There is an increasing need to improve crop water-use efficiency (WUE) (ratio of whole-plant biomass to cumulative transpiration) due to decreased water availability and increased food and energy demands throughout the world. The objective of the study was to estimate the genetic variation and genetic basis for transpiration efficiency A:E (CO2 assimilation rate (A) divided by transpiration rate (E)) trait and its relationship to WUE related to pre-flower drought tolerance in recombinant inbred lines (RILs) of sorghum and associated QTLs. A greenhouse study was conducted at Bushland, TX, 2008, using 71 RILs derived from cross of Tx430 x Tx7078. A randomized complete block experimental design was used, with both genotype and water regime (40 and 80 percent water regime) as experimental factors, and four replications. Genotype had a significant effect on A, E and A:E under both the environments. Among the RILs, entry means for A:E ranged from 1.58 to 3.07 mmol CO2 mol^-1 H2O and 1.18 to 4.36 mmol CO2 mol^-1 H2O under 80 percent and 40 percent water regime, respectively. Heritability estimates based on individual environments for A:E , A and E were 0.77, 0.45 and 0.37 under 80 percent water regime and 0.90, 0.33 and 0.71 under 40 percent water regime, respectively. A genetic map was constructed by digital genotyping method using Illumina GAII sequencer with 261 informative indel/ single-nucleotide polymorphism (SNP's) markers distributed over 10 linkage groups. Three significant QTLs associated with transpiration efficiency were identified; two on SBI-09 and one on SBI-10 with one logarithmic of odds (LOD) interval length ranging from 5.3 to 5.7 cM and accounting for 17 percent - 21 percent of the phenotypic variation. In field and greenhouse evaluation of agronomic of traits at College Station and Halfway, TX, 91 QTL that control variation in six major agronomic traits such as plant height, flowering, biomass, leaf area, leaf greenness and stomatal density were identified. Co-localization of transpiration efficiency QTLs with agronomic traits such as leaf area, biomass, leaf width and stomatal density indicated that these agronomically important QTLs can be used for further improving the sorghum performance through marker assisted selection (MAS) under pre-flowering drought stress conditions.

Transposable elements (Transposons; TEs) constitute the majority of DNA in genomes and are a major source of genetic polymorphisms. TEs act as potential regulators of gene expression and lead to phenotypic plasticity in plants and animals. In crops, several TEs were identified to influence alleles associated with important agronomic traits, such as apical dominance in maize and seed number in rice. Crops may harbor more TE-mediated genetic regulations than expected in view of multifunctional TEs in genomes. However, tools that accurately annotate TEs and clarify their associations with agronomic traits are still lacking, which largely limits applications of TEs in crop breeding. Here we 1) evaluate performances of popular tools and strategies to identify TEs in genomes, 2) develop a tool 'DeepTE' to annotate TEs based on deep learning models, and 3) develop a tool 'TE-marker' to identify potential TE-regulated alleles associated with agronomic traits. As a result, we propose a series of recommendations and a guideline to develop a comprehensive library to precisely identify TEs in genomes. Secondly, 'DeepTE' classifies TEs into 15-24 super families according to sequences from plants, metazoans, and fungi. For unknown sequences, this tool can distinguish non-TEs and TEs in plant species. Finally, the 'TE-marker' tool builds a TE-based marker system that is able to cluster rice populations similar to a classical SNP marker approach. This system can also detect association peaks that are equivalent to the ones produced by SNP markers. 'TE-marker' is a novel complementary approach to the classical SNP markers that it assists in revealing population structures and in identifying alleles associated with agronomic traits. / Doctor of Philosophy / Transposable elements (Transposons; TEs) are DNA fragments that can jump and integrate into new positions in the genome. TEs potentially act as regulators of gene expression and alter traits of plants and animals. In crops, several TEs were identified to influence functions of genes that control important agronomic traits, such as branching in maize and seed number in rice. However, tools that identify these associations in the crops are still lacking, which largely limits applications of TEs in crop breeding. Here we evaluated performance of popular tools and strategies that identify TEs, and provide a series of recommendations to efficiently apply these tools to the TE identification. In view of structural and sequence differences, TEs are classified into multiple families. We developed a 'DeepTE' tool to precisely cluster TEs into different families using a deep learning method. Finally, a 'TE-marker' tool was developed to build TE-based genetic markers to identify nearby alleles associated with agronomic traits. Overall, this work could promote the use of TEs as markers in improving quality and yielding crops.

