperature throughout the areas such beans are distributed. With an emphasis on drought stress, an adapted tube-screening method in greenhouse conditions enabled the phenotyping of several drought-related traits in the wild collection. Interestingly, our data revealed a correlation between root depth, plant height and biomass and the environmental data of the location of the accessions. Correlation was also observed between the population structure determined through PvDREB6B and the environmental data. An association study combining data from the SNP array and DREB polymorphisms enabled the detection of SNP associated with drought-related traits through a compressed mixed linear model (CMLM) analysis. This thesis highlighted important features of DREB genes in common bean, revealing candidates for further strategies aimed at improvement of abiotic stress tolerance, with emphasis on drought tolerance / O feijoeiro é um componente essencial na dieta em diversos países, no entanto, sua produção é afetada negativamente por estresses abióticos. O estudo de genes candidatos envolvidos na adaptação aos estresses é uma etapa fundamental para o melhoramento da performance do feijoeiro sob tais estresses. Desse modo, esta tese apresenta uma análise sistemática da subfamília de genes DEHYDRATION RESPONSIVE ELEMENT-BINDING (DREB), que reúne genes envolvidos em diversos processos em resposta a estresses, mas pouco estudados no feijoeiro. Primeiramente, uma série de análises in silico com sequências de feijoeiro obtidas da plataforma Phytozome possibilitaram a categorização de 54 genes PvDREB putativos, distribuídos em seis subgrupos (A-1 até A-6) nos 11 cromossomos da espécie. Posteriormente, quatro novos genes PvDREB foram clonados e seus padrões de inducibilidade foram determinados. PvDREB1F e PvDREB5A foram induzidos por desidratação, baixa temperatura e salinidade, enquanto PvDREB2A e PvDREB6B foram predominantemente induzidos por desidratação e baixa temperatura. Polimorfismos de nucleotídeos foram buscados através de sequenciamento por método derivado de Sanger, revelando elevado número de SNP no gene PvDREB6B. A nomenclatura desse gene foi discutida detalhadamente ao longo da tese. A plataforma de marcadores SNP BARCBean6K_3 foi acessada para identificar o SNP mais próximo de cada um dos 54 PvDREB. O gene PvDREB6B foi selecionado para um estudo mais amplo, envolvendo uma coleção de acessos selvagens de origem Mesoamericana. A estrutura populacional destes genótipos foi analisada a partir de polimorfismos na sequência de PvDREB6B. Os grupos genéticos apresentaram associação parcial com variação da latitude, altitude, precipitação e temperatura das áreas em que os acessos naturalmente ocorrem. Com ênfase no estudo do déficit hídrico, uma plataforma de fenotipagem destes acessos em casa de vegetação, utilizando um sistema de tubos plásticos, foi elaborada para a análise de diversos parâmetros relacionados ao estresse por déficit hídrico. Os dados revelaram correlação entre profundidade de raízes, altura das plantas e a biomassa e as variáveis ambientais de cada local. A correlação também foi detectada entre a estrutura populacional estudada por PvDREB6B e os dados ambientais. Finalmente, um estudo de associação genética foi realizado entre os SNP da plataforma e ligados a DREB e os parâmetros fenotípicos, permitindo a identificação de marcadores SNP associados a caracteres específicos, usando um modelo linear misto (CMLM). Esta tese apresentou importantes aspectos sobre os genes DREB em feijoeiro, revelando candidatos para seu uso em estratégias de melhoramento para tolerância a estresses abióticos, com ênfase em déficit hídrico

Philosophiae Doctor - PhD / Drought is the most complex phenomenon that remained to be a potential and historic challenge to human welfare. It affects plant productivity by eliciting perturbations related to a pathway that controls a normal, functionally intact biological process of the plant. Sorghum (Sorghum bicolor (L.) Moench), a drought adapted model cereal grass is a potential target in the modem agricultural research towards understanding the molecular and cellular basis of drought tolerance. This study reports on the genomic and proteomic findings of drought tolerance in sorghum combining the results from in silica and experimental analysis. Pipeline that includes mapping expression data from 92 normalized cDNAs to genomic loci were used to identify drought tolerant genes. Integrative analysis was carried out using sequence similarity search, metabolic pathway, gene expression profiling and orthology relation to investigate genes of interest. Gene structure prediction was conducted using combination of ab initio and extrinsic evidence-driven information employing multi-criteria sources to improve accuracy. Gene ontology was used to cross-validate and to functionally assign and enrich genes. An integrated approach that subtly combines functional ontology based semantic data with expression profiling and biological networks was employed to analyse gene association with plant phenotypes and to identify and genetically dissect complex drought tolerance in sorghum. The gramene database was used to identify genes with direct or indirect association to drought related ontology terms in sorghum. Where direct association for sorghum genes were not available, genes were captured using Ensemble Biomart by transitive association based on the putative functions of sorghum orthologs in closely related species. Ontology mapping represented a direct or transitive association of genes to multiple drought related ontology terms based on sorghum specific genes or orthologs in related species. Correlation of genes to enriched gene ontology (GO)-terms (p-value < 0.05) related to the whole-plant structure was used to determine the extent of gene-phynotype association across-species and environmental stresses.

