No abstract available. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2001.

Bibliography: leaves 128-146. / x, 146 leaves : ill. (some col.), maps ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Study was undertaken to determine the occurence and species incidence of wild oats in a major cropping region of southern Australia. Population dynamic studies were undertaken at two sites to define the seed bank decline and emergence pattern of several wild oat populations over a three year period. Management studies were conducted to determine appropriate strategies for the control of wild oats in southern Australian farming systems. / Thesis (Ph.D.)--Dept. of Agronomy and Farming Systems, The University of Adelaide, Roseworthy Campus, 1998

Made available in DSpace on 2014-06-11T19:26:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-07-05Bitstream added on 2014-06-13T20:14:42Z : No. of bitstreams: 1 000738209.pdf: 517669 bytes, checksum: 01eee58693e0de5b0d8e251e6653e038 (MD5) / O melhoramento genético de plantas é considerado um processo complexo que gera múltiplas informações e, em muitos casos, de difícil compreensão. O objetivo deste trabalho foi selecionar progênies com caracteres superiores provenientes de cruzamentos bi-parentais de soja com fonte de resistência ao glifosato (RR), além de identificar cruzamentos e genitores mais eficientes, por meio de abordagens multivariadas. Além disso, objetivou-se ainda testar a eficiência dos métodos no processo seletivo para múltiplos caracteres de interesse. O experimento foi conduzido no delineamento experimental do tipo famílias com testemunhas intercalares, no ano agrícola 2010/2011 e 2011/2012 em Jaboticabal-SP sendo que, nas populações F3 foram selecionadas seis plantas fenotipicamente superiores e avaliadas para os caracteres: número de dias para o florescimento (NDF), número de dias para a maturidade (NDM), altura de inserção da primeira vagem (AIV), altura de planta na maturidade (APM), acamamento (Ac), valor agronômico (VA), número de ramos (NR), número de vagens por planta (NV), peso de cem sementes (PCS), número de sementes por planta (NS) e produção de grãos (PG). Os dados foram analisados utilizando-se o software Statistica 7.0. Os resultados obtidos possibilitaram a seleção de 77 progênies superiores através da Análise de Componentes Principais. A análise de Agrupamentos, pelo do método de K-means, agregou as progênies em seis grupos de acordo com os caracteres de maior importância em cada um e, através do método de Ward, identificou por meio do dendrograma a estrutura de similaridade e divergência entre as progênies selecionadas. Por fim, comparou-se os métodos de agrupamentos e verificou-se que houve concordância entre ambos quanto aos resultados obtidos / The plant breeding is considered to be a complex process that generates multiple information sources and in many cases, difficult to understand. The aim of this work was to select progenies with superior characters from bi-parental crosses with soy source of resistance to glyphosate (RR), and identify intersections and parents more efficient through multivariate approaches. Furthermore, aimed to further test the efficiency of the methods in the selection process for multiple traits of interest. The experiment was conducted in the experimental design of type families to witness progress in the agricultural year 2010/2011 and 2011/2012 in Jaboticabal being that in F3 populations selected six plants were phenotypically superior and evaluated for the traits: number of days to flowering (NDF), number of days to maturity (NDM), height of the first pod (AIV), plant height at maturity (APM), lodging (Ac), agronomic value (VA), number of branches (NR), number of pods per plant (NV), one hundred seed weight (PCS), number of seeds per plant (NS) and grain yield (GY). Data were analyzed using the software Statistica 7.0. The results allowed the selection of 77 superior progenies by Principal Component Analysis. Cluster analysis by the K-means method, all progenies added into six groups according to the characters in each of utmost importance, and by the method of Ward identified by the dendrogram structure similarity and divergence between the progenies. Finally, we compared the clustering methods and found that there was an agreement between them as to the results obtained

