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The use of nitrogen (N) fertilizers is both costly to farmers and contributes to environmental degradation. N applied to wheat accounts for 18% of N applied to farmland globally, making it a prime target for reducing and optimizing N application. Chapter I is a review on nitrogen use efficiency (NUE) in wheat, with emphasis on breeding efforts and genetic resources available to increase NUE. The concept of effective use of nitrogen (EUN) as yield per unit N applied as a measure of N use, is also introduced. Chapter II is a study using two bi-parental double haploid families to evaluate genetic variability of both the genetic main effects (intercept) and linear response to N (slope) and determine the feasibility of selection for EUN in wheat. Using cross validation, a genomic prediction accuracy of 0.68 for intercept and 0.50 for slope was found, indicating that EUN is under genetic control and can be selected for. The prospect of breeding for EUN under limited resources, i.e., using fewer N rates and fewer experimental plots, is also explored. It was found that two different N treatments can be used to produce accurate predictions of intercept and slope as high as 0.98 and 0.95, respectively. Chapter III uses the same population described in chapter II to further investigate feasibility of selection for EUN using a normalized difference vegetation index (NDVI) obtained from multi-spectral aerial images gathered throughout the growing season. Cumulative photosynthesis across the growing season was estimated by integration across the NDVI curve, and compared to grain yield estimates to determine the efficacy of aerial imaging to identify high EUN lines. NDVI values and the area under the NDVI curve were able to predict yield and had the strongest ability to predict yield in moderate to low N treatments, with R2 values as high as 0.81 and 0.78 respectively. / Master of Science / Chapter I is a review on nitrogen use efficiency (NUE) in wheat, with emphasis on breeding efforts and genetic resources available to increase NUE. The concept of effective use of nitrogen (EUN) defined as grain yield per unit N applied, is contrasted to NUE as a more economic breeding goal. Chapter II uses two bi-parental mapping populations to evaluate genetic variability of both the genetic main effects and the linear response to N and determine the feasibility of selection for EUN in wheat. The efficacy of genomic prediction for EUN is explored and the prospect of breeding for EUN under limited resources is also explored. Chapter III uses the same populations described in chapter II to further investigate the feasibility of selection for EUN using a normalized difference vegetation index (NDVI) obtained from multi-spectral aerial images gathered throughout the growing season. Cumulative photosynthesis across the growing season was estimated and found to be predictive of grain yield estimates at accuracies ranging from 0.31 to 0.78.

Powdery mildew, caused by the pathogen Blumeria graminis (DC) Speer (Syn. Erysiphe graminis DC) f. sp. tritici, is a major disease of wheat (Triticum aestivum L.). Race-specific resistance is easily identified in the field due to its qualitative phenotype and it is easy to incorporate because it is inherited as a single gene. Unfortunately, this type of resistance is easily overcome by the pathogen. Traits associated with quantitative trait loci (QTL) such as adult-plant resistance (APR), have become popular with plant breeders because of their durability over a wide geographic range and time. Due to the quantitative nature of these genes, they are difficult to study requiring multiple assessments of disease development under natural conditions in more than one location over a period of several weeks. Numerous QTL for APR to powdery mildew have been mapped in independent studies in different wheat backgrounds. The wheat cultivar Massey has been the subject of several studies due to its APR to powdery mildew that has remained effective for several decades. However, it has been difficult to identity simple sequence repeat (SSR) markers that are tightly linked to the QTL for APR in Massey. Such markers give breeders an advantage by allowing them to quickly identify and select for traits that would be difficult to distinguish in the field among breeding progeny from several backgrounds. Therefore, identification of tightly linked markers associated with APR to powdery mildew is necessary so that these traits can be selected for reliably in progeny. / Master of Science