The main goal of soybean breeding is to increase yield with improved seed quality characters. The objectives of this thesis were: i) to identify yield quantitative trait loci (QTL) across different mega-environments (ME); ii) to evaluate the relationship between yield and yield components and the co-localization of QTL; iii) to analyze environmental factors that affect QTL expression and identify different ME. Two Canadian x Chinese soybean populations were tested across Canada, northern United States and China. Yield QTL were identified at one, two and three hypothetical ME. Most of them were co-localized with agronomic trait QTL. These results give strong evidence that Canada, northern United States and China are different ME. Novel alleles from plant introductions can favorably contribute directly or indirectly to seed yield and the use of QTL would facilitate their introgression into breeding populations in both North America and China. / National Science and Engineering Research Council of Canada (NSERC) and the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA)

Master of Agribusiness / Department of Agricultural Economics / Major Professor Not Listed / Different dry bean crop varieties with different colors are produced in Malawi. Yet, little is known about the drivers of consumer preferences for the different dry bean varieties grown based on color. Literature shows that consumers link bean color to taste, cooking time, gravy quality and other desirable characteristics. The main objective of this research was to assess factors that determine consumption of different types of dry beans in Malawi based on color to determine preferences for different consumer segments and hence the potential value of these preferences communicated across the dry bean supply chain, to enhance the probability of success for breeders’ efforts and the bean value chain’s initiatives. The research used survey data that was collected by the Bean Value Chain Research Network in Lilongwe District, Malawi. The sample size of the dataset was 687 households from three different economic strata. The research focused on four dry bean colors: Red, Red Mottled, White and Cream Mottled bean. These were found to be the most prominent colors by sales and stated preference in Malawi. Two econometric approaches were used in the data analysis. A bivariate analysis using Pearson’s chi-square was used to test the significance of the association between bean consumption (dependent variable) and household as well as product characteristics explanatory variables. A logit model was run on each of the four color types to assess the extent to which the explanatory variables influence consumer preferences for alternative colors of dry bean products. Results showed that 40.8% of the respondents consumed red beans, 12.6% consumed red mottled, 14.6% consumed White and 32% consumed Cream mottled beans. In terms of demographic characteristics, respondents’ marital and employment status as well as household size were found to have no significant influence the consumption of all the four colors. Being educated decreased probability of consuming white and cream mottled beans. Household characteristics were also found to influence preferences for color. For example, households in low and middle-income households were shown to have a lower likelihood of consuming white beans. The characteristics of the beans were also important in influencing preferences. For example, medium grain size beans influenced preference for red beans while fast cooking beans negatively affected the consumption of mottled red beans. The results provide insights for bean breeders in their attempts to contribute to increased producer incomes through a careful response to consumer preferences and not just producer demands for agronomic traits.