Made available in DSpace on 2014-06-11T19:26:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-04-18Bitstream added on 2014-06-13T19:13:01Z : No. of bitstreams: 1 amaral_al_me_jabo.pdf: 755163 bytes, checksum: 38fef006637923d725907da11533302e (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Estudos laboratoriais foram realizados com o objetivo de estudar a caracterização genética de plantas de Euphorbia heterophylla, provenientes de áreas em que a resistência aos herbicidas inibidores da ALS (Acetolactase) estava caracterizada (Santo Ângelo, RS), em processo de desenvolvimento (Sonora, MS) e onde nunca havia sido aplicado herbicida com este mecanismo de ação (Jaboticabal, SP). Testes preliminares comprovaram elevada resistência para as plantas provenientes de Santo Ângelo, moderada resistência para plantas de Sonora e elevada susceptibilidade para plantas provenientes de Jaboticabal. A análise dos resultados através das isoenzimas revelou que existem pequenas diferenças entre as três populações estudadas. A análise do DNA dos indivíduos das diferentes populações através de marcadores moleculares RAPD, permitiu a construção do Dendrograma de Cluster, que mostra uma similaridade mínima de 88% e máxima de 99% entre os diferentes indivíduos, quer pertencentes à mesma população, quer pertencentes às diferentes populações. Tal análise permitiu inferir que, apesar dos indivíduos analisados mostrarem grande similaridade entre si, apresentam variabilidade genética entre os indivíduos e as populações estudadas, de acordo com a conclusão obtida quando da utilização das isoenzimas. Crescendo em condições similares, o biótipo da Santo Ângelo apresentou maior absorção de fósforo em comparação com os demais, e maior absorção de potássio em relação ao biótipo de Jaboticabal. Comparando a densidade estomática, houve diferença estatística entre os três biótipos, sendo maior para o biótipo mais tolerante ao herbicida e menor para o susceptível. Não foi possível estabelecer qualquer relação confiável entre as características morfológicas e de crescimento das plantas e a resistência ao imazethapyr. / Laboratory studies were carried out aim to characterize genetically Euphorbia heterophylla plants were collect in three regions. At Santo Ângelo (RS) region this plant is highly resistant to ALS inhibitors herbicides, but moderately at Sonora (MS) and susceptible at Jaboticabal region. Greenhouse tests confirmed the plants reaction in face of imazethapyr spraying. The isoenzymes studies showed small differences between the three populations. The DNA analysis using molecular markers make feasible the Cluster dendrogram showing 88-99% of similarity comparing plants, regardless the plant origin. Besides the high similarity index between the plants, it was possible to determine lower genetic variation in Jaboticabal and Santo Ângelo populations using isoenzymes technique. The nitrogen and potassium contents in the plants shoot was higher in the Santo Ângelo byotipe, although there was no difference between the K contents when the Jaboticabal and Sonora byotipes were compared. The stomata and trichomes densities decreased in the same order of the plant tolerance to herbicide: Santo Ângelo > Sonora > Jaboticabal. None correlation between biotype resistance to imazethapyr and the plant morphology features for the three biotypes studied. The differences in the plant feature may be attributable to the adaptative mechanism of the plant to the regional characteristics they were collected.

