O presente trabalho teve por objetivo avaliar diferentes espaçamentos entre linhas e densidades de plantas em três cultivares de algodoeiro com diferentes arquiteturas de plantas. Os experimentos foram conduzidos no ano agrícola 2005/2006 no Centro Experimental Central, do Instituto Agronômico, em Campinas-SP, no Pólo Regional do Noroeste Paulista, da APTA, em Votuporanga-SP e na Fazenda de Ensino e Pesquisa da Unesp, Campus de Ilha Solteira, em Selvíria-MS. O delineamento experimental utilizado foi em blocos ao acaso, em esquema fatorial 2x2x3, com 4 repetições, sendo dois espaçamentos entre linhas (0,45 e 0,90 m), duas densidades de semeadura (6 e 10 plantas.m-1) e três cultivares (IAC 24, DeltaOpal e Fibermax 966). Em cada parcela experimental foram tomadas 4 plantas ao caso e avaliadas as seguintes variáveis: altura final das plantas, altura de inserção do 1° ramo frutífero, diâmetro do caule, número de ramos reprodutivos e número de capulhos por planta. Em Votuporanga foram determinadas a incidência de podridão de maçãs e a espessura do pericarpo de maçãs jovens. Amostras de 20 capulhos foram colhidas em cada parcela experimental, para a avaliação dos componentes da produção: massa de um capulho, massa de 100 sementes e porcentagem de fibra (apenas no experimento de Campinas); e para as análises das características tecnológicas da fibra: comprimento, uniformidade de comprimento, tenacidade, micronaire e maturidade. Em Campinas foi determinada a produção de algodão em caroço na área útil de cada parcela do experimento. De acordo com os dados obtidos, pôde-se concluir que: a utilização de espaçamentos mais largos acarreta maior altura final das plantas, maior diâmetro do caule, maior número de ramos reprodutivos e número de capulhos por planta; a utilização de espaçamentos entre 0,45 e 0,90 m e densidades de plantas entre 6 e 10 plantas.m-1 não acarreta em diferenças na produtividade do algodoeiro; em condições de menor competição entre plantas e maior penetração de luz no dossel, isto é, sob espaçamentos mais largos e/ou menor densidade de plantas na linha, o algodoeiro prioriza a produção de fibras; independente da cultivar e do espaçamento adotado, o índice micronaire pode aumentar com a redução do número de plantas na linha; a incidência de podridão de maçãs do algodoeiro, bem como sua severidade, estão relacionadas ao genótipo utilizado, quer seja pela arquitetura da planta como também pela espessura do pericarpo dos frutos. / The aim of this work was to evaluate different row spacings and plant population densities for three cotton cultivars with different plant architecture. The experiments were carried out in experimental areas belonging to Instituto Agronômico, in Campinas- SP, at Pólo Regional do Noroeste Paulista, from APTA, in Votuporanga-SP and at Unesp Campus de Ilha Solteira, in Selvíria-MS. A randomized block design was used, with four replicates, in a factorial 2x2x3 scheme, with two row spacings (0.45 and 0.90 m), two plant population densities (6 and 10 plants.m-1) and three cotton cultivars (IAC 24, DeltaOpal e Fibermax 966). Four plants per plot were labeled and analyzed for the plant height, insertion height of the first fruit branch, stem diameter, number of fruit branches and open bolls per plant. In Votuporanga were also analyzed the boll rot incidence and the pericarp thickness of young bolls. Samples of 20 open bolls randomized chosen per plot were analyzed for yield components: average open boll mass, 100 seeds mass, and fiber percentage, just on the Campinas experiment; and for fiber technological characteristics: length, length uniformity, strength, micronaire and maturity. In Campinas the cotton yield was determinated in the useful area of each plot. According to the experimental data obtained it was possible to conclude: the use of wider row spacing leads to a greater plant height, larger stem diameter, greater number of fruit branches and bolls per plant. The use of row spacing varying from 0.45 to 0.90 and plant densities varying from 6 to10 plants.m-1 do not affect cotton yield; under lower plant competition and higher light levels in the canopy, that is, in wider row spacing and/or lower plant population, the fiber production is prioritized by the cotton plant; independently of the cultivar and row spacing, the micronaire may increase with plant population reduction; the boll rot incidence, as well as its severity, are related to plant genotype, due to either plant architecture and pericarp thickness.