Issues surrounding water scarcity will become topical in future as global fresh water resources become more limited thus threaten crop production. Predicted climate change and increasing population growth will place more pressure on agriculture to produce more food using less water. As such, efforts have now shifted to identifying previously neglected underutilised species (NUS) as possible crops that could be used to bridge the food gap in future. Taro (Colocasia esculenta L. Schott) and bambara groundnut (Vigna subterranea L. Verdc) currently occupy low levels of utilisation in South Africa. Both crops are cultivated using landraces with no improved varieties available. Information describing their agronomy and water–use is limited and remains a bottleneck to their promotion. The aim of this study was to determine the drought tolerance and water–use of selected landraces of taro and bambara groundnut from KwaZulu-Natal, South Africa. In order to meet the specific objectives for taro and bambara groundnut management, an approach involving conventional and modelling techniques was used. Three taro landraces [Dumbe Lomfula (DL), KwaNgwanase (KW) and Umbumbulu (UM)] were collected from the North Coast and midlands of KwaZulu-Natal, South Africa, in 2010. The UM landrace was classified as Eddoe type taro (C. esculenta var. antiquorum) characterised by a central corm and edible side cormels. The DL and KW landraces were classified as Dasheen (C. esculenta var. esculenta), characterised by a large edible main corm and smaller side cormels. A bambara groundnut landrace was collected from Jozini, KwaZulu- Natal, and characterised into three selections (‘Red’, ‘Light-brown’ and ‘Brown’) based on seed coat colour. Seed colour was hypothesised to have an effect on seed quality. Field and rainshelter experiments were conducted for both taro and bambara landraces at Roodeplaat in Pretoria and Ukulinga Research Farm in Pietermaritzburg, over two growing seasons (2010/11 and 2011/12). The objective of the field trials for taro and bambara groundnut was to determine mechanisms associated with drought tolerance in taro and bambara groundnut landraces. Experiments were laid out in a split-plot design where irrigation [fully irrigated (FI) and rainfed (RF)] was the main factor and landraces (3 landraces of either taro or bambara groundnut) were sub-factors. Treatments were arranged in a randomised complete block design (RCBD), replicated three times. Rainfed trials were established with irrigation to allow for maximum crop stand. Thereafter, irrigation was withdrawn. Whilst experimental designs and layouts for taro and bambara groundnut were similar, differences existed with regards to plot sizes and plant spacing. Trials were planted on a total land area of 500 m2 and 144 m2, for taro and bambara groundnut, respectively. Plant spacing was 1 m x 1 m for taro and 0.3 m x 0.3 m for bambara groundnut. Irrigation scheduling in the FI treatment was based on ETo and Kc and was applied using sprinkler irrigation system. Separate rainshelter experiments were conducted for taro and bambara groundnut landraces at Roodeplaat, to evaluate growth, yield and water-use of taro and bambara groundnut landraces under a range of water regimes. The experimental design was similar for both crops, a RCBD with two treatment factors: irrigation level [30, 60 and 100% crop water requirement (ETa)] and landrace (3 landraces), replicated three times. Irrigation water was applied using drip irrigation system based on ETo and Kc. Data collection in field and rainshelter trials included time to emergence, plant height, leaf number, leaf area index (LAI), stomatal conductance and chlorophyll content index (CCI). For taro field trials, vegetative growth index (VGI) was also determined. Yield and yield components (harvest index, biomass, corm number and mass) as well as water–use efficiency (WUE) were determined at harvest. Intercropping of taro and bambara groundnut was evaluated under dryland conditions using farmers’ fields at Umbumbulu, KwaZulu–Natal, South Africa. The experimental design was a RCBD replicated three times. Intercrop combinations included taro and bambara groundnut sole crops, a 1:1 (one row taro to one row bambara groundnut) and 1:2 intercrop combinations. The taro UM landrace and ‘Red’ bambara groundnut landrace selection were used in the intercropping study. Lastly, data collected from field and rainshelter experiments were used to develop crop parameters to calibrate and validate the FAO’s AquaCrop model for taro and bambara groundnut landraces. The UM landrace was used for taro while the ‘Red’ landrace selection was used for bambara groundnut. AquaCrop was calibrated using observed data from optimum (FI) experiments conducted during 2010/11. Model validation was done using observations from field and rainshelter experiments conducted during 2011/12 as well as independent data. Results showed that all taro landraces were slow to emerge (≈ 49 days after planting). Stomatal conductance declined under conditions of limited water availability (RF, 60% and 30% ETa). The UM landrace showed better stomatal regulation compared with KW and DL landraces under conditions of limited water availability. Plant growth (plant height, leaf number, LAI and CCI) of taro landraces was lower under conditions of limited water availability (RF, 60% and 