Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus

Most of the cultivated species of citrus have narrow genetic basis. Relationships among species and cultivars are obscured by sexual compatibility, polyembryony, apomixis and a high incidence of somatic mutations. DNA analysis is crucial in genetic studies not only for citrus breeding programs but also for characterization of hybrids and species. In this paper, single nucleotide polymorphisms ( SNPs) were investigated in 58 accessions of Citrus, hybrids and related genera. Genomic sequences of 'Pera IAC' sweet orange ( Citrus sinensis L. Osbeck) were used for primer design and selection of sequence tagged sites (STSs) for identification of SNPs. Analysis of 36 STSs showed identical sequences among 40 of the 41 sweet orange accessions studied. However, these accessions were heterozygous for many SNPs. Ten selected STSs were analyzed in 17 additional accessions from 13 species and hybrids. Comparing to the 'Pera IAC' sweet orange accession, a total of 150 polymorphic nucleotides were identified and most of the alterations were transitions ( 52.7%). The greatest number of SNPs was observed in Poncirus trifoliata ( L.) Raf. and the smallest in 'Ponkan' mandarin ( Citrus reticulata Blanco). At the intra-specific level, 'Bafa Gigante' ( Citrus sinensis L. Osbeck) was the only sweet orange accession with a divergent SNPs genotype, which corroborates the hypothesis of a hybrid origin for this accession. Although the STSs analyzed represent randomly sampled genomic sequences, they provided consistent information about the level of polymorphism and showed the potential of SNPs markers for characterization and phylogenetic studies.

Pratylenchus jaehni sp n. from citrus in Brazil and its relationship with P-coffeae and P-loosi (Nematoda : Pratylenchidae)

A lesion nematode population infecting citrus in the state of São Paulo, Brazil is described and named Pratylenchus jaehni sp. n. Biological, molecular and morphological characteristics of this new species are compared with those of the morphologically similar P. coffeae and P. loosi. Results of mating experiments showed that R jaehni is reproductively isolated from P coffeae. Molecular (D2/D3 DNA sequences) dissimilarities among P. jaehni sp, n., P. coffeae and P. loosi were documented in a previous study. The morphology of seven R coffeae populations from tropical America and eastern Java and a P loosi population from Sri Lanka is used for comparison with the morphology of P. jaehni sp. n. Pratylenchus jaehni differs from R coffeae and P. loosi by only a few morphological ;characters of the females. The mean values of stylet length, stylet knob height, and vulva position are smaller (less than or equal to15 vs greater than or equal to15 mum, less than or equal to2.7 vs greater than or equal to2.7 mum, less than or equal to79 vs greater than or equal to79%) than those in P coffeae and P loosi. The tail terminus is usually subhemispherical and smooth in P jaehni sp. n.. whereas it is commonly truncate and indented in most P. coffeae populations and bluntly or finely pointed in P. loosi. Because of the morphological similarities among P. jaehni sp. n., P. coffeae and P. loosi, examination of at least ten specimens is required to obtain a reliable diagnosis based on morphology. Nineteen morphometric parameters for P. jaehni sp. n. and P. coffeae ranged from 0-13% smaller in fixed than in live specimens.

Partial purification and characterization of pectin methylesterase from orange (Citrus sinensis) cv. Pera-rio

The enzyme pectin methylesterase (PME) from orange was extracted and partially purified by filtration on Sephadex G-100. The extraction buffer for orange PME was borate-acetate containing 0.4 M NaCl. Orange PME showed optimum pH at 8.0 and optimum temperature at 50C. The PME enzyme was completely inactivated after 1 min of incubation at 90C. The specific activity increased in the presence of 0.15 M NaCl or 0.025 M Na2SO4, 0.10 M KCl, 0.025 M K2SO4, 0.05 and 0.1 M NH4Cl. Lithium chloride and Li(2)SO(4)inhibited the enzymatic activity at all concentrations studied. The K-m and V(max)value of PME were 0.36 mg/mL and 5.26 mu mol/mL-mg protein, respectively.

