Thesis--Auburn University, 2009. / Abstract. Vita. Includes bibliographic references.

Thesis--Auburn University, 2009. / Abstract. Includes bibliographic references.

Molecular diagnostic tests have been developed and utilized to diagnose and to confirm diagnoses of many plant-parasitic nematodes. We evaluate the potential of a qPCR assay to detect and quantify Rotylenchulus reniformis in Mississippi directly from soil. A novel pipeline utilizing multiple databases containing nematode DNA and EST sequences was developed to aid in the selection of R. reniformis primers used in a PCR and qPCR assays. In vitro testing showed that the primers and probes developed from the novel pipeline for the qPCR assays could accurately detect the presence of R. reniformis. Subsequent testing resulted in a trend of increasing observed number of R. reniformis resulting in increasing estimates by qPCR

Rotylenchulus reniformis is a nematode species affecting the cotton crop and quickly spreading throughout the southeastern United States. Effective use of nematicides at a variable rate is the only economic counter measure. It requires the intraield variable nematode population, which in turn depends on the collection of soil samples from the field and analyzing them in the laboratory. This process is economically prohibitive. Hence estimating the nematode infestation on the cotton crop using remote sensing and machine learning techniques which are cost and time effective is the motivation for this study. In the current research, the concept of multi-temporal remote sensing has been implemented in order to design a robust and generalized Nematode detection regression model. Finally, a user friendly web-service is created which is gives trustworthy results for the given input data and thereby reducing the nematode infestation in the crop and their expenses on nematicides.

Upland cotton (Gossypium hirsutum) is an important crop in Mississippi. Economic losses are incurred every year due to the feeding and treatment of crop pests and plant pathogens. Because it is often unclear what differentiates a pest from a pathogen, I will use the umbrella term “biotic stressor” or BST when referring to a plant pest or pathogen. BSTs employ a special set of proteins known as ‘effectors’ that function at the site of BST physical attack. Effectors dictate how the host-BST relationship will unfold. Effectors include the proteins produced by the BST that are recognized by the plant and invoke the subsequent plant immune responses to the BST. Moreover, some effectors are responsible for the successful modification of the host tissues for the survival of the pest. In this study I utilized Illumina sequencing and computational biology approaches to identify effectors within three evolutionarily diverse cotton BSTs; specifically, Lygus lineolaris (tarnished plant bug), Xanthomonas citri pv. malvacearum (Xcm) (bacterial cotton blight), and Rotylenchulus reniformis (reniform nematode). Transcripts from the Lygus lineolaris salivary gland were found to encode putative degradative proteins used for the extra-oral digestion of host tissues by the insect. Production, assembly, and comparison of a whole genome assembly of the first Xcm genome obtained from a strain isolated in the cotton producing region of the United States revealed that the cotton Xcm is similar to other reported Xcm assemblies and contains most of the proteins found in these other strains. Genome and life-stage specific transcriptome sequencing of the nematode Rotylenchulus reniformis resulted in the identification of 41,570 transcripts of which 3,033 were up-regulated in the parasitic sedentary female life-stage. These studies collectively provide insight into the mechanisms by which key cotton BSTs invade and damage cotton. Further study of the BST effectors and the plant biomolecules with which they interact should facilitate development of highly targeted mechanisms of minimizing/eliminating BST damage. Such customized BST management will increase profits for farmers and maximize resource utilization in an environmentally responsible manner.