Wheat (Triticum aestivum, L) and barley (Hordeum vulgare) are widely grown as winter annual grains in a double crop rotation with soybean (Glycine max, L. Merr.) in much of the U.S. Improved management strategies and the development cultivars that meet the quality requirements of higher value end-use markets is important to increase production and profitability of winter annual grains and the double crop rotation in the Eastern U.S. In Chapter I, fifteen commercially relevant winter wheat genotypes ranging in maturity were sown in a split-plot design (sowing date=main plot, genotype=subplot) at three different sowing dates (considered to be 'very early' (20-28 days before recommended), 'early (6-11 days before recommended)', or 'recommended') and replicated three times at eight environments (site-year) from 2015-2018 in VA and KY. Grain yield, tiller estimation, heading date, protein, and 1000-kernel weight were assessed for each yield plot. At all environments, sowing earlier in the fall achieved an earlier (P<0.05) heading date, while grain yields varied depending on environment and genotype. Genotype by sowing date interactions were non-significant (P<0.05) at five site-years and significant (P<0.05) at three site-years. Molecular markers can be associated with phenotypic traits via quantitative trait loci (QTL) mapping, these markers can be used by breeders in marker assisted selection (MAS) to indirectly select phenotypic traits that are difficult or expensive to measure. In Chapter II, the genetic architecture of end-use quality is investigated in two soft red winter wheat bi-parental (Pioneer '25R47' / 'Jamestown' and Pioneer '26R46' / 'Tribute'). Both populations were genotyped with a public 90,000 wheat iSelect SNP-Array, grown over two crop seasons at two Virginia sites, evaluated for quality traits at the USDA-ARS Soft Wheat Quality Lab (SWQL), and analyzed with QTL mapping. This chapter describes a total of 24 putative QTL that were identified on 13 different chromosomes and associated with grain characteristics, milling, and/or baking performance along with phenotypic data for both populations, other putative QTL, and transgressive progeny with exceptional flour yield and cookie diameters. A region on 3A (Qfy.vt.3A.Jtwn) is a strong candidate to be utilized for MAS in soft red winter wheat breeding programs as it explained 6.9-10.3% (Pioneer 25R47 / Jamestown) and 4.6-17.0% (Pioneer 26R46 / Tribute) of the phenotypic variation for flour yield. In Chapter III, malt quality genetic structure was investigated in two winter 'malt x feed' doubled haploid barley breeding populations. Both populations were genotyped with the iSelect InfiniumTM SNP assay consisting of 50,000 barley SNPs, grown in two to three Virginia environments (Blacksburg and Warsaw) during 2017 - 2019, and characterized for 11 phenotypic traits associated with malting quality. QTL mapping validated six previously reported regions (Mohammadi, et al., 2015, GrainGenes 3.0, 2019) that are strongly associated (LOD > 3.0) with relevant malt quality traits. Phenotypic variation for malt quality was largely and consistently explained by QTL on chromosomes 1H, 5H, and 7H in the Endeavor / VA09B-34 population and by two separate QTL on 1H in the Violetta / VA09B-34 population. A region on 4H corresponding with QDp.DiMo-4H, explained between 12.1 - 42.2% (Endeavor / VA09B-34) and 30.0 - 55.7% (Violetta / VA09B-34) of the phenotypic variation for diastatic power (DU). These QTL are recommended for MAS in order to aid breeding strategies that aim to select for improved malting characteristics in Eastern U.S. malt barley breeding material. / Doctor of Philosophy / Wheat (Triticum aestivum, L) and barley (Hordeum vulgare) are staple crops throughout the world, and are the third and fourth most produced cereals crop according to the FAO. Primarily grown for human consumption, wheat and barley provide a significant percentage of the nutritional requirements for the human populations. According to the United Nations, wheat contributes 20% of all calories consumed by humans. Barley is the primary ingredient used to make beer. Increased productivity of all cropping and livestock systems is required in order to feed a growing human population while also restoring and preserving natural ecosystems. This can be accomplished through breeding and improved cropping systems management. Planting of existing cropland more frequently is fundamental to the improvement of cropping system productivity. In much of the U.S. (southern two-thirds of the lower 48), annual winter grains such as wheat and barley can be grown over the winter and spring in between the typical corn (Zea mays subsp. mays) and soybean (Glycine max, L. Merr.) growing seasons. Therefore, producing three crops in two years, as opposed to only two. Only between 6 and 11 million acres are double cropped in the US annually, for perspective, in 2018, 89 million acres of both corn and soybeans, which can only grow in summer, were planted. Over half of the soybean (~45 million) acres in Midwestern and Southeastern states could support double cropping. This is a major opportunity to maximize output per unit area, freeing up less productive land to be restored as natural ecosystems, potentially increasing carbon sequestration and species biodiversity. Winter annual grains have a very similar composition (high carbohydrate, low protein and oil) to corn, and could fill similar end-use markets currently dominated by corn (i.e. ethanol or livestock feed). For double cropping to be more widely deployed, it must be more profitable. Increased profitability of growing three crops in two years as opposed to two must outweigh the added cost of planting, managing, harvesting, and marketing the additional winter crop. Therefore, it is important to investigate management