Determination of buprofezin, pyridaben, and tebufenpyrad residues by gas chromatography mass-selective detection in clementine citrus

A gas chromatography-mass-selective (GC-MS) detection method to determine buprofezin, pyridaben, and tebufenpyrad on the pulp, peel, and whole fruit of clementines is described. The extraction/partition procedure was performed in one step and no cleanup was necessary with the GC-MS in the SIM-mode pesticide determination. Recovery ranged from 75 to 124% with coefficients of variance ranging between 1 and 13%. The limit of determination was 0.01 mg/kg for all pesticides. The field trials showed a similar degradative behavior for all active ingredients (AI), with a great residue decrease during the first week and stability in the second. Just after treatment buprofezin and tebufenpyrad showed lower residues than the maximum residue limit (MRL) fixed in Italy, while pyridaben was below the MRL after a week.

Saprophytic colonization of citrus twigs by Diaporthe citri and factors affecting pycnidial production and conidial survival

Melanose, caused by Diaporthe citri, produces reddish brown lesions on the fruit, leaves, and twigs of citrus trees, and greatly reduces the marketability of fresh fruit. Most of the inoculum is produced in pycnidia on dead twigs in the tree canopy, which exude large numbers of conidia in slimy masses. In this study, detached twigs inoculated with conidia were readily colonized and produced large numbers of pycnidia within 30 to 40 days when they were soaked 3 to 4 h on alternate days. Conidial production was measured by wetting twigs in a rain tower periodically and collecting the conidia in the runoff water. Production began after 80 days and continued for nearly 300 days. In other experiments, production of mature pycnidia on detached twigs was greatest at 94 to 100% relative humidity (RH) and at 28 degrees C. Low RH and temperature, however, favored survival of conidia in exuded masses on twigs. In the field, colonization of detached twigs by D. citri was high in rainy season, moderate in spring and early fall, and minimal in late fall and winter. Twig colonization was positively related to the number of rain days and average temperature, but not to total rainfall. In another experiment, inoculated twigs placed in the tree canopy developed pycnidia and then produced conidial masses for about 200 days. D. citri is a serious pathogen, but a weak parasite, that survives primarily by colonization and reproduction on dead twigs.

Complete nucleotide sequence, genomic organization and phylogenetic analysis of Citrus leprosis virus cytoplasmic type

The complete nucleotide sequence of the genomic RNA 1 (8745 nt) and RNA 2 (4986 nt) of Citrus leprosis virus cytoplasmic type (CiLV-C) was determined using cloned cDNA. RNA 1 contains two open reading frames (ORFs), which correspond to 286 and 29 kDa proteins. The 286 kDa protein is a polyprotein putatively involved in virus replication, which contains four conserved domains: methyltransferase, protease, helicase and polymerase. RNA 2 contains four ORFs corresponding to 15, 61, 32 and 24 kDa proteins, respectively. The 32 kDa protein is apparently involved in cell-to-cell movement of the virus, but none of the other putative proteins exhibit any conserved domain. The 5' regions of the two genomic RNAs contain a 'cap' structure and poly(A) tails were identified in the 3'-terminals. Sequence analyses and searches for structural and non-structural protein similarities revealed conserved domains with members of the genera Furovirus, Bromovirus, Tobravirus and Tobamovirus, although phylogenetic analyses strongly suggest that CiLV-C is a member of a distinct, novel virus genus and family, and definitely demonstrate that it does not belong to the family Rhabdoviridae, as previously proposed. Based on these results it was proposed that Citrus leprosis virus be considered as the type member of a new genus of viruses, Cilevirus.

Pectin lyase from Aspergillus giganteus: Comparative study of productivity of submerged fermentation on citrus pectin and orange waste

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cloning, expression, purification and characterization of recombinant glutathione-S-transferase from Xylella fastidiosa

