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.

Submitted by Ana Luiza Azank Veltri null (anaveltri@hotmail.com) on 2017-03-30T23:04:18Z No. of bitstreams: 1 Dissertação_AnaVeltri_final.pdf: 3049259 bytes, checksum: 9daf03e3f66bf72133c07a9b3442b12d (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-03-31T13:21:29Z (GMT) No. of bitstreams: 1 veltri_ala_me_bot.pdf: 3049259 bytes, checksum: 9daf03e3f66bf72133c07a9b3442b12d (MD5) / Made available in DSpace on 2017-03-31T13:21:30Z (GMT). No. of bitstreams: 1 veltri_ala_me_bot.pdf: 3049259 bytes, checksum: 9daf03e3f66bf72133c07a9b3442b12d (MD5) Previous issue date: 2017-02-03 / O uso das plantas medicinais, aromáticas e condimentares pela humanidade desde os tempos mais remotos revela também a associação existente entre conhecimento empírico e conhecimento científico, bem como sua importância para diferentes setores da sociedade. Devido à crescente abrangência e demanda do mercado em relação a este grupo de plantas, tornam-se maiores as necessidades de investimentos para a produção contínua da matéria-prima, a fim de atender às diferentes áreas de interesse. Detentores de conhecimentos vivenciados na prática, os agricultores representam um elo essencial desta complexa cadeia produtiva. Sendo assim, a presente pesquisa buscou nas Etnociências, métodos para desenvolver um registro agronômico acerca das Boas Práticas Agrícolas de plantas medicinais, aromáticas e condimentares no município de Botucatu, SP, a partir do conhecimento empírico de oito famílias de agricultores produtores destas plantas. Pela importância deste grupo, um levantamento socioeconômico foi realizado para caracterizar os atores sociais envolvidos nesta produção agronômica e compreender o contexto em que estão inseridos. Os processos metodológicos realizados partem de pesquisas quantitativas e qualitativas. Para a investigação do tema, foi feita análise documental, complementada pelas entrevistas semiestruturadas para a coleta de informações, registradas em caderno de campo e recursos audiovisuais, via gravações de voz e fotografias. A observação participante possibilitou a compreensão mais profunda do contexto do grupo humano estudado. Durante o levantamento de dados, dois experimentos foram conduzidos em laboratório a partir das necessidades encontradas pelos agricultores em relação às Boas Práticas Agrícolas estudadas aqui. A análise quantitativa, por sua vez, foi realizada por métodos de estatística descritiva, com sínteses apresentadas em forma de gráficos e tabelas. Diante da ocorrência da espécie medicinal Passiflora incarnata L. na produção agronômica de todos os participantes, seu sistema de cultivo é analisado e discutido. Os dados analisados revelam não só o potencial produtivo dos agricultores, mas também as fragilidades encontradas por eles, no campo, e também, nos âmbitos socioeconômicos. A complexidade das relações humanas entre diferentes atores sociais que surge nos relatos reflete na cadeia produtiva do grupo de plantas estudado. A integração entre os conhecimentos, empírico e científico, que sustenta esta pesquisa, busca validá-los e reconhecê-los em diversos setores da sociedade envolvidos no complexo agroindustrial de plantas medicinais, aromáticas e condimentares. / The use of medicinal plants by humanity reveals the association between empirical and scientific knowledge, and also their significance for different sectors of society. Given the increasing demand for medicinal plants, additional investment in its production is needed in order to meet this demand. The small family farmers represent an essential bond in this production chain due to their experience and local knowledge. In order to validate their empirical knowledge of good agricultural practices, this study is supported by an Ethnosciences review. The sample group of this research is comprised by eight family farmers that produce medicinal plants in the city of Botucatu, SP. A socioeconomic data survey was also performed in order to characterize them and understand their social context. Methodological processes of this study are based in both quantitative and qualitative researches. A literature review and semi structured interviews were also conducted to collect information, which were recorded in a field journal and audio-visual resources. Participant observations enabled a deeper understanding of the family farmers’ social context. During the data survey, two Laboratory experiments were conducted in the University with the intention to meet some family farmers’ needs from agronomic production. The quantitative analyses are supported by statistical data. All participants mentioned the agronomic production of Passiflora incarnata L. at least once in their production processes. Consequently, the good agricultural practices of this medicinal species are analysed and discussed. As a result, this study shows the productive potential of the family farmers and the issues faced by them in the field and in the socioeconomic environment. The integration between empirical and scientific knowledge that consolidate this research, aims to validate them in the different social sectors involved in the medicinal plant production chain.