Made available in DSpace on 2016-08-12T19:15:24Z (GMT). No. of bitstreams: 1 GRACE KELLY LEITE DE LIMA.pdf: 277034 bytes, checksum: 56e3151fa502c6a92a30ec1e220a8c27 (MD5) Previous issue date: 2008-02-28 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / The objective of this work was to evaluate the reaction of watermelon cultivars and accessions to the parasitism of Rotylenchulus reniformis and Meloidogyne javanica, in two experiments carried out at a greenhouse of the Departmento de Ciências Vegetais of the Universidade Federal Rural do Semi-Árido (UFERSA), in a completely randomized design with nineteen treatments and five replications, being the experimental unity constituted of a seedling per pot. In the first experiment, it has been studied the resistance of six commercial cultivars ( Sugar Baby , Blowing , Crimson Sweet , Charleston Gray , Omaru Yamato and Mickylee ) and thirteen accessions ( M-03 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 and UP-18 ) of watermelon collected in the Mossoró and Upanema counties to the parasitism of Rotylenchulus reniformis. It was used the melon cultivar AF 646 as the control for the feasibility of the inoculum. The soil of each experimental unit was infested with 2,000 vermiformes forms of R. Reniformis (males, immature adult females and juveniles) and at 51 days after the infestation, it was evaluated to the following variables: number of nematodes into the soil, number of nematodes into the roots, total number of nematodes and reproduction factor. The cultivars Blowing and Charleston Gray , and the accession M-16 behaved themselves as nonefficient host to the population of R. reniformis. The cultivars Sugar Baby , Crimson Sweet , Omaru Yamato and Mickylee, and the accessions M-03 , M-08 , M-10 , M-14 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 and UP-18 behaved as poor host to the population of R. reniformis. In the second experiment was tested the resistance of four commercial cultivars ( Sugar Baby , Crimson Sweet , Charleston Gray and Mickylee ) and fifteen accessions ( M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 and UP-18 ) of watermelon collected also in the Mossoró and Upanema counties to the parasitism of M. javanica. It was used the tomato cultivar Santa Cruz Kada Gigante as the control for the feasibility of the inoculum. The soil of each experimental unit was infested with 5,000 eggs of M. Javanica and at 52 days after the infestation, it was evaluated to the following variables: root-gall and eggs- mass indexes and listed the ways of development of M. Javanica observed into the root system. The cultivars Sugar Baby , Crimson Sweet , Charleston Gray and Mickylee , and the accessions M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 and UP-18 were susceptible to M. Javanica in terms of root-gall index / Com o objetivo de verificar a reação de cultivares e acessos de melancia (Citrullus lanatus) ao parasitismo de Rotylenchulus reniformis e Meloidogyne javanica, foram desenvolvidos dois experimentos na casa de vegetação do departamento de Ciências Vegetais da Universidade Federal Rural do Semi-Árido (UFERSA), em delineamento inteiramente casualizado, com cinco repetições, sendo a unidade experimental constituída de uma plântula por vaso. No primeiro experimento foi estudada a reação, quanto à resistência, de seis cultivares comerciais ( Sugar Baby , Rajada , Crimson Sweet , Charleston Gray , Omaru Yamato e Mickylee ) e 13 acessos de melancia coletados nos municípios de Mossoró e Upanema ('M-03 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 e UP-18 ) ao parasitismo de R. reniformis. Utilizou-se meloeiro (Cucumis melo) cultivar AF 646 como testemunha de viabilidade de inóculo. O solo de cada unidade experimental foi infestado com 2.000 formas vermiformes de R. reniformis (machos, fêmeas adultas imaturas e juvenis) e 51 dias após avaliou-se as variáveis: número de nematóides no solo, número de nematóides na raiz, número total de nematóides e fator de reprodução. As cultivares Rajada , Charleston Gray e o acesso M-16 comportaram-se como não hospedeiras a população de R. reniformis. As cultivares Sugar Baby , Crimson Sweet , Omaru Yamato e Mickylee e, os acessos M-03 , M-08 , M-10 , M-14 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 e UP-18 comportaram-se como más hospedeiras a população de R. reniformis. No segundo experimento foi testada a reação, quanto à resistência, de quatro cultivares comerciais ( Sugar Baby , Crimson Sweet , Charleston Gray e Mickylee ) e 15 acessos de melancia coletados nos municípios de Mossoró e Upanema ( M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 e UP-18 ) ao parasitismo de M. javanica. Utilizou-se tomateiro (Lycopersicon esculentum) cultivar Santa Cruz Kada Gigante como testemunha de viabilidade de inóculo. O solo de cada unidade experimental foi infestado com 5.000 ovos de M. javanica e 52 dias após avaliou-se as variáveis: índices de galhas e massa de ovos e enumeradas as formas de desenvolvimento de M. javanica encontradas no interior do sistema radicular. As cultivares Sugar Baby , Crimson Sweet , Charleston Gray e Mickylee e, os acessos M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 e UP-18 foram suscetíveis a M. javanica quanto ao índice de galhas. Palavras-chaves: Citrullus lanatus. Rotylenchulus reniformis. Meloidogyne javanica