Xylella fastidiosa is an important pathogen bacterium transmitted by xylem-feedings leafhoppers that colonizes the xylem of plants and causes diseases on several important crops including citrus variegated chlorosis (CVC) in orange and lime trees. Glutathione-S-transferases (GST) form a group of multifunctional isoenzymes that catalyzes both glutathione (GSH)-dependent conjugation and reduction reactions involved in the cellular detoxification of xenobiotic and endobiotic compounds. GSTs are the major detoxification enzymes found in the intracellular space and mainly in the cytosol from prokaryotes to mammals, and may be involved in the regulation of stress-activated signals by suppressing apoptosis signal-regulating kinase 1. In this study, we describe the cloning of the glutathione-S-transferase from X. fastidiosa into pET-28a(+) vector, its expression in Escherichia coli, purification and initial structural characterization. The purification of recombinant xfGST (rxfGST) to near homogeneity was achieved using affinity chromatography and size-exclusion chromatography (SEC). SEC demonstrated that rxfGST is a homodimer in solution. The secondary and tertiary structures of recombinant protein were analyzed by circular dichroism and fluorescence spectroscopy, respectively. The enzyme was assayed for activity and the results taken together indicated that rxfGST is a stable molecule, correctly folded, and highly active. Several members of the GST family have been extensively studied. However, xfGST is part of a less-studied subfamily which yet has not been structurally and biochemically characterized. In addition, these studies should provide a useful basis for future studies and biotechnological approaches of rxfGST. (C) 2008 Elsevier B.V. All rights reserved.

Benomyl sensitivity of isolates of Colletotrichum acutatum and C. gloeosporioides from citrus

Postbloom fruit drop (PFD) of citrus, caused by Colletotrichum acutatum, produces orange-brown lesions on petals and results in premature fruit drop and the retention of calyces. C. gloeosporioides is common in groves and causes postharvest anthracnose on fruit. Both diseases are controlled effectively by the fungicide benomyl in research fields and commercial orchards. Highly sensitive and resistant isolates of C. gloeosporioides were found, whereas all isolates of C. acutatum tested were moderately resistant. In preliminary studies conducted in vitro with three isolates of each, mycelial growth of sensitive isolates of C. gloeosporioides was inhibited completely by benomyl (Benlate 50 WP) at 1.0 μg/ml, whereas resistant isolates grew well at 10 μg/ml. Growth of all isolates of C. acutatum was inhibited by about 55% at 0.1 μg/ml and by 80% at 1.0 μg/ml. Spore germination of C. acutatum was inhibited more at 0.1 μg/ml than at 1.0 μg/ml or higher concentrations. In all, 20 isolates of C. acutatum from 17 groves and 20 isolates of C. gloeosporioides from 7 groves were collected from locations with different histories of benomyl usage in São Paulo, Brazil, and Florida, United States. Benomyl at 1.0 μ.g/ml completely inhibited growth of 133 isolates of C. gloeosporioides, with the exception of 7 isolates that were highly resistant to the fungicide, whereas all isolates of C. acutatum were only partially inhibited at 0.1 and 1.0 μg/ml. Analysis of variance indicated that the sensitivity of the isolates of C. acutatum was not affected by benomyl usage or grove of origin, and country of origin had only minor effects. No highly resistant or sensitive isolate of C. acutatum was recovered. Partial sequencing of the β-tubulin gene did not reveal nucleotide substitutions in codons 198 or 200 in C. acutatum that usually are associated with benomyl resistance in other fungi.

Attractiveness of citrus pulp and orange albedo extracts to Atta sexdens rubropilosa (Hymenoptera: Formicidae)

The present study aimed to compare the attractiveness of industrial citrus pulp with the handmade orange albedo to the workers of Atta sexdens rubropilosa. For this, filter paper fragments were impregnated with organic extracts obtained through chemical extraction and sequential fractioning with hexane and dichloromethane and offered to different field nests. It was verified that the industrial citrus pulp extract is as good as the handmade orange albedo extract. This preference is discussed keeping in mind the chemical, behavioral and nutritional factors.

Response of rootstocks to stem canker and the production and quality of melon under protected cultivation