Inia 66 and Siete Cerros wheat varieties, and Steveland and Woodvale barley varieties were grown in mixtures and in pure stands for two years in irrigated nurseries at Logan. These four varieties were also grown the first year in a dryland nursery at Blue Creek. Another set of four varieties was used the second year in the dryland nursery. These four varieties as well as the first set, were tested in seven combinations, with the following percentages of one barley and one wheat variety : 100:0, 90:10, 75:25, 50:50, 25:75, 10:90, and 0:100. Grain yield of mixtures was higher than that of the mid-component value in most cases and was higher than that of the best component in a few cases. Only a few of the observed differences were statistically significant. All mixtures had significantly lower test weight than that of the best component. Ninety percent of the mixtures were significantly lower in test weight than the mid-component value. Tillering of both wheat varieties consistently decreased as the percentage of wheat in the seeded mixture decreased. Conversely, tillering in barley increased as the percentage of barley in the seeded mixture decreased. Most of the mixtures showed an excess of barley in the harvested crop, compared to that in the seeded mixture. These excesses were usually greatest around the 50:50 mixture level. A consistent pattern of slight increase in kernel weight of barley was observed as the amount of barley decreased in the seeded mixture. Wheat showed the reverse situation. None of these differences were statistically significant. Inter-relationships among yield components were evaluated by simple correlation coefficients. The correlations were subdivided into direct and indirect effects by the use of path coefficient analyses. Correlation coefficients and path coefficients showed consistent changes as the percentage of crop mixtures changed. Coefficients of determination for both wheat and barley decreased as the percentage of that crop in the seeded mixture was decreased.

Lately the rate of genetic gain in most agronomic crop species has been reduced due to several factors that limit breeding efficiency and genetic gain. New genetic tools and more powerful statistical analyses provide an alternative approach to enhance genetic improvements through the identification of molecular markers linked to genomic regions or QTLs controlling quantitative traits. The main objective of this research was to identify genomic regions associated with enhanced agronomic performance in lines per se and hybrid combination in Sorghum bicolor (L.) Moench. A population composed of 187 F5:6 recombinant inbred lines (RIL) was derived from the cross of restorer lines RTx430 and RTx7000. Also, a testcross hybrid population (TCH) was developed by using each RIL as a pollinator onto ATx2752. A linkage map was constructed using 174 marker loci generated from AFLP and SSR primer combinations. These markers were assigned to 12 different linkage groups. The linkage map covers 1573 cM with marker loci spaced at an averaged 9.04 cM. In this study, 89 QTL that control variation in seven different morphological traits were identified in the recombinant inbred line population, while in the testcross hybrid population, 79 QTL were identified. These traits included grain yield, plant height, days to mid-anthesis, panicle number, panicle length, panicle exsertion and panicle weight. These putative QTL explained from 4 to 42% of the phenotypic variation observed for each trait. Many of the QTL were not consistent across populations and across environments. Nevertheless, a few key QTL were identified and the source of the positive additive genetics isolated. RTx7000 was consistently associated with better agronomic performance in RIL, while in testcrosses, RTx430 was. Some genomic regions from RTx7000 may be utilized to improve RTx430 as a line per se. However, it is very unlikely that such regions will have a positive effect on the combining ability of RTx430 since testcross results did not reveal any transgressive segregants from the RIL population.