Orientador: Sandra Helena Unêda-Trevisoli / Coorientador: Antonio Orlando Di Mauro / Coorientador: Cibele Chalita Martins / Banca: Everton Luis Finoto / Banca: Ivana Marino Bárbaro Torneli / Banca: Rinaldo Cesar de Paula / Banca: Gustavo Vitti Môro / Resumo: O presente estudo foi realizado com os objetivos principais de: verificar as associações existentes entre caracteres agronômicos e caracteres relacionados à qualidade fisiológica de sementes de soja; determinar alterações fisiológicas e no teor de óleo em sementes de soja, ao longo do período de armazenamento, além de selecionar progênies superiores de soja por meio de análises multivariadas. Para isto, as relações existentes entre os caracteres agronômicos de plantas e fisiológicos de sementes foram verificadas por meio da análise de correlações canônicas em sete populações e duas cultivares comerciais, em três gerações: plantas F3 e sementes F4; plantas F4 e sementes F5; e sementes e plantas na geração F4. Os caracteres agronômicos de plantas (grupo I) avaliados foram: número de dias para maturidade, altura da planta na maturidade, altura de inserção da primeira vagem, número de vagens, produção de grãos e teor de óleo. A qualidade fisiológica das sementes (grupo II), foi avaliada por meio do teste de germinação, envelhecimento acelerado, emergência e índice de velocidade de emergência. As mesmas populações e cultivares também foram avaliadas antes do armazenamento e após seis meses, armazenadas em ambiente com temperatura e umidade controladas, através de testes de germinação, vigor, teor de água e teor de óleo, em esquema fatorial 2 x 9. Para as análises multivariadas, 20 populações segregantes de geração F4, foram avaliadas para os seguintes caracteres agronômicos: númer... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: This study aimed to examine the associations between agronomic traits and traits related to physiological seed quality in soybean seeds, determine physiological and oil content alterations during the storage and select superior progenies using multivariate analysis. For this, the relationships between agronomic traits and physiological of seed traits were evaluated using canonical correlation analysis in seven segregating populations and two commercial cultivars conducted in three generations: plants F3 and seeds F4, plants F4 and seeds F5 and seeds and plants in generation F4. The agronomic traits (group I) evaluated were: number of days to maturity, plant height at maturity, first pod height, number of pod per plant, grain yield and oil content. The seed physiological quality (group II) was evaluated by percentage of germination, percentage of emergence, emergence speed index and accelerated aging. The same populations and cultivars were also evaluated before the storage and after six months stored in cold room by germination test, vigor, seed moisture and oil content, arranged in a 2 x 9 factorial design. For the multivariate analysis, 20 segregating populations in generation F4 were evaluated using the following agronomic traits: number of days to flowering, number of days to maturity, plant height at maturity, first pod height, number of branches per plant, number of pod per plant, number of nodes per plant, grain yield and oil content. It was used the principal compone... (Complete abstract click electronic access below) / Doutor

Made available in DSpace on 2017-07-25T19:30:53Z (GMT). No. of bitstreams: 1 Lilian Schafascheck.pdf: 1885444 bytes, checksum: 0039d2e4db0312592da136c4b19798b8 (MD5) Previous issue date: 2015-12-10 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The wheat breeding starts with the selection of the parent to make the crossing blocks, aiming at segregating populations with high yield potential and divergent, to evaluate the adaptability and phenotypic stability in different wheat regions. Therefore, the objectives of this study were to estimate the genetic dissimilarity among wheat genotypes through agronomic characterization, molecular genotyping and coefficient parentage, cluster analyses of genotypes by means of multivariate statistical methods, and to evaluate the adaptability and phenotypic stability by GGE biplot methodology. It was evaluated 43 new wheat lines developed by the breeding program of UEPG and cultivar commercial Safira®. The genetic dissimilarity among the genotypes was obtained from the Generalized Mahalanobis Square Distance (D2) through seven agronomic traits, coefficient parentage (COP) and Jaccard index for SSR and AFLP markers. The genotypes were grouped according to the genetic dissimilarity through the UPGMA and principal component analysis (PCA) methods. The principal component analysis (PCA) enabled the reduction the set of seven