30% ETa) relative to optimum conditions (FI and 100% ETa). The UM landrace showed moderate reductions in growth compared with the DL and KW landraces, suggesting greater adaptability to water limited conditions. The VGI showed a large reduction in growth under RF conditions and confirmed the UM landrace’s adaptability to limited water availability. Limited water availability (RF, 60% and 30% ETa) resulted in lower biomass, HI, and final yield in taro landraces relative to optimum conditions (FI and 100% ETa). For all trials, the DL landrace failed to produce any yield. WUE of taro landraces was consistent for the three irrigation levels (30, 60 and 100% ETa); however, on average, the UM landrace was shown to have a higher WUE than the KW landrace. Bambara groundnut landraces were slow to emerge (up to 35 days after planting). ‘Red’ and ‘Brown’ landrace selections emerged better than the ‘Light-brown’ landrace selection, confirming the effect of seed colour on early establishment performance. Plant growth (stomatal conductance, CCI, plant height, leaf number, LAI and biomass accumulation) was lower under conditions of limited water availability (RF, 60% and 30% ETa) relative to optimum conditions (FI and 100% ETa). The ‘Red’ landrace selection showed better adaptation to stress. Limited water availability resulted in early flowering and reduced flowering duration as well as early senescence and maturity of bambara groundnut landrace selections. The ‘Red’ landrace selection showed delayed leaf senescence under conditions of limited water availability. Yield reductions of up to 50% were observed under water limited conditions (RF, 60% and 30% ETa) relative to optimum conditions (FI and 100% ETa). Water use efficiency increased at 60% and 30% ETa, respectively, relative to 100% ETa, implying adaptability to limited water availability. The ‘Red’ landrace selection showed better yield stability and WUE compared with the ‘Brown’ and ‘Light-brown’ landrace selections suggesting that seed colour may be used as a selection criterion for drought tolerance in bambara groundnut landraces. The intercropping study showed that intercropping, as an alternative cropping system, had more potential than monocropping. Evaluation of growth parameters showed that taro plant height was generally unaffected by intercropping but lower leaf number was observed as compared with the sole crop. Bambara groundnut plants were taller and had more leaves under intercropping relative to the sole crop. Although not statistically significant, yield was generally lower in the intercrops compared with the sole crops. Evaluation of intercrop productivity using the land equivalent ratio (LER) showed that intercropping taro and bambara groundnut at a ratio of 1:1 was more productive (LER = 1.53) than intercropping at a ratio of 1:2 (LER = 1.23). The FAO’s AquaCrop model was then calibrated for the taro UM landrace and ‘Red’ bambara groundnut landrace selection. This was based on observations from previous experiments that suggested them to be drought tolerant and stable. Calibration results for taro and bambara groundnut landraces showed an excellent fit between predicted and observed parameters for canopy cover (CC), biomass and yield. Model validation for bambara groundnut showed good model performance under field (FI and RF) conditions. Model performance was satisfactory for rainshelters. Validation results for taro showed good model performance under all conditions (field and rainshelters), although the model over-estimated CC for the declining stage of canopy growth under RF conditions. Model verification using independent data for taro showed equally good model performance. In conclusion, the taro UM landrace and ‘Red’ bambara groundnut landrace selection were shown to be drought tolerant and adapted to low levels of water–use. The mechanisms responsible for drought tolerance in the taro UM landrace and ‘Red’ bambara groundnut landrace selection were described as drought avoidance and escape. The taro UM landrace and ‘Red’ bambara groundnut landraces avoided stress through stomatal regulation, energy dissipation (loss of chlorophyll) as well as reducing canopy size (plant height, leaf number and LAI), which translates to minimised transpirational water losses. This indicated landrace adaptability to low levels of water–use. The ‘Red’ bambara groundnut landrace selection showed phenological plasticity and escaped drought by flowering early, delaying leaf senescence, and maturing early under conditions of limited water availability. Performance of the ‘Red’ landrace selection lends credence to the use of seed coat colour as a possible selection criterion for drought tolerance in bambara groundnut, and possibly for other landraces with variegated seed. The taro UM landrace escaped drought by maturing early under conditions of limited water availability. The FAO’s AquaCrop model was successfully calibrated and validated for taro UM and ‘Red’ bambara groundnut landraces. The calibration and validation of AquaCrop for taro is the first such attempt and represents progress in the modelling of neglected underutilised crops. The calibration and validation of AquaCrop for taro requires further fine-tuning while that for bambara groundnut still needs to be tested for more diverse landraces. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

