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Genomic platforms applied to citrus breeding

Grant number: 08/57909-2
Support Opportunities:Research Projects - Thematic Grants
Duration: May 01, 2009 - June 30, 2016
Field of knowledge:Agronomical Sciences - Agronomy - Plant Health
Convênio/Acordo: CNPq - INCTs
Principal Investigator:Marcos Antonio Machado
Grantee:Marcos Antonio Machado
Host Institution: Instituto Agronômico (IAC). Agência Paulista de Tecnologia dos Agronegócios (APTA). Secretaria de Agricultura e Abastecimento (São Paulo - Estado). Campinas , SP, Brazil
Associated grant(s):15/04776-9 - Transcriptional profile of sweet orange in response to chitosan and salicylic acid., PUB.ART
14/07910-5 - XVI international congress on molecular plant-microbe interactions, AR.EXT
13/20788-1 - RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response, PUB.ART
13/16823-6 - N-Acetylcysteine in agriculture, a novel use for an old molecule: focus on controlling the plant-pathogen Xylella fastidiosa, PUB.ART
13/05626-5 - Candidatus Liberibacter americanus induces significant reprogramming of the transcriptome of the susceptible citrus genotype, PUB.ART
Associated scholarship(s):15/13971-0 - Global gene expression of Candidatus Liberibacter asiaticus in different stages of development of the vector (Diaphorina citri)., BP.DR
15/14498-6 - Effectoromics: effectors as a new tool to control Phytophthora parasitica, causal agent of citrus root rot and gummosis., BP.PD
14/00366-8 - Arabidopsis thaliana e Citrus leprosis virus-C: a model for the plant-pathogen interaction study, BP.DR
+ associated scholarships 13/08569-2 - Evaluation of transgenic citrus expressing transcription factors in response to disease., BP.MS
12/18771-0 - Gene expression analysis of model plant in response to citrus leprosis, BP.MS
12/01917-2 - Functional genomics and genetic mapping of new citrus hybrids tolerant to huanglongbing (HLB or greening), BP.PD
11/16518-3 - Expression of genes of salicylic acid pathway in response to Candidatus Liberibacter spp. infection, the causal agent of citrus Huanglongbing, BP.MS


The citrus industry is one of the leading activities of the agribusiness in Brazil, with the states of Sao Paulo, Sergipe and Bahia as the main citrus producers. Brazil is by far the main producer and exporter of frozen concentrated (FCOJ) and not from concentrated (NFC) orange juice in the world. The low Brazilian yield (approximately 2 boxes 40.8 kg/tree/year) is highly associated to the incidence of pests and diseases (resulting in a substantial influence over the production costs), the production in non-irrigated areas, and the narrow genetic basis that has been used. It is estimated that more than 60 % of the costs for citrus production in Brazil are associated with control of pests and diseases. Diseases like citrus variegated chlorosis, leprosis, black and brown spot, sudden death, citrus canker, gummosis, tristeza and, recently, huanglongbing (HLB, former greening). Indeed, in recent years, the citrus industry has witnessed substantial structural changes in its structures due to diseases like HLB. Most of the models for the management of the disease vectors, including chemical control, have failed due to their high economic and environmental costs, which enhance even more the importance of studies on genetic breeding as a powerful and durable strategy to control diseases. The Centro de Citricultura Sylvio Moreira (CCSM) – IAC and Embrapa have been investigating citrus breeding for a long time as well as producing and evaluating new genetic materials by using biotechnological tools to accelerate