Brown stink bug, Euschistus servus (Heteroptera: Pentatomidae), is a recently re-emerged pest of cotton in Arizona. It has been present in southwestern desert-grown cotton since at least the early 1900’s, but dropped from primary pest status in the latter half of the twentieth century. Farmers and pest managers did not perceive it as a primary or economic pest until 2011, when elevated numbers of brown stink bugs were reported in isolated valleys of Arizona and southeastern California. Reports increased and became more widespread in the following years. In response to increased abundance of brown stink bug and corresponding cotton boll injury, research was needed to provide information to cotton farmers. First, pest managers needed information on which factors affect the susceptibility of cotton bolls to stink bug feeding (chapter 1). Young bolls are most vulnerable to stink bug injury, and injury is sustained in the first four days of feeding. In addition, research was needed to determine the effects of currently available brown stink bug chemical controls on the broader integrated pest management system in Arizona cotton (chapter 2). Current chemical control options disrupt natural enemy communities, which results in outbreaks and resurgences of other cotton pests. The negative outcomes and additional costs outweigh the benefits of brown stink bug management.

Orientador: Enes Furlani Junior / Resumo: O N é um dos elementos mais dinâmicos no solo, conforme sua transformação no meio. A lixiviação de nitrato e do amônio no solo é considerada a principal perda do N disponível às plantas, quanto maior for à aplicação deste elemento no solo, maior será o potencial de poluição do solo e da água. Objetivou-se, neste trabalho, avaliar a lixiviação de amônio e nitrato em um Latossolo Vermelho em diferentes profundidas do solo, em função de doses e fontes de N distintas, em sistemas irrigado e não irrigado nas condições de campo. O experimento foi conduzido no ano agrícola 2014/15, na área experimental da fazenda de ensino, pesquisa e extensão, localizada no município de Selvíria-MS. Utilizou-se o delineamento em blocos casualizados, com 20 tratamentos dispostos em fatorial 5x2x2, com 4 repetições. Aplicou-se 5 doses de nitrogênio (0 (testemunha); 25; 50; 100 e 150 kg de N ha-1), as fontes de N utilizadas foram: nitrato de amônio e a ureia, aplicados em uma única adubação de cobertura via solo aos 45 após a emergência. As amostras de solo colhidas foram analisadas em laboratório, para a determinação da concentração da lixiviação do NO3- e do NH4+ no solo. Avaliou – se os parâmetros de crescimento, estado nutricional e da produtividade do algodoeiro durante seu ciclo. Os resultados permitiram concluir que o sistema irrigado foi o que propiciou maior lixiviação dos teores de nitrato e amônio nas profundidades de 0 a 0,8 m do solo e o sistema não irrigado foi o que apresentou maior con... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The N is one of the most dynamic elements in the soil, according to its transformation in the environment. The leaching of nitrate and ammonium in the soil is considered the main loss of the N available to the plants, the greater the application of this element in the soil, the greater the pollution potential of soil and water. The objective of this work was to evaluate the leaching of ammonium and nitrate in a Red Latosol in different depths of the soil, as a function of different N sources and sources, in irrigated and non-irrigated systems under field conditions. The experiment was conducted in the agricultural year 2014/15, in the experimental area of the teaching, research and extension farm, located in the municipality of Selvíria, Brasil state of mato grosso do sul. A randomized complete block design was used, with 20 treatments arranged in 5x2x2 factorial, with 4 replications. Five nitrogen doses (0 (control), 25, 50, 100 and 150 kg of N ha-1) were applied, the N sources used were: ammonium nitrate and urea, applied in a single cover fertilization only at 45 after the emergency. The soil samples collected were analyzed in the laboratory for the determination of the leaching concentration of NO3- and NH4+ in the soil. The parameters of growth, nutritional status and yield of cotton during its cycle were evaluated. The results allowed to conclude that the irrigated system provided the highest leaching of the nitrate and ammonium contents in the 0 to 0,8 m depths of the ... (Complete abstract click electronic access below) / Mestre