Issues surrounding water scarcity will become topical in future as global fresh water resources become more limited thus threaten crop production. Predicted climate change and increasing population growth will place more pressure on agriculture to produce more food using less water. As such, efforts have now shifted to identifying previously neglected underutilised species (NUS) as possible crops that could be used to bridge the food gap in future. Taro (Colocasia esculenta L. Schott) and bambara groundnut (Vigna subterranea L. Verdc) currently occupy low levels of utilisation in South Africa. Both crops are cultivated using landraces with no improved varieties available. Information describing their agronomy and water–use is limited and remains a bottleneck to their promotion. The aim of this study was to determine the drought tolerance and water–use of selected landraces of taro and bambara groundnut from KwaZulu-Natal, South Africa. In order to meet the specific objectives for taro and bambara groundnut management, an approach involving conventional and modelling techniques was used. Three taro landraces [Dumbe Lomfula (DL), KwaNgwanase (KW) and Umbumbulu (UM)] were collected from the North Coast and midlands of KwaZulu-Natal, South Africa, in 2010. The UM landrace was classified as Eddoe type taro (C. esculenta var. antiquorum) characterised by a central corm and edible side cormels. The DL and KW landraces were classified as Dasheen (C. esculenta var. esculenta), characterised by a large edible main corm and smaller side cormels. A bambara groundnut landrace was collected from Jozini, KwaZulu- Natal, and characterised into three selections (‘Red’, ‘Light-brown’ and ‘Brown’) based on seed coat colour. Seed colour was hypothesised to have an effect on seed quality. Field and rainshelter experiments were conducted for both taro and bambara landraces at Roodeplaat in Pretoria and Ukulinga Research Farm in Pietermaritzburg, over two growing seasons (2010/11 and 2011/12). The objective of the field trials for taro and bambara groundnut was to determine mechanisms associated with drought tolerance in taro and bambara groundnut landraces. Experiments were laid out in a split-plot design where irrigation [fully irrigated (FI) and rainfed (RF)] was the main factor and landraces (3 landraces of either taro or bambara groundnut) were sub-factors. Treatments were arranged in a randomised complete block design (RCBD), replicated three times. Rainfed trials were established with irrigation to allow for maximum crop stand. Thereafter, irrigation was withdrawn. Whilst experimental designs and layouts for taro and bambara groundnut were similar, differences existed with regards to plot sizes and plant spacing. Trials were planted on a total land area of 500 m2 and 144 m2, for taro and bambara groundnut, respectively. Plant spacing was 1 m x 1 m for taro and 0.3 m x 0.3 m for bambara groundnut. Irrigation scheduling in the FI treatment was based on ETo and Kc and was applied using sprinkler irrigation system. Separate rainshelter experiments were conducted for taro and bambara groundnut landraces at Roodeplaat, to evaluate growth, yield and water-use of taro and bambara groundnut landraces under a range of water regimes. The experimental design was similar for both crops, a RCBD with two treatment factors: irrigation level [30, 60 and 100% crop water requirement (ETa)] and landrace (3 landraces), replicated three times. Irrigation water was applied using drip irrigation system based on ETo and Kc. Data collection in field and rainshelter trials included time to emergence, plant height, leaf number, leaf area index (LAI), stomatal conductance and chlorophyll content index (CCI). For taro field trials, vegetative growth index (VGI) was also determined. Yield and yield components (harvest index, biomass, corm number and mass) as well as water–use efficiency (WUE) were determined at harvest.Intercropping of taro and bambara groundnut was evaluated under dryland conditions using farmers’ fields at Umbumbulu, KwaZulu–Natal, South Africa. The experimental design was a RCBD replicated three times. Intercrop combinations included taro and bambara groundnut sole crops, a 1:1 (one row taro to one row bambara groundnut) and 1:2 intercrop combinations. The taro UM landrace and ‘Red’ bambara groundnut landrace selection were used in the intercropping study. Lastly, data collected from field and rainshelter experiments were used to develop crop parameters to calibrate and validate the FAO’s AquaCrop model for taro and bambara groundnut landraces. The UM landrace was used for taro while the ‘Red’ landrace selection was used for bambara groundnut. AquaCrop was calibrated using observed data from optimum (FI) experiments conducted during 2010/11. Model validation was done using observations from field and rainshelter experiments conducted during 2011/12 as well as independent data. Results showed that all taro landraces were slow to emerge (≈ 49 days after planting). Stomatal conductance declined under conditions of limited water availability (RF, 60% and 30% ETa). The UM landrace showed better stomatal regulation compared with KW and DL landraces under conditions of limited water availability. Plant growth (plant height, leaf number, LAI and CCI) of taro landraces was lower under conditions of limited water availability (RF, 60% and 