genetic gains. As the leading member of the Millennium Institute of CNPq /MCT (2002-2005), CCSM constructed an extensive database on expressed citrus genome (CitEST), which comprises tools for studying genetic breeding and comparative and functional genomics of citrus and some of its pathogens. Besides producing the largest collection of genomic data worldwide, the project enlarged profoundly the number of new citrus hybrids under field evaluation, molecular markers for genetic mapping and discovery of new genes discovery with potential association to disease resistance. This proposal reflects the continuation of the program “Millennium Institute”, not only bringing together the main groups that investigate citrus in Brazil, but also focusing on subjects related to genetic breeding and functional genomics of the citrus group, looking forward on the integration of three platforms: Platform of Genomic Information, which focuses on studies regarding comparative and functional genomics to enlarge the basis of information, including the complete genome associated with the International Consortium on Citrus Genome and the database on expressed citrus genome, studies on gene expression (microarrays) of citrus and some of its pathogens, support to bioinformatics and genetic transformation to produce modified plants based on data from the citrus genome. Platform for Genomic Application, which the focus is the plant-pathogen interaction in limiting pathosystems faced by the citrus industry and the plant-environment interaction (water stress). Such studies will allow enlarging the knowledge useful in other activities of the Program. Platform of Apllied Genetics, which represents the advanced interface of breeding from which previously generated data (markers, maps, genes, promoters), as well as genetic material (hybrids of controlled crosses and events of transformation already available) will be validated under field conditions, to permit a reliable approach to the strategy of marker-assisted breeding. From this platform, new materials will be released for the Brazilian citrus industry. The multi-disciplinar and multi-institutional network of the Program includes, besides the CCSM as the coordinator member, Embrapa Mandioca e Fruticultura and its network for citrus breeding, Embrapa Recursos Genéticos e Biotecnologia, Escola Superior de Agricultura Luiz de Queiróz (ESALQ/USP) and Centro de Energia Nuclear na Agricultura (Cena), Universidade Estadual de Campinas (Unicamp), Instituto Biológico, Universidade Federal de Campina Grande, Universidade Estadual do Sudoeste da Bahia (Vitória da Conquista), Universidade de Mogi das Cruzes (UMC), and University of Florida. (AU)

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Scientific publications (26)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
PICCHI, S. C.; TAKITA, M. A.; COLETTA-FILHO, H. D.; MACHADO, M. A.; DE SOUZA, A. A.. N-acetylcysteine interferes with the biofilm formation, motility and epiphytic behaviour of Xanthomonas citri subsp citri. PLANT PATHOLOGY, v. 65, n. 4, p. 561-569, . (08/57909-2)
RAMOS-GONZALEZ, PEDRO LUIS; SARUBBI-ORUE, HUMBERTO; GONZALES-SEGNANA, LUIS; CHABI-JESUS, CAMILA; FREITAS-ASTUA, JULIANA; KITAJIMA, ELIOT WATANABE. Orchid Fleck Virus Infecting Orchids in Paraguay: First Report and Use of Degenerate Primers for its Detection. JOURNAL OF PHYTOPATHOLOGY, v. 164, n. 5, p. 342-347, . (08/57909-2, 14/08458-9)
NIZA, BARBARA; MERFA, MARCUS V.; ALENCAR, VALQUIRIA C.; MENEGIDIO, FABIANO B.; NUNES, LUIZ R.; MACHADO, MARCOS A.; TAKITA, MARCO A.; DE SOUZA, ALESSANDRA A.. Draft Genome Sequence of 11399, a Transformable Citrus-Pathogenic Strain of Xylella fastidiosa. GENOME ANNOUNCEMENTS, v. 4, n. 5, p. 2-pg., . (13/10957-0, 13/17485-7, 11/14307-5, 13/02014-9, 08/57909-2)