variables on three principal components, explaining 67% of the total phenotypic variance. The coefficients of the eigenvectors indicated that the CP1 was more related to grain quality (thousand kernels weight and weight hectoliter) and the vegetative cycle. CP2 in most was influenced by the grain yield (48.4%) and CP3 negatively associated with the plant height (72.08%). CP analysis allowed the identification of groups of different wheat genotypes through agronomic characteristics. The dendrograms obtained through molecular genotyping (SSR and AFLP) and agronomic characterization demonstrated the formation of eight groups, while the coefficient parentage only five groups of genotypes. The cophenetic correlations between the matrices of genetic dissimilarity were low. Nevertheless, the analysis methods were efficient in estimating the genetic dissimilarity among the genotypes and enabled highlight wheat lines which showed higher agronomic performance. To estimate the adaptability and stability of wheat genotypes were evaluated in crops 2010, 2011 and 2012 in Ponta Grossa, for characteristics plant height, reproductive cycle and grain yield. From the results of the graphical analysis, it could identify the ideals genotypes characterized by high agronomic adaptation combined with phenotypic stability. The lines of the UEPG program L8, L15, L17, L31, L34, L38 and L40 showed high adaptation agronomic and phenotypic stability for grain yield. This group of wheat lines showed higher potential productive than that commercial cultivar Safira®, making them strong candidates in the future as new commercial cultivars recommended for the municipality of Ponta Grossa. / O melhoramento genético de trigo inicia com a seleção dos parentais para compor os blocos de cruzamentos, visando populações segregantes com alto potencial produtivo e divergente, até a avaliação da adaptabilidade e estabilidade fenotípica nas diferentes regiões tritícolas. Diante disso, os objetivos deste trabalho foram estimar a dissimilaridade genética entre genótipos de trigo através da caracterização agronômica, da genotipagem molecular e do coeficiente de parentesco, realizar a análise de agrupamento dos genótipos por meio de métodos estatísticos multivariados, bem como avaliar a adaptabilidade e estabilidade fenotípica através da metodologia GGE biplot. Foram avaliadas 43 novas linhagens de trigo desenvolvidas pelo programa de melhoramento da UEPG e a cultivar comercial Safira®. A dissimilaridade genética entre os genótipos foi obtida a partir da Distância Quadrada Generalizada de Mahalanobis (D2) através de sete características agronômicas, do coeficiente de parentesco (COP) e do índice de Jaccard para os marcadores SSR e AFLP. Os genótipos de trigo foram agrupados de acordo com a dissimilaridade genética através dos métodos UPGMA e da análise de componentes principais (ACP). A análise de componentes principais (ACP) possibilitou a redução do conjunto de sete variáveis em três componentes principais, explicando 67% da variância fenotípica total. Os coeficientes dos autovetores indicaram que o CP1 foi mais relacionado a qualidade de grãos (peso de mil grãos e peso do hectolitro) e ao ciclo vegetativo. O CP2 em maior parte foi influenciado pelo rendimento de grãos (48,4%) e o CP3 associado negativamente com a estatura de plantas (72,08%). A análise CP permitiu a identificação de diferentes grupos de genótipos de trigo a partir da caracterização agronômica. Os dendrogramas obtidos da genotipagem molecular (SSR e AFLP) e da caracterização agronômica demonstraram a formação de oito grupos, enquanto pelo coeficiente de parentesco apenas cinco grupos de genótipos. As correlações cofenéticas entre as matrizes de dissimilaridade genética foram baixas. Apesar disso, as metodologias de análise foram eficientes em estimar a dissimilaridade genética entre os genótipos e possibilitaram destacar as linhagens de trigo que evidenciaram desempenho agronômico superior. Para estimar a adaptabilidade e estabilidade os genótipos de trigo foram avaliados nas safras de 2010, 2011 e 2012 em Ponta Grossa, para as características estatura de planta, ciclo reprodutivo e rendimento de grãos. A partir dos resultados da análise gráfica, foi possível identificar os genótipos ideais, caracterizados pela alta adaptação agronômica e estabilidade fenotípica. As linhagens do programa de melhoramento da UEPG L8, L15, L17, L31, L34, L38 e L40 evidenciaram alta adaptação agronômica e estabilidade fenotípica para o rendimento de grãos. Esse grupo de linhagens de trigo apresentou potencial produtivo superior a cultivar comercial Safira®, tornando-as no futuro fortes candidatas como novas cultivares comerciais recomendadas para o município de Ponta Grossa.