30% ETa) relative to optimum conditions (FI and 100% ETa). The UM landrace showed moderate reductions in growth compared with the DL and KW landraces, suggesting greater adaptability to water limited conditions. The VGI showed a large reduction in growth under RF conditions and confirmed the UM landrace’s adaptability to limited water availability. Limited water availability (RF, 60% and 30% ETa) resulted in lower biomass, HI, and final yield in taro landraces relative to optimum conditions (FI and 100% ETa). For all trials, the DL landrace failed to produce any yield. WUE of taro landraces was consistent for the three irrigation levels (30, 60 and 100% ETa); however, on average, the UM landrace was shown to have a higher WUE than the KW landrace. Bambara groundnut landraces were slow to emerge (up to 35 days after planting). ‘Red’ and ‘Brown’ landrace selections emerged better than the ‘Light-brown’ landrace selection, confirming the effect of seed colour on early establishment performance. Plant growth (stomatal conductance, CCI, plant height, leaf number, LAI and biomass accumulation) was lower under conditions of limited water availability (RF, 60% and 30% ETa) relative to optimum conditions (FI and 100% ETa). The ‘Red’ landrace selection showed better adaptation to stress. Limited water availability resulted in early flowering and reduced flowering duration as well as early senescence and maturity of bambara groundnut landrace selections. The ‘Red’ landrace selection showed delayed leaf senescence under conditions of limited water availability. Yield reductions of up to 50% were observed under water limited conditions (RF, 60% and 30% ETa) relative to optimum conditions (FI and 100% ETa). Water use efficiency increased at 60% and 30% ETa, respectively, relative to 100% ETa, implying adaptabilityto limited water availability. The ‘Red’ landrace selection showed better yield stability and WUE compared with the ‘Brown’ and ‘Light-brown’ landrace selections suggesting that seed colour may be used as a selection criterion for drought tolerance in bambara groundnut landraces. The intercropping study showed that intercropping, as an alternative cropping system, had more potential than monocropping. Evaluation of growth parameters showed that taro plant height was generally unaffected by intercropping but lower leaf number was observed as compared with the sole crop. Bambara groundnut plants were taller and had more leaves under intercropping relative to the sole crop. Although not statistically significant, yield was generally lower in the intercrops compared with the sole crops. Evaluation of intercrop productivity using the land equivalent ratio (LER) showed that intercropping taro and bambara groundnut at a ratio of 1:1 was more productive (LER = 1.53) than intercropping at a ratio of 1:2 (LER = 1.23). The FAO’s AquaCrop model was then calibrated for the taro UM landrace and ‘Red’ bambara groundnut landrace selection. This was based on observations from previous experiments that suggested them to be drought tolerant and stable. Calibration results for taro and bambara groundnut landraces showed an excellent fit between predicted and observed parameters for canopy cover (CC), biomass and yield. Model validation for bambara groundnut showed good model performance under field (FI and RF) conditions. Model performance was satisfactory for rainshelters. Validation results for taro showed good model performance under all conditions (field and rainshelters), although the model over-estimated CC for the declining stage of canopy growth under RF conditions. Model verification using independent data for taro showed equally good model performance. In conclusion, the taro UM landrace and ‘Red’ bambara groundnut landrace selection were shown to be drought tolerant and adapted to low levels of water–use. The mechanisms responsible for drought tolerance in the taro UM landrace and ‘Red’ bambara groundnut landrace selection were described as drought avoidance and escape. The taro UM landrace and ‘Red’ bambara groundnut landraces avoided stress through stomatal regulation, energy dissipation (loss of chlorophyll) as well as reducing canopy size (plant height, leaf number and LAI), which translates to minimised transpirational water losses. This indicated landrace viii adaptability to low levels of water–use. The ‘Red’ bambara groundnut landrace selection showed phenological plasticity and escaped drought by flowering early, delaying leaf senescence, and maturing early under conditions of limited water availability. Performance of the ‘Red’ landrace selection lends credence to the use of seed coat colour as a possible selection criterion for drought tolerance in bambara groundnut, and possibly for other landraces with variegated seed. The taro UM landrace escaped drought by maturing early under conditions of limited water availability. The FAO’s AquaCrop model was successfully calibrated and validated for taro UM and ‘Red’ bambara groundnut landraces. The calibration and validation of AquaCrop for taro is the first such attempt and represents progress in the modelling of neglected underutilised crops. The calibration and validation of AquaCrop for taro requires further fine-tuning while that for bambara groundnut still needs to be tested for more diverse landraces. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.