strategies that could increase production per unit area and develop new winter annual cultivars with improved end-use characteristics in order to make the winter annual more desirable to the end-users. Chapter I investigates sowing winter wheat earlier in the fall (i.e. 1st week of Oct. or last week of Sept.) in order to achieve an earlier harvest in the spring and earlier soybean planting (yield decreases 0.5 to 1 bu/ac per day that sowing is delayed), while also offering other benefits such as better-established root systems going into winter, which improves water infiltration and reduces erosion. At all environments, sowing earlier in the fall achieved an earlier heading date, while grain yields varied depending on environment and genotype. Genotype by sowing date interactions were non-significant at five site-years and significant at three site-years. Chapters II and III investigate the genetic architecture of winter wheat and winter barley breeding populations for end-use quality traits (milling/baking and malting). This was done in order to identify molecular markers that could be used to screen breeding material for improved end-use quality. The markers could then be used to assist breeders in developing soft red winter wheat cultivars with greater flour yields/improved baking performance and winter malt barley cultivars that can be grown in the Eastern U.S. and are suitable for the craft beer market. Chapter II describes 24 genomic regions that influences milling/baking performance in two soft red winter wheat breeding populations. Chapter III describes 6 genomic regions that influence malting performance in two winter barley breeding populations.

Natto and sprout soybeans are produced using small-seeded soybeans and their production is a high value alternative to grow grain soybeans for food in U.S. The development of soybean cultivars with improved natto and sprout quality is crucial for maintaining and increasing the soyfood market. However, there is insufficient information on sprout soybean characteristics. Therefore, the first objective of this study was to evaluate seed and sprout traits as potential selection criteria and study the storage effect on sprout quality. Seeds can be a vehicle for transmission of pathogens capable of causing human illness. That is why, the second objective was to identify seed-borne pathogens on a commercial soybean cultivar and to evaluate different seed decontamination treatments. Finally, seed coat deficiency is an undesirable trait for natto soybean seeds because it causes inferior appearance of the product. Thus, the third objective was to identify quantitative trait loci (QTL) underlying seed coat deficiency (SCD) and associated markers. Results showed that seed size, high-, average- and low-quality sprout percentage, hypocotyl thickness and length and sprout yield are the most important variables for breeding sprout cultivars; and one-year seed storage at room temperature reduced sprout quality. Fusarium, Alternaria and Diaphorte were the most frequent genera isolated from soybean seeds, and 2% calcium hypochlorite and 5% acetic acid were promising seed disinfection treatments. A stable QTL, qSCD20_1, was identified across two years explaining up to 25% of the variation of SCD; and eight molecular markers tightly linked and nearby qSCD20_1 were identified. Information presented will be helpful for sprout and natto soybean cultivar development. / Master of Science / Natto and sprout soybeans are produced using by small-seeded soybeans and their production is a high value alternative to grow grain soybeans for feed in U.S. The development of soybean cultivars with improved natto and sprout quality is crucial for maintaining and increasing the soyfood market. However, there is insufficient information on sprout soybean characteristics. Therefore, the first objective of this study was to evaluate important seed and sprout traits as potential selection criteria of soybean cultivars and study the storage effect on sprout quality. Seeds can be contaminated with fungi capable of causing human illness. So, the second objective was to identify fungus species associated with seeds of a sprout soybean cultivar and evaluate different seed disinfection treatments. Finally, seed coat deficiency is an undesirable trait for natto soybean seeds because it causes inferior appearance of the product. Thus, the third objective was to identify molecular markers associated with seed coat deficiency. Results showed that seed size, high-, average- and low-quality sprout percentage, hypocotyl thickness and length and sprout yield are the most important variables for breeding sprout cultivars; and one-year seed storage at room temperature reduced sprout quality. Fungal species that may cause human illness were isolated from sprout soybean seeds and calcium hypochlorite and acetic acid are promising seed disinfection treatment for reducing fungus incidence. Finally, eight molecular markers associated with seed coat deficiency were identified which may be potentially used in selecting natto soybean cultivars with low seed coat deficiency. Information presented will be helpful for sprout and natto soybean cultivar development.