Made available in DSpace on 2016-08-12T19:18:45Z (GMT). No. of bitstreams: 1 GRACE KELLY LEITE DE LIMA.pdf: 277034 bytes, checksum: 56e3151fa502c6a92a30ec1e220a8c27 (MD5) Previous issue date: 2008-02-28 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / The objective of this work was to evaluate the reaction of watermelon cultivars and accessions to the parasitism of Rotylenchulus reniformis and Meloidogyne javanica, in two experiments carried out at a greenhouse of the Departmento de Ciências Vegetais of the Universidade Federal Rural do Semi-Árido (UFERSA), in a completely randomized design with nineteen treatments and five replications, being the experimental unity constituted of a seedling per pot. In the first experiment, it has been studied the resistance of six commercial cultivars ( Sugar Baby , Blowing , Crimson Sweet , Charleston Gray , Omaru Yamato and Mickylee ) and thirteen accessions ( M-03 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 and UP-18 ) of watermelon collected in the Mossoró and Upanema counties to the parasitism of Rotylenchulus reniformis. It was used the melon cultivar AF 646 as the control for the feasibility of the inoculum. The soil of each experimental unit was infested with 2,000 vermiformes forms of R. Reniformis (males, immature adult females and juveniles) and at 51 days after the infestation, it was evaluated to the following variables: number of nematodes into the soil, number of nematodes into the roots, total number of nematodes and reproduction factor. The cultivars Blowing and Charleston Gray , and the accession M-16 behaved themselves as nonefficient host to the population of R. reniformis. The cultivars Sugar Baby , Crimson Sweet , Omaru Yamato and Mickylee, and the accessions M-03 , M-08 , M-10 , M-14 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 and UP-18 behaved as poor host to the population of R. reniformis. In the second experiment was tested the resistance of four commercial cultivars ( Sugar Baby , Crimson Sweet , Charleston Gray and Mickylee ) and fifteen accessions ( M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 and UP-18 ) of watermelon collected also in the Mossoró and Upanema counties to the parasitism of M. javanica. It was used the tomato cultivar Santa Cruz Kada Gigante as the control for the feasibility of the inoculum. The soil of each experimental unit was infested with 5,000 eggs of M. Javanica and at 52 days after the infestation, it was evaluated to the following variables: root-gall and eggs- mass indexes and listed the ways of development of M. Javanica observed into the root system. The cultivars Sugar Baby , Crimson Sweet , Charleston Gray and Mickylee , and the accessions M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 and UP-18 were susceptible to M. Javanica in terms of root-gall index / Com o objetivo de verificar a reação de cultivares e acessos de melancia (Citrullus lanatus) ao parasitismo de Rotylenchulus reniformis e Meloidogyne javanica, foram desenvolvidos dois experimentos na casa de vegetação do departamento de Ciências Vegetais da Universidade Federal Rural do Semi-Árido (UFERSA), em delineamento inteiramente casualizado, com cinco repetições, sendo a unidade experimental constituída de uma plântula por vaso. No primeiro experimento foi estudada a reação, quanto à resistência, de seis cultivares comerciais ( Sugar Baby , Rajada , Crimson Sweet , Charleston Gray , Omaru Yamato e Mickylee ) e 13 acessos de melancia coletados nos municípios de Mossoró e Upanema ('M-03 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 e UP-18 ) ao parasitismo de R. reniformis. Utilizou-se meloeiro (Cucumis melo) cultivar AF 646 como testemunha de viabilidade de inóculo. O solo de cada unidade experimental foi infestado com 2.000 formas vermiformes de R. reniformis (machos, fêmeas adultas imaturas e juvenis) e 51 dias após avaliou-se as variáveis: número de nematóides no solo, número de nematóides na raiz, número total de nematóides e fator de reprodução. As cultivares Rajada , Charleston Gray e o acesso M-16 comportaram-se como não hospedeiras a população de R. reniformis. As cultivares Sugar Baby , Crimson Sweet , Omaru Yamato e Mickylee e, os acessos M-03 , M-08 , M-10 , M-14 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-10 , UP-12 e UP-18 comportaram-se como más hospedeiras a população de R. reniformis. No segundo experimento foi testada a reação, quanto à resistência, de quatro cultivares comerciais ( Sugar Baby , Crimson Sweet , Charleston Gray e Mickylee ) e 15 acessos de melancia coletados nos municípios de Mossoró e Upanema ( M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 e UP-18 ) ao parasitismo de M. javanica. Utilizou-se tomateiro (Lycopersicon esculentum) cultivar Santa Cruz Kada Gigante como testemunha de viabilidade de inóculo. O solo de cada unidade experimental foi infestado com 5.000 ovos de M. javanica e 52 dias após avaliou-se as variáveis: índices de galhas e massa de ovos e enumeradas as formas de desenvolvimento de M. javanica encontradas no interior do sistema radicular. As cultivares Sugar Baby , Crimson Sweet , Charleston Gray e Mickylee e, os acessos M-03 , M-04 , M-08 , M-10 , M-14 , M-16 , M-17 , M-18 , M-19 , UP-02 , UP-04 , UP-05 , UP-10 , UP-12 e UP-18 foram suscetíveis a M. javanica quanto ao índice de galhas. Palavras-chaves: Citrullus lanatus. Rotylenchulus reniformis. Meloidogyne javanica