Dans l'optique de produire des agro‐carburants, le sorgho sucré est aujourd'hui proposé comme une alternative à d'autres espèces cultivées à grande échelle comme la canne à sucre et le maïs car il présente plusieurs avantages : le sorgho est résistant à la sécheresse et à la chaleur, il nécessite peu d'intrants, a en moyenne un cycle de culture relativement court (3‐4 mois) comparé à la canne à sucre. Il offre une grande diversité génétique à explorer et exploiter, tout en étant génétiquement moins complexe que la canne à sucre. Finalement, il peut être cultivé pour un double usage, le grain pouvant être utilisé comme source d'alimentation pour l'homme ou le bétail (à partir du grain) et le jus sucré contenu par les tiges comme source d'agrocarburant. Cette polyvalence en fait une culture idéale pour lutter contre la compétition entre cultures énergétiques et cultures vivrières et assurer des rendements dans des environnements de culture sujets au stress hydrique et thermique comme c'est le cas en Afrique de l'Ouest. Cependant, le caractère sucré du sorgho est complexe, car sous l'influence d'interactions Génotype X Environnement (GxE). Aussi, les mécanismes métaboliques, morphologiques ou phénologiques constituant la cinétique d'accumulation des glucides dans la tige et son éventuelle compétition avec le remplissage des grains restent mal connus ou très controversés dans la littérature. La présente thèse, réalisée dans le cadre du projet européen Sweetfuel, vise à comprendre ces mécanismes, afin de contribuer à la définition d'idéotypes de sorgho double usage, pour les environnements soudano‐sahéliens.Sur la base d'études expérimentales au champ au Mali et en serre en France, il a pu être démontré que les glucides sont accumulés dans les entrenoeuds des tiges par un jeu d'activités enzymatiques (favorisant l'accumulation d'hexoses puis de saccharose) dès le début de leur élongation, donc potentiellement avant la floraison. Au Mali, l'étude au champ de 14 génotypes adaptés aux conditions locales, plus ou moins sensibles à la photopériode et semés à trois dates différentes, a démontré le bénéfice d'un rallongement de la phase végétative sur la quantité de sucre accumulée dans les tiges de la plante à floraison, du fait d'un plus grand nombre d'entrenoeuds allongés et du temps à leur disposition pour accumuler des glucides avant ce stade. Ce bénéfice était cependant plus lié à la plus grande quantité de biomasse accumulée (taille des tiges) qu'à la concentration en sucre dans les entrenoeuds (plutôt stable entre dates de semis).Ainsi, la durée de la phase végétative et la sensibilité à la photopériode sont proposés comme des paramètres clés favorisant la quantité de glucides accumulée dans les tiges de la plante à floraison. D'autre part, il a été montré que la quantité de glucides présente à maturité dans les tiges des mêmes génotypes ne différait pas ou peu de celle à floraison, une éventuelle réduction pour quelques génotypes n'étant généralement pas significative et évitable par l'allongement du cycle. De plus, cette quantité de glucides dans les tiges à maturité n'a tiré aucun bénéfice de l'ablation de la panicule à floraison chez les mêmes génotypes. Ces résultats suggèrent que la compétition entre le remplissage du grain et la production de sucre est faible chez le sorgho, d'autant plus faible que la plante présente de grandes tiges et donc un grand compartiment de stockage des glucides, tamponnant cette éventuelle compétition. D'ailleurs, à une échelle plus fine, aucune différence n'a pu être mise en évidence en termes d'activité des principales enzymes du métabolisme carboné dans la tige d'un génotype dans sa version stérile (pas de remplissage du grain) et fertile.Ce travail a démontré le potentiel du sorgho pour une double utilisation dans un contexte soudano‐sahélien et la pertinence d'exploiter la diversité génétique de cette espèce pour cette objectif de sélection. Les résultats ob / Sweet sorghum offers many advantages as an alternative to widely cultivated crops such as corn and sugarcane to produce biofuels: it is resistant to water stress, it requires few inputs; it has a shorter growth cycle compared to sugarcane in particular. Sorghum also exhibits a great genetic diversity and is genetically less complex than sugarcane. Finally, sorghum can be cultivated for dual‐purpose uses, using grains for food or feed and sweet juice for biofuel production. Hence, sorghum is a promising option to reduce the competition for land and (water) resource use between food and fuel, in particular in cropping environments with high drought and heat stress frequency, as in West Africa. However, stem sweetness is a complex trait prone to genotype x environment interactions (GxE). The metabolic, morphological and phenological mechanisms involved in the kinetic of stem sugar accumulation and its possible competition with grain filling are largely unknown or controversial in the literature. The present work is part of the European project Sweetfuel and aims at better understanding these mechanisms and contributing to define dual‐purpose sorghum ideotypes for soudano‐sahelian conditions.Based on field and greenhouse experiments respectively in Mali and France, it was found that sugars start accumulating in stem internodes at the onset of their elongation, i.e. potentially soon before the plant flowers. The successive accumulation of hexose and then sucrose in internodes could be dynamically explained by changes in the activity of key enzymes related to sucrose metabolism. In Mali, a field experiment performed on 14 genotypes, contrasted for photoperiod sensitivity and sown at three planting dates, highlighted the interest of increasing vegetative phase duration to increase sugar yield. This was explained first of all by the higher number of internodes that could expand during a longer vegetative phase, and thus, by the higher production of stem biomass, and, to a minor extent, by the longer time for internodes to mature and accumulate sugar (sugar concentration in the stem was however fairly stable across sowing dates). Also, vegetative phase duration and photoperiod sensitivity can be considered as two key parameters promoting stem sugar content before grain filling. In the same time, it was shown that stem sugar content kept remarkably constant between anthesis and maturity in most of studied genotypes and that the reduction observed for some genotypes was overcome with an early sowing. Moreover, sugar accumulation in the stem between flowering and maturity did not benefit from panicle pruning. These results together suggest that the competition for carbohydrates between stem sugar reserves and grain filling is weak; it is even weaker for big/large stem genotypes with huge sugar reserves in the stem that would buffer a post‐flowering allocation of sugar from the stem to the grains if required. This low competition was confirmed at a finer scale, as no differences were observed in the activity of key enzymes of sucrose metabolism between the sterile and the fertile line of a same genotype.This work demonstrates the potential of sorghum for dual‐purpose in particular for soudano‐sahelian cropping conditions and the interest of using its genetic diversity for this breeding purpose. It provides further knowledge for revisiting the phenotyping strategies to be adopted to investigate the genetic basis of sugar and grain production and their combination. The results are also currently used to improve the way the source‐sink relationships underlying this dual production are formalized in crop and plant models at CIRAD. Such models will be then useful to assist sorghum ideotype exploration for dual purpose.

The aims of this work were 1) to assess whether sorghum (Sorghum bicolor (L.) Moench) genotypes originating from the India can be grown and analyzed in the climatic conditions of central Europe and 2) to find out the utilization potential of selected non- destructive and destructive methods based mostly on the chlorophyll a fluorescence measurements and the determination of photosynthetic pigments' content for the differentiation of sorghum genotypes based on their presumed drought tolerance. Field experiments made during 2 years compared 15 genotypes of this species (2 stay-green parental lines, 2 senescent parental lines and 11 introgression lines with stay-green loci), 2 of these genotypes were further analyzed in greenhouse conditions where the water deficit was induced by a cessation of watering for 12 days. The field-grown plants showed some differences between individual genotypes in all measured parameters; however, for the majority of the genotypes these differences were not statistically significant. The stay-green parental genotype B35 differred the most from the other ones in both field seasons, but the other stay-green genotypes usually did not differ from the senescent genotypes. No significant differences between both greenhouse-tested genotypes (presumably contrasting in their...