Understanding the composition, evolution, and function of the cotton (Gossypium) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). Specifically, read-mapping (a fundamental part of next-generation sequence analysis) cannot adequately differentiate reads as belonging to one genome or the other. These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we developed PolyCat to categorize reads according to their genome of origin based on homoeo-SNPs that differentiate the two genomes. We re-sequenced the genomes of extant diploid relatives of tetraploid cotton that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium raimondii) genomes. We identified 24 million SNPs between the A-diploid and D-diploid genomes. These analyses facilitated the construction of a robust index of conserved SNPs between the A-genomes and D-genomes at all detected polymorphic loci. This index can be used by PolyCat to assign reads from an allotetraploid to its genome-of-origin. Continued characterization of the Gossypium genomes will further enhance our ability to manipulate fiber and agronomic production of cotton. We re-sequenced 34 allotetraploid cotton lines, representing all 7 tetraploid cotton species. The analysis of these genomes-using PolyCat and PolyDog-provides us with the beginnings of a HapMap-like resource for cotton species, including indices of both homoeo-SNPs and allele-SNPs. With this information, we explore the phylogenetic relationships among cotton species, including the newly characterized species G. ekmanianum and G. stephensii. We examine gene conversion both recent and ancient, discovering that recent gene conversion is extremely rare, and ancient gene conversion is far less extensive than previously believed, with many previously identified conversion events being more probably due to autapamorphic SNPs in the descent of diploid relatives. In order to carry out these experiments, many tools for next-generation sequence analysis were developed. These tools, along with PolyCat and PolyDog, comprise the tool suite BamBam.

Orientador: Renato de Melo Prado / Resumo: Os valores de referências dos teores de nutrientes foliares de nitrogênio (N), fósforo (P) e boro (B) obtidos por métodos uni, bi e multivariados são publicados sem ter a sua eficiência comprovada. Sendo importante usar o teste de acurácia (APD) de forma integrada para se realizar os ajustes necessários na metodologia para melhorar a eficiência dos diagnósticos, mas isso ainda não é conhecido para cultura do algodão. Diante disso, objetivou-se usar o método APD para disponibilizar valores de referência, pelo método Distribuição Normal Reduzida (DNR), Chance Matemática (CHMAT), Sistema Integrado de Diagnose e Recomendação (DRIS) e Diagnose da Composição Nutricional (CND), eficientes para a diagnose nutricional de N, P e B da cultura do algodão, em Chapadão do Sul - MS. Para obter os valores de referência foram amostradas 144 lavouras comerciais de algodão do município de Chapadão do Sul - MS. No diagnóstico nutricional do DRIS e CND foram usados os fatores 0,5 e 1,0 para ajustar o Índice de balanço Nutricional médio (IBNm). Na mesma região foram realizados três experimentos de calibração, constituídos de quatro doses para cada nutriente (N, P e B), com cinco repetições. Os experimentos foram utilizados para confrontar o diagnóstico obtido pelo método da DNR, CHMAT, DRIS e CND com o Verdadeiro Estado Nutricional (VEN) da planta. O VEN da planta foi definido como deficiente quando a planta apresentava Incremento Real na Produtividade (IRP) acima de 5%, ou 10%, e como suficiente ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The leaf nutrient content of nitrogen (N), phosphorus (P) and boron (B) reference values are reproduced by uni, bi and multivariate methods are published without their proven efficacy. It is important to use the accuracy test (APD) in an integrated manner to make the necessary adjustments to the methodology to improve diagnostic efficiency, but this is not yet known for cotton cultivation. Thus, we aim to use the APD method to provide efficient reference values, the Normal Reduced Distribution (DNR), Mathematical Chance (CHMAT), Integrated Diagnostic and Recommendation System (DRIS) and Diagnostic Nutritional Composition (CND) method. nutritional status of cotton crop N, P and B, in Chapadão do Sul - MS. To obtain the reference values, 144 commercial cotton crops in Chapadão do Sul - MS were sampled. No nutritional diagnosis of DRIS and CND was used by factors 0.5 and 1.0 to adjust the mean nutritional balance index (IBNm). In the same region, three calibration experiments were performed, consisting of four doses for each nutrient (N, P and B), with five replications. The experiments were used to compare or diagnose DNR, CHMAT, DRIS and CND methods with the plant's True Nutritional Status (VEN). Plant VEN was defined as deficient when a plant had a Real Productivity Increase (IRP) above 5%, or 10%, and as sufficient when the increase was lower. The adjustments applied in this study result in an increase of 31%, 98% and 89% for N, P and B, respectively. The CND was the most ef... (Complete abstract click electronic access below) / Doutor

Plant MAP3Ks have expanded significantly compared to their metazoan counterparts. A new, sequential workflow combining multispecies ortholog clustering and newly built, family-specific HMMs is used to identify the MAP3K gene family within seven plant species, allowing for a refinement of previously proposed gene family cladding and the novel identification of the MAP3K gene families in the allotetraploid cotton Gossypium hirsutum and newly sequenced monocot seagrass Zostera marina. The MAP3K gene family architecture is further refined and validated using bioinformatics analyses before the recently characterized Arabidopsis Raf-like MAP3K ILK1 is identified and characterized in upland cotton. Transient gene silencing reveals an increase in RKN susceptibility following GhILK1.1 silencing in the susceptible TM1 cultivar. No changes in susceptibility were seen in the resistant M240 cultivar or against reniform nematodes. GhILK1.1 is only the second cotton gene characterized to have a direct role in mediating RKN resistance.