Groat oil content and composition are important quality traits in oats (Avena sativa L). These traits are controlled by many genes with additive effects. The chromosomal regions containing these genes, known as quantitative trait loci (QTL), can be discovered through their close association with markers. This study investigated total oil content and fatty acid components in an oat breeding population derived from a cross between high oil ('Dal') and low oil ('Exeter') parents. A genetic map consisting of 475 DArT (Diversity Array Technology) markers spanning 1271.8 cM across 40 linkage groups was constructed. QTL analysis for groat oil content and composition was conducted using grain samples grown at Aberdeen, ID in 1997. QTL analysis for multiple agronomic traits was also conducted using data collected from hill plots and field plots in Ottawa, ON in 2010. QTLs for oil content, palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2) and linolenic acid (18:3) were identified. Two of the QTLs associated with oil content were also associated with all of the fatty acids examined in this study, and most oil-related QTL showed similar patterns of effect on the fatty acid profile. These results suggest the presence of pleiotropic effects on oil-related traits through influences at specific nodes of the oil synthesis pathway. In addition, 12 QTL-associated markers (likely representing nine unique regions) were associated with plant height, heading date, lodging, and protein content. The results of this study will provide information for molecular breeding as well as insight into the genetic mechanisms controlling oil biosynthesis in oat.

Estudos genético quantitativos e moleculares são fundamentais para o melhoramento animal e sua realização com a raça Nelore é de grande importância devido a ampla participação dessa no rebanho de corte nacional. A estimação constante dos parâmetros genéticos das características de produção é necessário para a adequada condução do processo de seleção dos animais. A melhoria de características relacionadas à carcaça bovina é essencial para a eficiência e sustentabilidade da atividade e a implementação de métodos de seleção animal baseados em informações moleculares pode revolucionar a produção zootécnica e deve ser profundamente estudado. Sendo assim, os objetivos do presente estudo foram estimar parâmetros genéticos e componentes de variância através de diferentes modelos matemáticos para um total de 14 características fenotípicas (o peso ao nascimento, peso a desmama, peso ao sobreano, ganho de peso entre a desmama e o sobreano ajustado para um intervalo de 345 dias, perímetro escrotal ao sobreano, altura de garupa ao sobreano, escores visuais avaliados ao sobreano de conformação, precocidade, musculosidade, comprimento de umbigo e ossatura, e ainda características de carcaça mensuradas por ultrassonografia realizada após 30 a 45 dias de confinamento como a área de olho de lombo, espessura de gordura subcutânea, espessura de gordura na picanha). Foram estimadas correlações entre todas estas características com as de carcaça mensuradas por ultrassonografia. Sob o enfoque molecular, desenvolveu-se um programa para imputação de genótipos faltantes e estudaram-se diferentes métodos de associação de marcadores moleculares do tipo mutação de base nitrogenada única (SNP) a características de produção incluídas no índice de seleção de um programa de melhoramento da raça Nelore, utilizando inferência bayesiana. Todas as características estudadas podem ser selecionadas esperando-se progresso genético na população. Os efeitos maternos foram importantes em algumas características onde normalmente estes efeitos não têm sido considerados atualmente. A quantidade de escores atribuídos a uma característica categórica assim como o número de observações fenotípicas resultam em diferenças nas estimativas quando avaliadas por modelos lineares ou de limiar. Não deverão ser obtidos resultados satisfatórios na melhoria das características de carcaça se a seleção for baseada nas tradicionais avaliações visuais utilizadas no momento. Os métodos utilizados na análise de associação