South Africa is classified as a semi-arid environment with limited natural water sources. Amenity landscapes provide broad ranging benefits for society. Amenity landscapes account for between 31% - 50% of water supplied for domestic and urban use. To reduce water use and water conservation in amenity landscapes, strategies, regulations and interventions are required. Every landscape is a unique complex system with a large number of variables that differ from each other. The variability can be summarized into management/design, irrigation, climatological, edaphic and plant related aspects. Several amenity landscape water use models have been developed around the world and two in South Africa. This study developed a comprehensive South African hydrozone based plant database and an Amenity Landscape Water Use Model South Africa (ALWUMSA). This will improve hydrozoning of amaneity landscapes and ultimately also improve water conserbvation for these sites. It allows users/owners to determine water use requirements through an extensive data gathering, from aspects such as design, management, microclimate, environmental, edaphic, irrigation and plant related factors. Comparisons of results from ALWUMSA to three test sites, selected existing models and a range of scenarios produced results demonstrating that ALWUMSA consistently projected lower water requirements. The model also allows for site aspects to be changed thus encouraging end users to implement specific water saving intiatives with the amenity landscape to reduce water use. These savings will be translated into both water-use savings as well as financial savings for users of the amenity landscape water use model. / Environmental Sciences / Ph. D. (Environmental Science)

Os efeitos da aplicação foliar de fósforo (Pi) na condutância estomática (gs) e na fotossíntese (A), foram avaliados em genótipos de feijoeiro, A320, Carioca e Ouro Negro, cultivados em potes numa casa de vegetação. Este estudo foi feito durante o dia após a aplicação foliar de 10 g de Pi L-1, em plantas hidratadas, e durante um período de deficiência hídrica iniciada dois ou cinco dias após a aplicação. Durante o dia após a aplicação de Pi, não foi observado nenhuma diferença, entre os tratamentos com e sem Pi, nas trocas gasosas de ambas as cultivares. Durante a desidratação, a aplicação de Pi não causou aumento de gs, mas causou aumento de A, nas medições às 0900, 1200 e 1500 horas, nas cultivares (Carioca e Ouro Negro), mas com um efeito maior na cultivar Ouro Negro, principalmente às 1200 horas. A eficiência intrínseca do uso da água (EIUA) também foi superior nas plantas com suprimento foliar de Pi. Quanto aos componentes da produção, a aplicação de Pi causou aumento do número de vagens das plantas da cultivar Ouro Negro, sob desidratação. Portanto, a aplicação de Pi foliar pode reduzir o efeito de uma desidratação quando aplicado dois dias antes da suspensão da irrigação. Além disso, o potencial fotossintético (Ac) de Ouro Negro com Pi foi superior ao de A320, com e sem Pi, na seca máxima, e ao A320 sem Pi, na reidratação. A dissipação térmica, não fotoquímica (NPQ), do genótipo A320 sem Pi foi maior que com Pi e que a do Ouro Negro, com e sem Pi, na reidratação, provavelmente devido aos menores valores de A neste tratamento sem Pi. O uso de fosfato de amônio substituindo a uréia ou o sulfato de amônio, que são aplicados aos 25 DAE, é recomendável. / The effects of foliar Pi supplying (Pi) on stomatal conductance (gs) and photosynthesis (A) were measured in genotypes, A320, Carioca and Ouro Negro, grown under greenhouse condition. Measurements of gs and A were taken one day after Pi application (10 g L-1) on well-irrigated plants, and during drought stress period beginning two or five days after Pi supplying. During the day after Pi application, it was not observed any difference on gas exchange of genotypes (Carioca and Ouro Negro) due to the treatments with and without Pi. During water stress, the Pi supplying did not cause increase of gs, however, caused increase of A at 0900, 1200 and 1500 h in both genotypes. This effect was higher when considered Ouro Negro at 1200 h. The intrinsic water use efficiency (IWUE) was also increased in Pi-supplied plants. The Pi supplying caused increase on pod number of Ouro Negro plants under water deficit. These results suggest that the foliar Pi application may reduce the effect of water deficit on photosynthesis when supplied two days before the water withholding. In addition, the O2 evolution (Ac) on Ouro negro with extra Pi was higher than for A320, with or without Pi, at the last day of the mild water deficit, and it was higher than A 320 with extra Pi at rehydration. The non-photosynthetic quenching (NPQ), was higher for A320 without Pi at recovery, probably due to the smaller values of A at this treatment. The use of ammonium phosphate, instead of urea or ammonium sulphate to be applied as usual 25 DAS, is recommended.

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