Two tests were performed. In the first, resistance to Didymella bryoniae was determined for the following genotypes: the pumpkins 'Ikky', 'Agroceres', 'Kirameki' and 'Shelper', watermelon progenies 1a, 2a, 3a, 5a, 1b, 2b, 3b and 5b, and 'Gherkin' (C. anguria). The plants were inoculated with the fungus during transplanting. The evaluations of the test were performed every 15 d according to a scoring scale adopted by Dusi et al. (1994). The second test examined compatibility among the rootstocks x grafts, and their effects on production. The rootstocks, 5 pumpkins including 'Ikky', 'Agroceres', 'Kirameki', 'Shelper', six watermelon progenies 1a, 2a, 5a, 1b, 2b and 5b, and one 'Gherkin', were planted one week before planting of the grafted 'Bônus No. 2' melon. The experiments were carried out with 12 treatments, including the control ('Bônus No. 2') with 3 replications with 14 grafted plants per each replication. For the first test, the first three evaluations (at 15, 30 and 45 d after inoculation) did not show characteristic lesions of stem canker, but progeny 3b was found to be susceptible in evaluations performed at 60 and 75 d after inoculation. Progeny 3a demonstrated intermediate susceptibility, while progenies 1a, 2a, 5a, 1b, 2b and 5b, the pumpkins 'Kirameki', 'Shelper', 'Ikky' and 'Agroceres', and 'Gherkin', showed resistance to Didymella bryoniae. In the second test, watermelon progenies 1a, 5a, 1b and 2b, and the pumpkins 'Kirameki', 'Shelper', 'Ikky' and 'Agroceres' showed a level of grafting success of 100%, while results with progenies 2a and 5b, and 'Gherkin' were different in grafting success, respectively 91.67, 98.33 and 43.33%. For other fruit parameters, weight, longitudinal and transverse diameters, pulp thickness and level of total soluble solids, there were no differences among the treatments.

Oxidative stability and α-tocopherol retention in soybean oil with lemon seed extract (Citrus limon) under thermoxidation

The synergistic effect of lemon seed extract with tert-butylhydroquinone (TBHQ) in soybean oil subjected to thermoxidation by Rancimat was investigated, and the influence of these antioxidants on α-tocopherol degradation in thermoxidized soybean oil. Control, LSE (2,400 mg/kg Lemon Seed Extract), TBHQ (50 mg/kg), Mixture 1 (LSE + 50 mg/kg TBHQ) and Mixture 2 (LSE + 25 mg/kg TBHQ) were subjected to 180°C for 20 h. Samples were taken at time 0, 5, 10, 15 and 20 h intervals and analysed for oxidative stability and α-tocopherol content. LSE and Mixtures 1 and 2 showed the capacity of retarding lipid oxidation when added to soya oil and also contributed to α-tocopherol retention in oil heated at high temperatures. However, Mixtures 1 and 2 added to the oil presented a greater antioxidant power, consequently proving the antioxidants synergistic effect.

Relationship between citrus productivity and indicators of uniformity in trickle irrigation system

In trickle irrigation systems, the design is based on the pre-established emission uniformity (EU) which is the combined result of the equipment characteristics and its hydraulic configuration. However, this desired value of the EU may not be confirmed by the final project (in field conditions) and neither by the yield uniformity. The hypotheses of this research were: a) the EU of a trickle irrigation system at field conditions is equal to the emission uniformity pre-established in the its design; b) EU has always the lowest value when compared with other indicators of uniformity; c) the discharge variation coefficient (VC) is not equal to production variation coefficient in the operational unit; d) the difference between the discharge variation coefficient and the productivity variation coefficient depends on the water depth applied. This study aimed to evaluate the relationship between EU used in the irrigation system design and the final yield uniformity. The uniformity indicators evaluated were: EU, distribution uniformity (UD) and the index proposed by Barragan & Wu (2005). They were compared estimating the performance of a trickle irrigation system applied in a citrus orchard with dimensions of 400m x 600m. The design of the irrigation system was optimized by a Linear Programming model. The tree rows were leveled in the larger direction and the spacing adopted in the orchard was 7m x 4m. The manifold line was always operating on a slope condition. The sensitivity analysis involved different slopes, 0, 3, 6, 9 and 12%, and different values of emission uniformity, 60, 70, 75, 80, 85, 90 and 94%. The citrus yield uniformity was evaluated by the variation coefficient. The emission uniformity (EU) after design differed from the EU pre-established, more sharply in the initial values lower than 90%. Comparing the uniformity indexes, the EU always generated lower values when compared with the UD and with the index proposed by Barragan. The emitter variation coefficient was always lower than the productivity variation coefficient. To obtain uniformity of production, it is necessary to consider the irrigation system uniformity and mainly the water depth to be applied.