Abamectin is a blend of B1a and B1b avermectins that is being used as a seed treatment to control plant-parasitic nematodes on cotton. Data on the toxicity of abamectin and its effectiveness as a seed treatment to control Meloidogyne incognita or Rotylenchulus reniformis on cotton are lacking. The toxicity of abamectin was based on an assay of nematode mobility, LD50 values of 1.56 µg/ml and 32.9 µg/ml were calculated based on 2 hr exposure for M. incognita and R. reniformis, respectively. There was no recovery of either nematode after exposure for 1 hr to its LD50 concentration. Sublethal concentrations greater than 0.39 µg/ml for M. incognita and 8.2 µg/ml for R. reniformis reduced (P = 0.05) infectivity on tomato. In field trials, suppression (P = 0.05) of M. incognita was observed 32 DAP by abamectin seed treatment whereas no suppression of R. reniformis was observed. No suppression of M. incognita was perceived by abamectin seed treatment in microplots. Suppression of M. incognita was observed in microplots by harpinEA and harpingαβ as a seed treatment and foliar spray, respectively. Seed cotton yields were variable for abamectin-treated seed, but numerically positive for harpin-treated cotton. Initial gall formation on developing taproots was suppressed (P = 0.001), and penetration of 5-cm long taproots by M. incognita and R. reniformis was numerically suppressed by abamectin-treated compared to non-treated seed, but infection increased with root development. Using an assay of nematode mobility, the proportion of dead second-stage juveniles (J2) was higher (P = 0.05) following exposure to an excised radicle from abamectin-treated seed than non-treated seed, but lower (P = 0.05) than J2 exposed to the abamectin-treated seed coat. Thus a higher concentration of abamectin remained on the seed coat than emerging radicle. The concentration of abamectin transferred from the seed coat to the developing roots was limited, which contributed to the variability in suppression of plant-parasitic nematodes on cotton.

Abamectin is a blend of B1a and B1b avermectins that is being used as a seed treatment to control plant-parasitic nematodes on cotton. Data on the toxicity of abamectin and its effectiveness as a seed treatment to control Meloidogyne incognita or Rotylenchulus reniformis on cotton are lacking. The toxicity of abamectin was based on an assay of nematode mobility, LD50 values of 1.56 µg/ml and 32.9 µg/ml were calculated based on 2 hr exposure for M. incognita and R. reniformis, respectively. There was no recovery of either nematode after exposure for 1 hr to its LD50 concentration. Sublethal concentrations greater than 0.39 µg/ml for M. incognita and 8.2 µg/ml for R. reniformis reduced (P = 0.05) infectivity on tomato. In field trials, suppression (P = 0.05) of M. incognita was observed 32 DAP by abamectin seed treatment whereas no suppression of R. reniformis was observed. No suppression of M. incognita was perceived by abamectin seed treatment in microplots. Suppression of M. incognita was observed in microplots by harpinEA and harpingαβ as a seed treatment and foliar spray, respectively. Seed cotton yields were variable for abamectin-treated seed, but numerically positive for harpin-treated cotton. Initial gall formation on developing taproots was suppressed (P = 0.001), and penetration of 5-cm long taproots by M. incognita and R. reniformis was numerically suppressed by abamectin-treated compared to non-treated seed, but infection increased with root development. Using an assay of nematode mobility, the proportion of dead second-stage juveniles (J2) was higher (P = 0.05) following exposure to an excised radicle from abamectin-treated seed than non-treated seed, but lower (P = 0.05) than J2 exposed to the abamectin-treated seed coat. Thus a higher concentration of abamectin remained on the seed coat than emerging radicle. The concentration of abamectin transferred from the seed coat to the developing roots was limited, which contributed to the variability in suppression of plant-parasitic nematodes on cotton.