Submitted by Leandro Bianchi (leandro_bianchii@hotmail.com) on 2018-04-16T19:41:47Z No. of bitstreams: 1 Leandro final.pdf: 3197976 bytes, checksum: 442c110e13ec1198a874c1285f176bbc (MD5) / Approved for entry into archive by Maria Lucia Martins Frederico null (mlucia@fca.unesp.br) on 2018-04-16T20:03:09Z (GMT) No. of bitstreams: 1 bianchi_l_me_botfca.pdf: 3197898 bytes, checksum: 5bd6736d1b7a1e530435ae5e7c91c884 (MD5) / Made available in DSpace on 2018-04-16T20:03:09Z (GMT). No. of bitstreams: 1 bianchi_l_me_botfca.pdf: 3197898 bytes, checksum: 5bd6736d1b7a1e530435ae5e7c91c884 (MD5) Previous issue date: 2018-02-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Devido ao uso frequente do glyphosate na agricultura, o capim-amargoso (Digitaria insularis) tornou-se uma das plantas daninhas mais problemáticas no Brasil, por adquirir resistência a esse herbicida. Biótipos resistentes em estádios iniciais são facilmente controlados por graminicidas, porém em estádio mais avançado o controle é reduzido. O herbicida clethodim é um graminicida com alta eficiência, portanto, verificar o controle de biótipos resistentes ao glyphosate em diferentes estádios, com o uso isolado de clethodim e em mistura com o glyphosate é fundamental para auxiliar no manejo desta invasora. Assim o presente trabalho teve como objetivo avaliar o desempenho de glyphosate, clethodim e glyphosate + clethodim, em biótipo de D. insularis resistente e suscetível. O ensaio foi realizado em casa de vegetação, inteiramente casualizado, com quatro repetições e repetido em duas épocas do ano. As aplicações foram realizadas em estádio inicial (15 – 20 cm) e em florescimento. Avaliou-se o controle aos 21 dias e o peso da biomassa seca. Para a mistura dos produtos, foi verificada a interação entre os herbicidas: efeito sinérgico, antagônico ou aditivo. No ensaio com plantas em estádio inicial, avaliou-se a concentração de lipídeos na biomassa seca. De forma geral, a aplicação de clethodim aplicado isoladamente controlou o biótipo resistente em estádio inicial, porém em florescimento a eficácia foi reduzida. A mistura mostrou-se eficiente para controle de biótipo resistente em estádio inicial e em florescimento. Considerando as avaliações visuais de controle, a interação entre glyphosate e clethodim apresentou efeito sinérgico para doses intermediárias e aditivo para as maiores doses considerando o estádio inicial; em plantas florescidas, predominaram os efeitos aditivos para todas as doses. Para massa seca, a mistura teve interação sinérgica em todas as doses e estádios avaliados. As menores doses dos dois herbicidas reduziram os teores de lipídeos. / Due to frequent use of glyphosate in agriculture, sourgrass (Digitaria insularis) has become one of the most problematic weeds in Brazil for purchase resistance to this herbicide. Resistant biotypes in initial stages are easily controlled by graminicides, but in a more advanced stage the control is reduced. The herbicide clethodim is a graminicide with high efficiency, therefore, to check the control of resistant biotypes of glyphosate in different stages, with the isolated use of clethodim and in mixture with the glyphosate is fundamental to assist in the management of this weed. Thus the experiment was aimed at evaluate the action of glyphosate, clethodim and glyphosate + clethodim, in a resistant and susceptible biotype of D. insularis. The experiment was carried out in a greenhouse, completely randomized, with four replications and repeated at two times of the year. The applications were performed in the initial stage (15 - 20 cm) and flowering. Plants were evaluated at 21 days after application (DAA) and dry biomass weight. For the mixture of products, the interaction between the herbicides was also verified: synergistic, antagonistic or additive effect. In the experiment with plants at the initial stage, was evaluated the lipid concentration in the dry biomass. In general, the application of clethodim applied alone controlled the resistant biotype at the initial stage, but in flowering the efficiency was reduced. The mixture showed to be efficient for control of resistant biotype in initial and flowering stages. Considering the visual evaluations of control, the interaction between glyphosate and clethodim showed synergic effect for intermediate doses and additive for the highest doses considering the initial stage; in flowered plants, with the additive effects predominating for all as doses, the additive effect prevailed for all doses. For dry mass, the mixture had synergistic interaction at all doses and evaluated stages. Lower doses of both herbicides reduced lipid levels.

Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.

Master of Science / Department of Agronomy / Randall S. Currie / Mithila Jugulam / Italian ryegrass (Lolium perenne L. ssp. multiflorum (Lam.) Husnot), one of the problem weeds of the US, evolved resistance to multiple herbicides including glyphosate due to selection in Arkansas (AR). Glyphosate is a 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) inhibitor and amplification of EPSPS gene, the molecular target of glyphosate confers resistance to this herbicide in several weed species, including Italian ryegrass from AR. The objective of this study was to determine the expression of EPSPS gene and protein as well as distribution of EPSPS copies on the genome of glyphosate-resistant Italian ryegrass (ARR) using a known susceptible Italian ryegrass (ARS) from AR. EPSPS gene copies and expression of ARR and ARS were determined using quantitative PCR with appropriate endogenous controls. EPSPS protein expression was determined using Western blot analysis. Fluorescence in situ hybridization (FISH) was performed on somatic metaphase chromosomes to determine the location of EPSPS copies. Based on qPCR analysis, ARR plants showed a wide range of 12 to 118 EPSPS copies compared to a single copy in ARS. EPSPS gene expression correlated with the gene copy number in both ARR and ARS. Individuals with high EPSPS copies showed high protein expression in Western blot analysis. FISH analysis showed presence of brighter EPSPS signals, distributed randomly throughout the genome of ARR individuals compared to a faint signal in ARS plants. Random distribution of EPSPS copies was previously reported in glyphosate-resistant Palmer amaranth. Overall, the results of this study will help understand the origin and mechanism of EPSPS gene amplification in Italian ryegrass.