dos marcadores podem originar diferentes resultados. Os marcadores que apresentaram efeitos altamente relevantes (P<0,01) geralmente apresentaram resultados semelhantes, independentemente do método utilizado. Certos marcadores podem ter efeitos positivos para algumas características componentes do índice de seleção e negativos para as demais. A análise em conjunto com todos os SNP\'s e todos os dados fenotípicos disponíveis é viável e parece ser a mais adequada. O método desenvolvido de imputação de genótipos faltantes a partir do parentesco de animais genotipados foi eficiente. / Quantitative and molecular genetic studies are very important for animal breeding and studies with Nellore cattle have great importance due to the large participation of that breed in the Brazilian beef cattle industry (around 80% of the herd). The constant estimation of genetic parameters for traits linked to production is necessary for properly perform selection of animals. The improvement of carcass traits is essential for efficiency and profitability of the activity. The implementation of methods for animal selection based on molecular information could revolutionize animal production and should be deeply studied. Thus, the objectives of this study were to estimate genetic parameters and variance components using different mathematical models for a total of 14 traits, such as birth weight, weaning weight, yearling weight, post-weaning weight gain between weaning and yearling adjusted for 345 days, yearling scrotal circumference, yearling hip height, yearling visual scores like conformation, finishing, muscularity, bone structure and navel length. Ultrasound measurements for carcass traits performed at feedlot (30 to 45 days, at approximate age of 20 months) such as rib-eye area, fat thickness, rump fat thickness were, also, evaluated. Estimate correlations between all these traits with the carcass traits measured by ultrasound were estimated. As concerned to molecular study, an algorithm for imputation of missing genotypes was developed and different methods to analyze molecular marker (single nucleotide polymorphism - SNP) association with traits components of the selection index of a breeding program that is applied to the population studied, using bayesian inference, were used. Genetic progress will be expected for selection of all the traits studied. Maternal effects were important in some traits in which those effects are not usually considered. The amount of scores assigned to a categorical trait and the number of observations could result in different estimates when evaluated by linear or threshold models. The selection for visual scores traditionally used in that population will not improve carcass traits. The methods used to analyze the association of markers may lead to different results. The SNP\'s with association effects of high relevance (P<0.01) generally express their effects regardless of the method used to analyze. Some markers may have positive effects for some traits of selection index, but negative for others. The joint analysis with all SNPs and with all available phenotypes is feasible and appears to be more appropriate. The algorithm developed for imputation of missing genotypes from pedigree information of genotyped animals was efficient.

Dados de desenvolvimento ponderal de 3.844 bovinos da raça Nelore, criados em pastagens em duas fazendas do sudoeste do Brasil, dos quais 1.889 tiveram suas carcaças avaliadas por ultra-sonografia e 674 foram confinados por 90 a 120 dias e abatidos por volta dos 24 meses de idade tiveram análises de associação com dezenas de marcadores genéticos realizadas, visando detectar a associação desses marcadores com características economicamente relevantes. Foram analisadas as características de crescimento, peso ao nascer (PNAS), peso a desmama (PDES), peso ao sobreano (PSOB), ganho de peso pós-desmama (GP345), escores visuais de conformação frigorífica (CONF), precocidade de acabamento (PREC), musculosidade (MUSC) e de carcaça área de olho de lombo medida por ultra-sonografia (AOL_US), espessuras de gorduras medida por ultra-som na região lombar (EGS_US) e