Made available in DSpace on 2014-06-11T19:33:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-04-03Bitstream added on 2014-06-13T19:04:50Z : No. of bitstreams: 1 corbani_rz_dr_jabo.pdf: 1269053 bytes, checksum: bdd1f9eb7c4759323348b6f58db3d09d (MD5) / Biocarbo Industria e Comercio / No Japão, uma solução aquosa, referida como extrato pirolenhoso, resultante da carbonização de madeira ou bambu, obtida através da condensação da fumaça, vem sendo estudada com fins agrícolas, inclusive como alternativa para os defensivos químicos convencionais. O presente estudo teve como objetivo avaliar a ação do extrato pirolenhoso Biopirol® sobre a eclosão e a atividade de juvenis de segundo estádio de Meloidogyne incognita, Meloidogyne. javanica e Tylenchulus semipenetrans, sobre o manejo de populações de nematóides, a campo, em cana-deaçúcar e citros, e em alface sob ambiente protegido. No Laboratório de Nematologia do Departamento de Fitossanidade da Universidade Estadual Paulista, Câmpus de Jaboticabal, foram preparadas câmaras de eclosão para a avaliação do extrato pirolenhoso Biopirol®, em diferentes concentrações, variando de 0,5% até 2,0%, sobre a eclosão e atividade dos nematóides in vitro. Nos experimentos a campo, as concentrações do produto variaram de 0,5% até 8,0%. Os dados foram submetidos à análise de variância, e as médias foram comparadas pelo Teste de Tukey, a 5% de probabilidade. Os resultados evidenciaram que o extrato pirolenhoso Biopirol® reduz a eclosão de juvenis de M. incognita, de M. javanica e de T. semipenetras in vitro e a formação de galhas formadas por M. incognita e por M. javanica em raízes de tomateiro. Nas concentrações de até 4%, não foi eficaz para a redução da população de Pratylenchus zeae e Meloidogyne sp. em cana-de-açúcar e de T. semipenetrans em laranjeira “Natal’ enxertada sobre limoeiro cravo. Nas concentrações de até 8,0%, também, não foi eficaz para a redução da população de Rotylenchulus reniformis e M. incognita em alface ‘Lucy Brown’, em ambiente protegido. / In Japan, an aqueous solution resulting from the carbonization of wood or bamboo, obtained by the condensation of smoke, referred to as pyroligneous acid has been studied with agricultural purposes, including as an alternative to the conventional chemical control of pests and diseases. This study aimed to evaluate the effect of the pyroligneous acid Biopirol® on the hatching and activity of second stage juvenile of Meloidogyne incognita, M. Javanica and Tylenchulus semipenetrans; as well as on the management of populations of nematodes, at field conditions in sugar cane and citrus and lettuce under protected environment. In Nematology Laboratory of the Department of Plant Protection of the Universidade Estadual Paulista, Câmpus of Jaboticabal, hatching chambers were prepared for the evaluation of different concentrations ranging from 0.5 % until 2.0 % of the pyroligneous acid Biopirol® on the hatching and activity of the nematodes in vitro. In the field experiments, the concentrations of the product ranged from 0.5% to 8.0%. The data were submitted to the analysis of variance and the means were compared by Tukey test of a 5% probability. Results showed that the pyroligneous acid Biopirol® reduces the hatching of the second stage juveniles of Meloidogyne incognita, M. Javanica and Tylenchulus semipenetrans in vitro. Also, reduces the formation of galls by M. incognita and M. Javanica in roots of tomato. At the concentrations of up to 4% was not effective in reducing the population of Pratylenchus zeae and Meloidogyne sp. in sugar cane and of Tyelenchulus semipenetras in orange cv. Natal grafted on Rangpur lime. In concentrations of up to 8,0% has not been effective in reducing the population of Rotylenchulus reniformis and M. incognita in lettuce cv. Lucy Brown in protected environment.