No description available.

<p>Tall waterhemp management in agronomic crops continues to be an increasing problem due to widespread resistance to herbicides, including protoporphyrinogen oxidase (PPO)-inhibitors. With limited effective postemergence herbicides, especially in soybeans, research to further understand the selection of PPO-resistant (PPO-R) tall waterhemp and identification of new herbicide resistance mechanisms is crucial for improving weed management decisions in order to slow selection for herbicide resistance and prolong the effectiveness of PPO-inhibiting herbicides.</p> <p> Previous research has shown that soil-applied applications of PPO-inhibiting herbicides can increase the frequency of the PPO resistance trait (∆G210) in surviving tall waterhemp plants, even when applied in combination at the same ratio with the very long chain fatty acid inhibitor (VLCFA), <i>s-</i>metolachlor. Field experiments were conducted to determine if selection for tall waterhemp resistant individuals to PPO-inhibitors could be reduced when the soil residual activity of <i>s</i>-metolachlor persisted longer than the PPO-inhibitor herbicide. The frequency of ∆G210 in surviving individual plants increased as the fomesafen rate increased, but was independent of the rate of <i>s</i>-metolachlor. Additionally, heterozygosity of ∆G210 in surviving individuals did not change with any rate or combination of fomesafen and <i>s</i>-metolachlor. However, saflufenacil, standard PPO-inhibitor with relatively short soil residual activity, applied alone increased the number of homozygous PPO-R tall waterhemp by 15% compared to the high rate of <i>s</i>-metolachlor and the combination of saflufenacil and <i>s</i>-metolachlor. Furthermore, this research demonstrated that end of season control of tall waterhemp plays a more vital role in delaying a large-scale shift towards herbicide resistance through reduced seed production. This can be achieved through the combination of multiple effective herbicide sites of action, including soil residual PPO-inhibitors. Tall waterhemp control and density were greatest with the high rates of fomesafen plus <i>s</i>-metolachlor, which resulted in the lowest number of PPO-R tall waterhemp that survived herbicide treatment at the end of season.</p> <p> Prior to the research conducted in this thesis, the only known resistance mechanism to PPO-inhibiting herbicides in tall waterhemp has been the ∆G210 target site mutation. A previously developed TaqMan assay used to determine the presence or absence of the ∆G210 mutation has allowed accurate, high throughput screening of this mutation. However, suspected PPO-R tall waterhemp do not always receive positive confirmation indicating the presence of an alternative resistance mechanism. Identification of additional resistance mechanisms can provide valuable insight in regards to resistance to PPO-inhibiting herbicides as well as cross resistance to other herbicide modes of action, which can lead to improved tall waterhemp management decisions. Of 148 tall waterhemp populations collected across the Midwestern U.S., 84% of the populations sampled contained at least one PPO-R biotype with the ∆G210 mutation, although several individual plants across the Midwest U.S. exhibited phenotypic resistance to fomesafen that could not be explained by ∆G210. The percentage of PPO-R tall waterhemp without ∆G210 was 19, 5, 2, 1, and 2% for Iowa, Illinois, Indiana, Minnesota, and Missouri, respectively. Following the initial greenhouse screening, subsequent tall waterhemp populations were selected that exhibited low-, mid-, and high-level resistance to fomesafen that resulted in resistance ratios from 0.6 to 17X in response to fomesafen. This research documents the variability in fomesafen response to multiple tall waterhemp populations in addition to revealing the presence of additional resistance mechanism(s), other than the previously known ∆G210 mutation that has been the benchmark for resistance to PPO-inhibiting herbicides in tall waterhemp.</p> <p> Lastly, greenhouse and lab experiments were conducted to investigate the role of antioxidant enzymes with PPO-R tall waterhemp via ∆G210. The objectives of this research were to determine if the variability in resistance ratios for PPO-R tall waterhemp documented in greenhouse and field scenarios could be due to an enhanced antioxidant enzyme pathway. Basal levels of antioxidant enzymes in PPO-S populations were not different from PPO-R populations when pooled together by respective phenotype. However, enzyme activity of tall waterhemp populations varied at the individual level, but independent of the ∆G210 mutation. This indicates that an inherent enhanced antioxidant enzyme pathway does not cause the variability in fomesafen response in tall waterhemp. With the exception of glutathione reductase, antioxidant enzyme activity following fomesafen application was generally the same for PPO-R and PPO-S populations by increasing, decreasing, or remaining unchanged. Glutathione reductase activity in PPO-S populations decreased compared to PPO-R populations from 9 to 36 HAT. By 36 HAT, all antioxidant enzyme activity for PPO-S populations was lower compared to PPO-R populations most likely a consequence of more lipid peroxidation. This research shows that antioxidant enzyme activity correlated with fomesafen application and documents the variability observed within tall waterhemp populations with and without the ∆G210 mutation. </p>