na picanha (EGP8). Adicionalmente, foram analisadas as características medidas post-mortem, relacionadas a qualidade de carcaça, peso de carcaça quente (PCQ), área de olho de lombo (AOL), espessura de gordura no músculo Longissimus dorsi (EGS) e as características ligadas à qualidade de carne, perdas por exsudação após 7, 14 ou 21 dias de maturação da carne (PEX7, PEX14, PEX21), perdas por cocção e maciez após os mesmos períodos de maturação (PCO7, PCO14 e PCO21, MAC7, MAC14 e MAC21), além de teor de lipídeos totais e colesterol em amostras após 7 dias de maturação. Os genótipos dos polimorfismos de base única (SNP) foram obtidos em laboratórios licenciados por empresa parceira, com uso de placas de micro-arranjos dessa empresa. Foram analisados os efeitos de substituição em análises de marcador único e multi-polimorfismos e os efeitos de aditividade e desvio de dominância de cada marcador genético. Vários dos polimorfismos de DNA analisados apresentaram ou fixação ou freqüências muito altas, maiores que 99%, de um dos alelos impossibilitando as análises de associação. No entanto, muitos outros polimorfismos apresentaram freqüências gênicas adequadas às análises de associação. Cada uma das características avaliadas apresentou, no mínimo, dois marcadores com efeitos significativos (P&le;0,05) ou sugestivos (0,05&lt;P&le;0,20), o que indica que polimorfismos de DNA podem ser critérios adicionais e auxiliares nos processos seletivos ligados às 24 características de desenvolvimento ponderal, qualidade de carcaça e carne na raça Nelore. Como os efeitos de substituição alélica são responsáveis apenas por parte da determinação de cada característica, em geral uma pequena parte, recomenda-se que as previsões de efeitos de marcadores sejam feitas com análise conjunta dos mesmos. / Data on of 3,844 Nellore cattle, reared under pasture conditions on two different farms in southwestern Brazil, 1,889 of them measured by ultra-sound for carcass traits and 674 bulls finished in a feedlot for 90 to 120 days and slaughtered around 24 month of age were analyzed to verify the association with genetic markers (DNA Single nucleotide polymorphism or SNP) with the objective of detecting association of those markers with traits economically important relevant for Brazilian beef business. Growth traits considered were birth weight (PNAS), weaning weight (PDES), yearling weight, measured at 18 mo (PSOB), weight gain after weaning (GP345), visual scores for carcass conformation (CONF), finishing (PREC) and muscle (MUSC). Carcass traits, measured by ultra-sound were ribeye area (AOL_US), backfat (EGS_US) and fat depth at rump (EGP8). Additionally, carcass traits measured after slaughter were hot carcass weight (PCQ), ribeye area (AOL), fat depth on Longissimus muscle (EGS). Meat quality traits were measured after 7, 14 and 21 days of ageing: weep loss (PEX7, PEX14 and PEX21), shrink loss (PCO7, PCO14 and PCO21) and tenderness (MAC7, MAC14 and MAC21). Total lipids and cholesterol content on samples aged for 7 days, were, also, included on the analysis. The genotypes of DNA markers were carried out in laboratories licensed by a private company using its micro-array panels. Allele substitution effects were estimated in single or multi-polymorphism analysis. Additive and dominance effects were also estimated. Many DNA polymorphisms analyzed showed to be fixed or the frequencies for one of the alleles were too high, more than 99 %. In those cases, analysis could not be performed. However, for many others polymorphisms there was observed variability on allele frequencies what make possible to do the association analysis. All traits analyzed were influenced by, at least, two polymorphisms with statistically significant (P&le;0,05) or suggestive (0,05&lt;P&le;0,20) effects, thus DNA polymorphisms can be used as additional and auxiliary criteria on selection process of those 24 traits related to animal growth, carcass and meat quality in Nellore cattle. As allele substitution effects explain only a small part of the phenotype, the results of this paper suggest that the effect of those markers should be considered together.