Gossypium herbaceum is a species of cotton native to Africa and Asia. As part of a larger effort to investigate structural variation in assorted diploid and polyploid cotton genomes we have sequenced and assembled the genome of G. herbaceum. Cultivated G. herbaceum is an A1-genome diploid from the Old World (Africa) with a genome size of approximately 1.7 Gb. Long range information is essential in constructing a high-quality assembly, especially when the genome is expected to be highly repetitive. Here we present a quality draft genome of G. herbaceum (cv. Wagad) using a multi-platform sequencing strategy (PacBio RS II, Dovetail Genomics, Phase Genomics, BioNano Genomics). PacBio RS II (60X) long reads were de novo assembled using the CANU assembler. Illumina sequence reads generated from the PROXIMO library method from Phase Genomics, and BioNano high-fidelity whole genome maps were used to further scaffolding. Finally, the assembly was polished using PILON. This multi-platform long range sequencing strategy will help greatly in attaining high quality de novo reconstructions of genomes. This assembly will be used towards comparative analysis with G. arboreum, which is also a domesticated A2-genome diploid. Not only will this provide a quality reference genome for G. herbaceum, it also provides an opportunity to assess recent technologies such as Dovetail Genomics, Phase Genomics, and Bionano Genomics. The G. herbaceum genome sequence serves as an example to the plant genomics community for those who have an interest in using multi-platform sequencing technologies for de novo genome sequencing.

The tarnished plant bug (TPB), Lygus lineolaris (Palisot de Beauvois), has been a devastating insect pest in cotton agroecosystems in mid-southern cotton for several decades. Similar to related Heteropteran insect pests, L. lineolaris uses piercing-sucking mouthparts to penetrate harvestable fruiting structures on the cotton plant (i.e., squares, flowers, small bolls) leading to significant reductions in lint yield when infestations are above economic injury levels. Economically damaging infestations of L. lineolaris have occurred in Virginia and North Carolina cotton since 2013. In response, cotton area sprayed with broad-spectrum insecticides for L. lineolaris has increased in these states. As such, this dissertation research sought to answer a variety of questions to address this issue including 1) mapping the spatiotemporal abundance of L. lineolaris across Virginia as well as creating models to predict landscape and climate factors increasing infestation risk, 2) using a systems approach to provide growers with cost-effective and sustainable integrated pest management (IPM) solutions including economic spray thresholds, 3) investigating the incidence and transmission of fungal pathogens by L. lineolaris increasing Fusarium hardlock disease, further impacting yield loss at harvest, and 4) conducting insecticide resistance monitoring of L. lineolaris across the Southeast including biochemical lab assays to determine possible mechanisms of insecticide resistance. These findings will help form compressive IPM and insect resistant management (IRM) plans to equip southeastern cotton growers with practical management tools as well as useful information on "high-risk" areas to invest management resources, increasing economic returns while minimizing environmental impacts of over-spraying foliar insecticides. / Doctor of Philosophy / The tarnished plant bug (Lygus lineolaris) is an important pest in cotton from July through September that causes reduced yields and lower quality of lint and seed. Tarnished plant bugs cost the cotton industry hundreds of millions of dollars in losses annually. However, tarnished plant bug infestations were rare and sporadic in Virginia and North Carolina before 2013. In recent years, tarnished plant bug infestations have nearly doubled in these states, and research is needed to better understand how to manage recent pest outbreaks to avoid substantial economic losses. To address this issue, this dissertation research investigated a variety of questions including 1) the distribution of tarnished plant bugs in this region and the effects of geography and climate on infestation risk, 2) best practices for managing this pest in cotton fields, 3) possible associations between tarnished plant bugs and cotton boll diseases further impacting yield, and 4) whether tarnished plant bugs in this region are resistant to frequently used broad-spectrum insecticides as well as potential mechanisms driving resistance levels. Findings from this research will equip southeastern cotton growers with regionally specific recommendations for managing and monitoring tarnished plant bugs that minimize management costs and increase the quality and quantity of cotton yields.