In Canada, flax (<i>Linum usitatissimum</i> L.) is grown for its seed oil. However, a major disadvantage associated with growing oilseed flax is that the straw is difficult to incorporate into the soil after harvest. Instead, the majority of flax straw is burned in the field, increasing the workload for farmers, as well as creating air pollution. Agronomic concerns are also associated with burning, since it leaves fields vulnerable to wind and water erosion. A small market exists for Canadian flax straw for making high quality paper products and some plastic composites. However, fibre-based and fibre-using industries are growing world wide, and flax straw fibre is becoming an important product. Flax straw fibre concentration varies among cultivars and environments. Consistently high fibre concentrations are essential if the fibre in oilseed flax is to become an important product for Canadian farmers. This study assembled the agronomic information necessary to select for increased straw fibre concentration in the Crop Development Centre (CDC) Flax Breeding Program. Three experiments were conducted to determine: how seeding rate and row spacing effects straw fibre concentration, the effects of seeding date on straw fibre concentration, and how nitrogen fertilizer rates effects straw fibre concentration. Seeding in mid-May at either an 18 or 36 cm row spacing at a seeding rate of 30 or 45 kg/ha resulted in high straw fibre concentration without reducing other important oilseed characteristics such as seed yield, oil content and straw fibre yield. Nitrogen fertilizer did not have an effect on either straw fibre concentration or straw fibre yield.

In Canada, flax (<i>Linum usitatissimum</i> L.) is grown for its seed oil. However, a major disadvantage associated with growing oilseed flax is that the straw is difficult to incorporate into the soil after harvest. Instead, the majority of flax straw is burned in the field, increasing the workload for farmers, as well as creating air pollution. Agronomic concerns are also associated with burning, since it leaves fields vulnerable to wind and water erosion. A small market exists for Canadian flax straw for making high quality paper products and some plastic composites. However, fibre-based and fibre-using industries are growing world wide, and flax straw fibre is becoming an important product. Flax straw fibre concentration varies among cultivars and environments. Consistently high fibre concentrations are essential if the fibre in oilseed flax is to become an important product for Canadian farmers. This study assembled the agronomic information necessary to select for increased straw fibre concentration in the Crop Development Centre (CDC) Flax Breeding Program. Three experiments were conducted to determine: how seeding rate and row spacing effects straw fibre concentration, the effects of seeding date on straw fibre concentration, and how nitrogen fertilizer rates effects straw fibre concentration. Seeding in mid-May at either an 18 or 36 cm row spacing at a seeding rate of 30 or 45 kg/ha resulted in high straw fibre concentration without reducing other important oilseed characteristics such as seed yield, oil content and straw fibre yield. Nitrogen fertilizer did not have an effect on either straw fibre concentration or straw fibre yield.

Lately the rate of genetic gain in most agronomic crop species has been reduced due to several factors that limit breeding efficiency and genetic gain. New genetic tools and more powerful statistical analyses provide an alternative approach to enhance genetic improvements through the identification of molecular markers linked to genomic regions or QTLs controlling quantitative traits. The main objective of this research was to identify genomic regions associated with enhanced agronomic performance in lines per se and hybrid combination in Sorghum bicolor (L.) Moench. A population composed of 187 F5:6 recombinant inbred lines (RIL) was derived from the cross of restorer lines RTx430 and RTx7000. Also, a testcross hybrid population (TCH) was developed by using each RIL as a pollinator onto ATx2752. A linkage map was constructed using 174 marker loci generated from AFLP and SSR primer combinations. These markers were assigned to 12 different linkage groups. The linkage map covers 1573 cM with marker loci spaced at an averaged 9.04 cM. In this study, 89 QTL that control variation in seven different morphological traits were identified in the recombinant inbred line population, while in the testcross hybrid population, 79 QTL were identified. These traits included grain yield, plant height, days to mid-anthesis, panicle number, panicle length, panicle exsertion and panicle weight. These putative QTL explained from 4 to 42% of the phenotypic variation observed for each trait. Many of the QTL were not consistent across populations and across environments. Nevertheless, a few key QTL were identified and the source of the positive additive genetics isolated. RTx7000 was consistently associated with better agronomic performance in RIL, while in testcrosses, RTx430 was. Some genomic regions from RTx7000 may be utilized to improve RTx430 as a line per se. However, it is very unlikely that such regions will have a positive effect on the combining ability of RTx430 since testcross results did not reveal any transgressive segregants from the RIL population.

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)

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