Dados de desenvolvimento ponderal de 3.844 bovinos da raça Nelore, criados em pastagens em duas fazendas do sudoeste do Brasil, dos quais 1.889 tiveram suas carcaças avaliadas por ultra-sonografia e 674 foram confinados por 90 a 120 dias e abatidos por volta dos 24 meses de idade tiveram análises de associação com dezenas de marcadores genéticos realizadas, visando detectar a associação desses marcadores com características economicamente relevantes. Foram analisadas as características de crescimento, peso ao nascer (PNAS), peso a desmama (PDES), peso ao sobreano (PSOB), ganho de peso pós-desmama (GP345), escores visuais de conformação frigorífica (CONF), precocidade de acabamento (PREC), musculosidade (MUSC) e de carcaça área de olho de lombo medida por ultra-sonografia (AOL_US), espessuras de gorduras medida por ultra-som na região lombar (EGS_US) e na picanha (EGP8). Adicionalmente, foram analisadas as características medidas post-mortem, relacionadas a qualidade de carcaça, peso de carcaça quente (PCQ), área de olho de lombo (AOL), espessura de gordura no músculo Longissimus dorsi (EGS) e as características ligadas à qualidade de carne, perdas por exsudação após 7, 14 ou 21 dias de maturação da carne (PEX7, PEX14, PEX21), perdas por cocção e maciez após os mesmos períodos de maturação (PCO7, PCO14 e PCO21, MAC7, MAC14 e MAC21), além de teor de lipídeos totais e colesterol em amostras após 7 dias de maturação. Os genótipos dos polimorfismos de base única (SNP) foram obtidos em laboratórios licenciados por empresa parceira, com uso de placas de micro-arranjos dessa empresa. Foram analisados os efeitos de substituição em análises de marcador único e multi-polimorfismos e os efeitos de aditividade e desvio de dominância de cada marcador genético. Vários dos polimorfismos de DNA analisados apresentaram ou fixação ou freqüências muito altas, maiores que 99%, de um dos alelos impossibilitando as análises de associação. No entanto, muitos outros polimorfismos apresentaram freqüências gênicas adequadas às análises de associação. Cada uma das características avaliadas apresentou, no mínimo, dois marcadores com efeitos significativos (P&le;0,05) ou sugestivos (0,05&lt;P&le;0,20), o que indica que polimorfismos de DNA podem ser critérios adicionais e auxiliares nos processos seletivos ligados às 24 características de desenvolvimento ponderal, qualidade de carcaça e carne na raça Nelore. Como os efeitos de substituição alélica são responsáveis apenas por parte da determinação de cada característica, em geral uma pequena parte, recomenda-se que as previsões de efeitos de marcadores sejam feitas com análise conjunta dos mesmos. / Data on of 3,844 Nellore cattle, reared under pasture conditions on two different farms in southwestern Brazil, 1,889 of them measured by ultra-sound for carcass traits and 674 bulls finished in a feedlot for 90 to 120 days and slaughtered around 24 month of age were analyzed to verify the association with genetic markers (DNA Single nucleotide polymorphism or SNP) with the objective of detecting association of those markers with traits economically important relevant for Brazilian beef business. Growth traits considered were birth weight (PNAS), weaning weight (PDES), yearling weight, measured at 18 mo (PSOB), weight gain after weaning (GP345), visual scores for carcass conformation (CONF), finishing (PREC) and muscle (MUSC). Carcass traits, measured by ultra-sound were ribeye area (AOL_US), backfat (EGS_US) and fat depth at rump (EGP8). Additionally, carcass traits measured after slaughter were hot carcass weight (PCQ), ribeye area (AOL), fat depth on Longissimus muscle (EGS). Meat quality traits were measured after 7, 14 and 21 days of ageing: weep loss (PEX7, PEX14 and PEX21), shrink loss (PCO7, PCO14 and PCO21) and tenderness (MAC7, MAC14 and MAC21). Total lipids and cholesterol content on samples aged for 7 days, were, also, included on the analysis. The genotypes of DNA markers were carried out in laboratories licensed by a private company using its micro-array panels. Allele substitution effects were estimated in single or multi-polymorphism analysis. Additive and dominance effects were also estimated. Many DNA polymorphisms analyzed showed to be fixed or the frequencies for one of the alleles were too high, more than 99 %. In those cases, analysis could not be performed. However, for many others polymorphisms there was observed variability on allele frequencies what make possible to do the association analysis. All traits analyzed were influenced by, at least, two polymorphisms with statistically significant (P&le;0,05) or suggestive (0,05&lt;P&le;0,20) effects, thus DNA polymorphisms can be used as additional and auxiliary criteria on selection process of those 24 traits related to animal growth, carcass and meat quality in Nellore cattle. As allele substitution effects explain only a small part of the phenotype, the results of this paper suggest that the effect of those markers should be considered together.

Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2015-10-13T22:42:35Z No. of bitstreams: 1 Tese_Renata Nat?lia_PPG_RGV.pdf: 4534182 bytes, checksum: 0d860c2ab1b6041788983d56cd000549 (MD5) / Made available in DSpace on 2015-10-13T22:42:35Z (GMT). No. of bitstreams: 1 Tese_Renata Nat?lia_PPG_RGV.pdf: 4534182 bytes, checksum: 0d860c2ab1b6041788983d56cd000549 (MD5) Previous issue date: 2015-07-24 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / The powdery mildew is one of the most important foliar diseases that attack the watermelon and other cucurbits in Brazil and in the world. The principal identification elements by the consumer are based on the external appearance and quality of the fruit. The objective of this study was to identify microsatellite markers linked to resistance to powdery mildew and to the stripe pattern of watermelon fruits with microsatellite markers. Plants of the parents, F1 and F2, which are the result of a cross between the cultuvars BRS Opara (powdery mildew resistant and with clearly defined stripes fruit) and P?rola (powdery mildew susceptible and with diffuse stripes fruit), were phenotyped in the field for resistance or susceptibility to powdery mildew and, after of the harvest, the fruits was morphologically characterized. For these characteristics, 116 microsatellite markers were analyzed and the linkage analysis done in JoinMap 2.0. Segregation in the F2 population demonstrated that resistance powdery mildew and the stripe pattern are controlled by a single dominant gene. The microsatellite loci MCPI_11, CYSTSIN and BVWS02441 showed linked to the powdery mildew resistance gene at 2.6 cM with LODs ?score? of 31.42 and are located in chromosome two of the watermelon genome. The microsatellite loci MCPI_05 and MCPI_16 showed a linkage to the stripe patterns of watermelon fruits at a distance of 1.5 and 1.8 cM with a LODs ?scores? of 39.28 and 38.11 respectively, and are located in the chromosome six of the watermelon genome. These markers can be used in the marker assisted selection process in watermelon improvement programs. / O o?dio ? uma das principais doen?as foliares que acomete a melancia e outras cucurbit?ceas, no Brasil e no mundo. Os principais elementos de identifica??o de uma cultivar pelo consumidor est?o relacionados com a apar?ncia externa e qualidade do fruto. O objetivo deste trabalho foi identificar marcadores microssat?lites ligados ? resist?ncia ao o?dio e ao padr?o de listras de frutos de melancia. Plantas dos parentais, de F1 e de F2, resultantes do cruzamento entre as cultivares BRS Opara (resistente ao o?dio e com padr?o de listras claramente definidas) e P?rola (suscet?vel ao o?dio e com padr?o de listras difusas) foram fenotipadas em campo para resist?ncia ou suscetibilidade ao o?dio e, ap?s a colheita, os frutos foram caracterizados quanto ao padr?o de listras. Para essas duas caracter?sticas foram analisados 116 marcadores microssat?lites e as an?lises de liga??o foram realizadas no programa JoinMap 2.0. A segrega??o da popula??o F2 demonstrou que a resist?ncia ao o?dio e o padr?o de listras de frutos de melancia s?o caracter?sticas monog?ncias e dominantes. Os microssat?lites MCPI_11, CYSTSIN e BVWS02441 mostraram-se ligados ao gene que confere resist?ncia ao o?dio a 2,6 cM com LODs ?score? de 31,42 e est?o localizados no cromossomo dois no genoma da melancia. Os microssat?lites MCPI_05 e o MCPI_16 est?o ligados ao padr?o de listras de frutos de melancia a uma dist?ncia de 1,5 e 1,8 cM com LODs ?score?de 39,28 e 38,11, respectivamente, e est?o localizados no cromossomo seis do genoma da melancia. Esses marcadores poder?o ser utilizados no processo de sele??o assistida por marcadores em programas de melhoramento de melancia.