Thesis (M.Sc. Agriculture (Crop Science)) -- University of Limpopo, 2011 / The nature and magnitude of the genotype by environment interactions is important to identify superior and stable genotypes under the target environments. This will assist to maximize specific adaptation and to speed up the transfer of new cultivars to growers. The objective of this study was to determine the stability of selected soybean genotypes with regards to the agronomic traits, high yield and nodule formation. Field experiments were conducted under dryland conditions during the 2007/2008 and 2008/2009 growing seasons at the University of Limpopo’s experimental farm (Syferkuil) and at a farmer’s field at Gabaza community, Mopani District near Tzaneen. Ten selected soybean cultivars were evaluated under a randomised complete block design with three replications. Stability was assessed via joint regression and superiority analyses. Significant differences were found for genotypes, environments and genotype by environment interactions. Stability analysis after Eberhart and Russell’s model suggested that the genotypes showed marked differences to environmental changes. The cultivar superiority measure for seed yield indicated that variety Clark was the most stable genotype with an average yield of 5235 kg/ha, followed by L81-4858 and Barc-2 that provided average yield of 4839 kg/ha and 4582 kg/ha, respectively. In terms of number of nodules Magoye was observed to be stable with average of five nodules per plant. Cultivar Barc-2 was found stable for number of active nodules with an average of 3.17 active nodules per plant. Most of the genotypes performed better at Syferkuil than at Gabaza. In general Barc-2 was found stable for yield and other agronomic traits considered in this study. This variety could be suitable for large scale production in these or other similar environments in Limpopo Province.

In this thesis, the relationships between 17 traits including starch, fibre, culinary quality and agronomic parameters of potato were investigated. In two studies, 12 genotypes were grown at three locations in Ontario and 18 genotypes were grown at four locations in Manitoba, Ontario and New Brunswick. Genotype by environment interactions were significant for fibre and agronomic traits, except bake score and specific gravity. Correlations were found between some, but not all, starch, fibre and agronomic parameters. Several genotypes containing desirable starch, fibre and agronomic profiles with high stability were identified. Although no single genotype was superior in all analyzed traits, certain genotypes excelled in specific attributes. CV96044-3 had the best starch and fibre profile, but low yields compared to other cultivars. Three genotypes, CV96044-3, F04037 and Goldrush, may be useful parents in a breeding program to improve starch and fibre characteristics, producing cultivars containing all desirable traits. / AAFC, Agricultural Bioproducts Innovation Program, BioPotato Network

High linoleic acid soybeans facilitate maximum production of soy-based polyurethane. The objectives of this study were to: 1) Evaluate environmental influence on yield and seed composition traits; 2) Estimate correlation coefficients between linoleic acid with agronomic traits; 3) Validate SSR markers associated with fatty acid QTL in multiple environments and across diverse genotypes; and 4) Evaluate the influence of fertilizers differing in P and K concentrations on seed fatty acids. RG25 was identified as the best genotype to be commercialized for polyurethane production. Strong marker-trait associations across environments included Satt_335, Satt389, Satt556 associated with palmitic and stearic, Satt389 with oleic, Satt389 and Satt537 with linoleic acid. A significant increase in linoleic acid content was observed when plants received modified Hoagland’s solution with 2×K compared to without K. Development of a high linoleic acid soybean line for polyurethane production is feasible using validated SSR markers and high K fertility. / Ontario Ministry of Agriculture, Food and Rural Affairs