Success in evaluating effects of a 75% oxygen atmosphere, containing an ambient concentration of carbon dioxide, on levels of protein and oxidative enzymes in cotton, Gossypium herbaceum L. C.B. 1697, leaf tissue was dependent upon generation of genetically uniform and physiologically similar leaves. Sufficient quantities of 2-4 week old leaves for experimental procedures were obtained from plants grown in a 1:1 perlite:vermiculite potting medium supplied with 20% Hoagland's nutrient and maintained in a controlled environment growth chamber under the following conditions: 16 hr day/8 hr night cycle, irradiances of 200-300 µE m⁻² sec⁻¹, 70% humidity, and 30°. Maximum yields of soluble protein (10-12 mg/g tissue) and active enzymes were obtained when freshly harvested leaves were crushed in liquid nitrogen and then homogenized in 0.1 M Tris-Cl, pH 6.9, containing 0.01 M isoascorbate and polyvinylpyrrolidone [2% (w/v) PVP-10 and 0.5 g dry Polyclar AT/g tissue]. Routinely 90% of the solubilized protein was obtained following centrifugation and chromatography on Sephadex G-50. Introduction of cotton plants into vinyl chambers of 95% humidity resulted in foliar symptoms of physiological stress, including chlorosis, cellular edema, leaf curling, and loss of turgidity. Of the oxidative enzymes analyzed, catalase activity decreased 30%, glycolate oxidase activity decreased 42%, and peroxidase. increased 89% while soluble protein decreased 27% in plants maintained in the high humidity for 5 days. Exposure of plants to 75% oxygen, 350 ppm carbon dioxide for 48 hr under these conditions resulted in a 70% increase in glutathione reductase and a 25% increase in malate dehydrogenase. Other enzymes, superoxide dismutase, catalase, peroxidase, glyoxylate reductase, and acid phosphatase, appeared to be independent of the oxygen treatment. When humidity was carefully controlled at 70%, treatment with 75% oxygen, 350 ppm carbon dioxide resulted in a 180% increase in glutathione reductase, an 85% increase in acid phosphatase, and a 22% increase in peroxidase. In the same experiment, catalase decreased by 32% and total soluble protein decreased by 15%. Activities of glyoxylate reductase and both cyanide-sensitive and insensitive superoxide dismutases appeared to be unaffected by the 75% oxygen treatment after 48 hr. Obviously the impact of humidity as a component of the regulation of metabolism in leaf tissue must be considered. It is concluded that oxidoreductase activities located in the chloroplast, peroxisome, and cytosol are not equally sensitive to high oxygen tensions, and effects of environmental oxygen are not restricted to oxidative enzymes. / Ph. D.

Cotton (Gossypium hirsutum L.) growth and development, lint yield, and fiber quality are influenced by many management decisions. Three field experiments examining the interaction of plant population and planting date, and cultivar or herbicide and plant growth regulator application on these parameters were conducted in Virginia during 2005 and 2006 and in North Carolina, South Carolina, and Louisiana during specific years. Experiment I: Plant Population and Planting Date Lint yields were highest with populations of 8.9 and 12.8 plants m¯² compared to 5.3 plants m¯² in Virginia and North Carolina, while in Louisiana the highest yields resulted from populations of 5.8 and 9.5 plants m¯² compared to 17.1 plants m¯². Earlier planted (1 May) cotton produced higher yields relative to later planted (21 May) cotton in Louisiana, while yield was not influenced by planting date in Virginia and North Carolina. The impact of plant population and planting date on cotton appeared to be influenced significantly by heat unit accumulation. Experiment II: Cultivar and Mepiquat Pentaborate Application Mepiquat pentaborate (MPB) application consistently decreased plant height, HNR, and enhanced maturity for all cultivars, compared to untreated cotton. A trend of decreasing yield with increasing MPB application in Virginia was observed. These data suggests that cotton response to MPB application is influenced by cultivar maturity or fruiting interval. Experiment III: Trifloxysulfuron-sodium and Mepiquat Chloride Application Trifloxysulfuron-sodium (TFS) did not influence vegetative growth, maturity, or yield in comparison to untreated cotton. Mepiquat chloride (MC) application reduced vegetative growth and enhanced maturity in most years. The results of this experiment demonstrate that TFS application does not have the same effects on plant growth as MC application. / Master of Science