Precise engineering of genomes holds great promise to advance our understanding of gene function and biotechnological applications. DNA double strand breaks are repaired via imprecise non-homologous end joining repair or via precise homology-directed repair processes. Therefore, we could harness the DSBs to engineer the genomes with a variety of genetic outcomes and with singlebase- level precision. The major barrier for genome engineering was the generation of site-specific DNA DSBs. Programmable DNA enzymes capable of making a complete and site-specific cut in the genome do not exist in nature. However, these enzymes can be made in in vitro as chimeric fusions of two modules, a DNA binding module and a DNA cleaving module. The DNA cleaving module can be programmed to bind to any user-defined sequence and the DNA cleaving module would generate DSBs in the target sequence. These enzymes called molecular scissors include zinc finger nucleases (ZFNs) and transcriptional activator like effector nucleases (TALENs). The programmability of these enzymes depends on protein engineering for DNA binding specificity which may be complicated, recourse intensive and suffer from reproducibility issues. Recently, clustered regularly interspaced palindromic repeats (CRISPR)/ CRISPR associated endonuclease 9 (Cas9) an adaptive immune system of bacterial and archaeal species has been developed for genome engineering applications. CRISPR/Cas9 is an RNA-guided DNA endonuclease and can be reprogrammed through the engineering of single guide RNA molecule (sgRNA). CRISPR/Cas9 activity has been shown across eukaryotic species including plants. Although the engineering of CRISPR/Cas9 is quite predictable and reproducible, there are many technological challenges and improvements that need to be made to achieve robust, specific, and efficient plant genome engineering. Here in this thesis, I developed a number of technologies to improve specificity, delivery and expression and heritability of CRISRP/Cas9-modification in planta. Moreover, I used these technologies to answer basic questions to understand the molecular underpinning of the interplay between splicing and abiotic stress. To improve Cas9 specificity, I designed and constructed a chimeric fusion between catalytically dead Cas9 (dCas9) and FOKI catalytic DNA cleaving domain (dCas9.FoKI). This synthetic chimeric fusion enzyme improved Cas9 specificity which enable precision genome engineering. Delivery of genome engineering reagents into plant cells is quite challenging, I developed a virus-based system to deliver sgRNAs into plants which facilitates plant genome engineering and could bypass the need for tissue culture in engineering plant genomes. To improve the expression of the CRISPR/Cas9 machinery in plant species, I developed a meiotically-driven expression of CRISPR/Cas9 which improved genome editing and heritability of editing in seed progeny, thereby facilitating robust genome engineering applications. To understand the molecular basis of the interplay between splicing stress and abiotic stress, I used the CRISPR/Cas9 machinery to engineer components of the U2snRNP complex coupled which chemical genomics to understand the splicing stress regulation in response to abiotic stress conditions. Finally, I harnessed the technological improvements and developments I have achieved with CRISPR/Cas9 system to develop a directed evolution platform for targeted trait engineering which expands and accelerates trait discovery and engineering of plant species resilient to climate change conditions.