Made available in DSpace on 2016-12-08T16:44:37Z (GMT). No. of bitstreams: 1 PGPV12MA064.pdf: 1012596 bytes, checksum: c4f66f0fa2a1b45c1ad39219f45c6b2d (MD5) Previous issue date: 2012-07-10 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The bacterial wilt (Curtobacterium flaccumfaciens pv. flaccumfaciens) has showed one of the most important diseases in the bean crop. Its symptoms occur from wilts at leaves to death of the infected plant. The control is based on the use of healthy seeds, crop rotation and especially resistant cultivars. The goal of this study was to estimate the efficiency of selection in segregating populations of beans for bacterial wilt resistance and indicate the best time of the cycle to make the selection of resistant plants and also to test in field the effectiveness selection at greenhouse for resistance to this disease. To achieve these objectives were used converging crosses between Aruã x Guará, Pyatã x Guará and Pyatã x Pérola, originating F2, F2:3, F3:4 which were subsequently inoculated with Curtobacterium flaccumfaciens pv. flaccumfaciens cff 2634 and evaluated according to a scale related to the common symptoms of the disease at 20, 40 and 60 days after inoculation. The field test of the effectiveness selection at greenhouse was used the same crosses, however, the populations used were in the generations F2:3, F3:4 and F4:5, subsequently measured the agronomic traits such as plant height, first pod, stem diameter, number of pods per plant, number of grains per plant, grain weight in grams per line and resistance to bacterial wilt. Through the data can be established that the populations of Aruã x Guará, Pyatã x Guará and Pyatã x Pérola have similar behavior in relation to resistance to the bacterial wilt symptoms. The selection was effected for the coming populations of Aruã x Guará and Pyatã x Pérola. The favorable time for distinguishing and selecting reliably segregating plants is between 40 and 60 days after inoculation. It was likewise observed that there is genetic diversity and superiority of selected plants on not select plants and their parents, indicating in the field that the greenhouse selection for resistance to bacterial wilt was effective / A murcha de curtobacterium (Curtobacterium flaccumfaciens pv. flaccumfaciens) tem se mostrado uma das doenças emergentes mais importantes na cultura do feijão. Seus sintomas ocorrem desde murchas nas folhas até à morte da planta infectada. O controle está baseado em uso de sementes sadias, rotação de cultura e principalmente cultivares resistentes. Assim, o objetivo deste trabalho foi estimar a eficiência da seleção em populações segregantes de feijão para resistentes à murcha de curtobacterium e indicar o melhor período do ciclo da cultura para proceder a seleção das plantas resistentes e também testar a campo a efetividade da seleção em casa de vegetação. Para atingir estes objetivos foram usados cruzamentos convergentes entre Aruã x Guará, Pyatã x Guará e Pyatã x Pérola, dando origem a populações segregantes que nas das gerações F2, F2:3 e F3:4 foram inoculadas com Curtobacterium flaccumfaciens pv. flaccumfaciens cff 2634 e avaliadas segundo uma escala de notas referentes aos sintomas comuns da doença aos 20, 40 e 60 dias após a inoculação. O teste a campo da efetividade da seleção em casa de vegetação usou os mesmos cruzamentos, entretanto as populações avaliadas são relativas às gerações F2:3, F3:4 e F4:5 sendo posteriormente mensurados os caracteres agronômicos como altura de planta, inserção do primeiro legume, diâmetro do caule, número de legumes por planta, número de grãos por planta, peso em gramas de grãos por linha e resistência à murcha de curtobacterium. Através dos dados pôde se estabelecer que as populações segregantes de Aruã x Guará, Pyatã x Guará e Pyatã x Pérola possuem comportamento semelhante em relação à resistência aos sintomas da murcha de curtobacterium. A seleção foi efetiva para as populações oriundas de Aruã x Guará e Pyatã x Pérola e o período propício para distinguir e selecionar de maneira confiável as plantas segregantes ocorre entre 40 e 60 dias após a inoculação. Foi da mesma forma observado que existe divergência genética e superioridade de plantas selecionadas sobre plantas não selecionadas e genitores, indicando a campo que a seleção em casa de vegetação visando resistência à murcha de curtobacterium foi efetiva