CURTOLO, MAIARA; CRISTOFANI-YALY, MARIANGELA; GAZAFFI, RODRIGO; TAKITA, MARCO AURELIO; FIGUEIRA, ANTONIO; MACHADO, MARCOS ANTONIO. QTL mapping for fruit quality in Citrus using DArTseq markers. BMC Genomics, v. 18, . (11/18605-0, 08/57909-2)
NIZA, B.; COLETTA-FILHO, H. D.; MERFA, M. V.; TAKITA, M. A.; DE SOUZA, A. A.. Differential colonization patterns of Xylella fastidiosa infecting citrus genotypes. PLANT PATHOLOGY, v. 64, n. 6, p. 1259-1269, . (13/17485-7, 08/57909-2, 11/14307-5)
CAMILLA DE ANDRADE PACHECO; EVANDRO HENRIQUE SCHINOR; FERNANDO ALVES DE AZEVEDO; MARINÊS BASTIANEL; MARIÂNGELA CRISTOFANI-YALY. Caracterização de frutos do tangor TMxLP 290 para mercado de fruta fresca. Revista Brasileira de Fruticultura, v. 36, n. 4, p. 805-812, . (11/18605-0, 08/57909-2)
GOULIN, EDUARDO; BOUFLEUR, THAIS REGINA; NEGRINI, FRANCESCA; CARNEIRO, GREICE AMARAL; BARALDI, ELENA; MACHADO, MARCOS ANTONIO; LE FLOCH, GAETAN; BARONCELLI, RICCARDO. Genome Sequence Resources of Colletotrichum abscissum, the Causal Agent of Citrus Post-Bloom Fruit Drop, and the Closely Related Species C. filicis. PHYTOPATHOLOGY, v. 113, n. 1, p. 4-pg., . (08/57909-2, 21/01606-6, 12/23381-7, 14/50880-0)
CASERTA, R.; PICCHI, S. C.; TAKITA, M. A.; TOMAZ, J. P.; PEREIRA, W. E. L.; MACHADO, M. A.; IONESCU, M.; LINDOW, S.; DE SOUZA, A. A.. Expression of Xylella fastidiosa RpfF in Citrus Disrupts Signaling in Xanthomonas citri subsp citri and Thereby Its Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS, v. 27, n. 11, p. 1241-1252, . (13/17485-7, 08/57909-2)
CASERTA, R.; SOUZA-NETO, R. R.; TAKITA, M. A.; LINDOW, S. E.; DE SOUZA, A. A.. Ectopic Expression of Xylella fastidiosa rpfF Conferring Production of Diffusible Signal Factor in Transgenic Tobacco and Citrus Alters Pathogen Behavior and Reduces Disease Severity. MOLECULAR PLANT-MICROBE INTERACTIONS, v. 30, n. 11, p. 866-875, . (08/57909-2, 13/10957-0)
GALDEANO, DIOGO MANZANO; BRETON, MICHELE CLAIRE; SPOTTI LOPES, JOAO ROBERTO; FALK, BRYCE W.; MACHADO, MARCOS ANTONIO. Oral delivery of double-stranded RNAs induces mortality in nymphs and adults of the Asian citrus psyllid, Diaphorina citri. PLoS One, v. 12, n. 3, . (14/03925-8, 08/57909-2, 13/02138-0)
MAXIMO, HEROS J.; DALIO, RONALDO J. D.; RODRIGUES, CAROLINA M.; BRETON, MICHELE C.; MACHADO, MARCOS A.. Reference genes for RT-qPCR analysis in Citrus and Poncirus infected by zoospores of Phytophthora parasitica. TROPICAL PLANT PATHOLOGY, v. 42, n. 2, p. 76-85, . (15/14498-6, 08/57909-2)
MURANAKA, LIGIA S.; TAKITA, MARCO A.; OLIVATO, JACQUELINE C.; KISHI, LUCIANO T.; DE SOUZA, ALESSANDRA A.. Global Expression Profile of Biofilm Resistance to Antimicrobial Compounds in the Plant-Pathogenic Bacterium Xylella fastidiosa Reveals Evidence of Persister Cells. Journal of Bacteriology, v. 194, n. 17, p. 4561-4569, . (08/57909-2)
CASERTA, R.; TAKITA, M. A.; TARGON, M. L.; ROSSELLI-MURAI, L. K.; DE SOUZA, A. P.; PERONI, L.; STACH-MACHADO, D. R.; ANDRADE, A.; LABATE, C. A.; KITAJIMA, E. W.; et al. Expression of Xylella fastidiosa Fimbrial and Afimbrial Proteins during Biofilm Formation. Applied and Environmental Microbiology, v. 76, n. 13, p. 4250-4259, . (08/57909-2)
NIZA, BARBARA; MERFA, MARCUS V.; ALENCAR, VALQUIRIA C.; MENEGIDIO, FABIANO B.; NUNES, LUIZ R.; MACHADO, MARCOS A.; TAKITA, MARCO A.; DE SOUZA, ALESSANDRA A.. Draft Genome Sequence of 11399, a Transformable Citrus-Pathogenic Strain of Xylella fastidiosa. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, v. 4, n. 5, . (13/02014-9, 11/14307-5, 13/17485-7, 13/10957-0, 08/57909-2)
DORTA, SILVIA DE OLIVEIRA; NOURI, SHAHIDEH; MACHADO, MARCOS ANTONIO. . Viruses-Basel, v. 8, n. 12, . (08/57909-2)
BOSCARIOL-CAMARGO, RAQUEL L.; TAKITA, MARCO A.; MACHADO, MARCOS A.. Bacterial resistance in AtNPR1 transgenic sweet orange is mediated by priming and involves EDS1 and PR2. TROPICAL PLANT PATHOLOGY, v. 41, n. 6, p. 341-349, . (09/00058-3, 08/57909-2)
DURIGAN DALIO, RONALDO JOSE; MAXIMO, HEROS JOSE; OLIVEIRA, TIAGO SILVA; AZEVEDO, THAMARA DE MEDEIROS; FELIZATTI, HENRIQUE LEME; CAMPOS, MAGNOLIA DE ARAUJO; MACHADO, MARCOS ANTONIO. Molecular Basis of Citrus sunki Susceptibility and Poncirus trifoliata Resistance Upon Phytophthora parasitica Attack. MOLECULAR PLANT-MICROBE INTERACTIONS, v. 31, n. 3, p. 386-398, . (08/57909-2, 15/14498-6, 14/50880-0)
RODRIGUES, CAROLINA MUNARI; TAKITA, MARCO AURELIO; SILVA, NICHOLAS VINICIUS; RIBEIRO-ALVES, MARCELO; MACHADO, MARCOS ANTONIO. Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host. BMC Genomics, v. 20, . (08/57909-2, 14/50880-0)
GOULIN, EDUARDO HENRIQUE; DE LIMA, THIAGO ANTONIO; DOS SANTOS, PAULO JOSE CAMARGO; MACHADO, MARCOS ANTONIO. RNAi-induced silencing of the succinate dehydrogenase subunits gene in Colletotrichum abscissum, the causal agent of postbloom fruit drop (PFD) in citrus. MICROBIOLOGICAL RESEARCH, v. 260, p. 10-pg., . (12/23381-7, 08/57909-2, 14/50880-0)
BOSCARIOL-CAMARGO, RAQUEL L.; TAKITA, MARCO A.; MACHADO, MARCOS A.. Bacterial resistance in AtNPR1 transgenic sweet orange is mediated by priming and involves EDS1 and PR2. ROPICAL PLANT PATHOLOG, v. 41, n. 6, p. 9-pg., . (09/00058-3, 08/57909-2)
MATSUMURA, EMILYN EMY; DELLA COLETTA FILHO, HELVECIO; DORTA, SILVIA DE OLIVEIRA; NOURI, SHAHIDEH; MACHADO, MARCOS ANTONIO. Genetic Structure and Molecular Variability Analysis of Citrus sudden death-associated virus Isolates from Infected Plants Grown in Brazil. Viruses-Basel, v. 8, n. 12, p. 17-pg., . (08/57909-2)
MAXIMO, HEROS J.; DALIO, RONALDO J. D.; RODRIGUES, CAROLINA M.; BRETON, MICHELE C.; MACHADO, MARCOS A.. Reference genes for RT-qPCR analysis in Citrus and Poncirus infected by zoospores of Phytophthora parasitica. ROPICAL PLANT PATHOLOG, v. 42, n. 2, p. 10-pg., . (08/57909-2, 15/14498-6)
OLIVEIRA COQUEIRO, DANILA SOUZA; DE SOUZA, ALESSANDRA ALVES; TAKITA, MARCO AURELIO; RODRIGUES, CAROLINA MUNARI; KISHI, LUCIANO TAKESHI; MACHADO, MARCOS ANTONIO. Transcriptional profile of sweet orange in response to chitosan and salicylic acid. BMC Genomics, v. 16, . (08/57909-2)
ARENA, GABRIELLA D.; RAMOS-GONZALEZ, PEDRO L.; NUNES, MARIA A.; RIBEIRO-ALVES, MARCELO; CAMARGO, LUIS E. A.; KITAJIMA, ELLIOT W.; MACHADO, MARCOS A.; FREITAS-ASTUA, JULIANA. Citrus leprosis virus C Infection Results in Hypersensitive-Like Response, Suppression of the JA/ET Plant Defense Pathway and Promotion of the Colonization of Its Mite Vector. FRONTIERS IN PLANT SCIENCE, v. 7, . (12/18771-0, 14/08458-9, 08/57909-2, 14/00366-8)
WU, G. ALBERT; PROCHNIK, SIMON; JENKINS, JERRY; SALSE, JEROME; HELLSTEN, UFFE; MURAT, FLORENT; PERRIER, XAVIER; RUIZ, MANUEL; SCALABRIN, SIMONE; TEROL, JAVIER; et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. NATURE BIOTECHNOLOGY, v. 32, n. 7, p. 656+, . (08/57909-2)
MURANAKA, LIGIA S.; GIORGIANO, THAIS E.; TAKITA, MARCO A.; FORIM, MOACIR R.; SILVA, LUIS F. C.; COLETTA-FILHO, HELVECIO D.; MACHADO, MARCOS A.; DE SOUZA, ALESSANDRA A.. N-Acetylcysteine in Agriculture, a Novel Use for an Old Molecule: Focus on Controlling the Plant-Pathogen Xylella fastidiosa. PLoS One, v. 8, n. 8, . (08/57909-2)

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