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INCT 2014: comparative and functional genomics and citrus-assisted breeding

Abstract

Citrus industry is one of the most important activities of the Brazilian agriculture. São Paulo, Sergipe and Bahia are the main citrus producers, and 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 strictly associated to the incidence of pests and diseases, resulting in a substantial influence over the production costs, groves in non-irrigated areas, and the narrow genetic basis especially of the industrial citrus production. It is estimated that more than 80 % of the costs for citrus production in Brazil are associated with the control of pests and diseases. Diseases like huanglongbing (HLB), citrus variegated chlorosis (CVC), leprosis, citrus black spot (CBS), sudden death, citrus canker, citrus brown spot, gummosis, and tristeza have expressive contribution in the increasing production costs. As headquarter of the NIST Citrus, the Citriculture Center, expanded the data base of citrus genomes, integrating breeding, comparative and functional genomics of citrus and some of their pathogens. Besides generating the largest database of citrus genomes in the world, this project greatly increased the number of new citrus hybrids evaluated in the field, molecular markers for genetic mapping, and identified new genes potentially associated with disease resistance. The proposal submitted to the Notice of 016/2014 NIST represents the continuation and expansion of the Citrus NIST program with leading research groups working on citrus in Brazil, focusing on topics related to breeding and comparative and functional genomics of citrus and their pathogens. This new NIST Citrus proposal maintains the structure of the three platforms, optimizing and integrating them, and focusing on the development of new knowledge and technology for the citrus industry. Platform of Comparative Genomics focuses on studies of comparative genomics of more citrus genotypes (genomes of nuclear core collection), completion of the genomes of important pathogens, in addition to expanding the database of miRNA and epigenetic regulation processes. Understanding the citrus pathogens and their relationships, the search for genes and promoters, the genomic diversity of the citrus group (platform SNPs), the regulation of genetic processes are the most relevant aspects of that platform. Platform for Functional Genomics gathers specific projects in all pathosystems with the goals of expanding the potentially applicable knowledge in the following phases of the program. All proposals have specific foci derived from the knowledge generated in the previous NIST. Platform of Assisted Breeding represents the advanced interface of breeding, from which previously generated data (markers, maps, genes, promoters), as well as genetic materials (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 program includes the participation of the leading research teams working in research and development in citrus in Brazil. Various external collaborators were invited to be leaders in their fields and the availability to receive students and researchers in their groups. The headquarters of NIST will again be the Centro de Citricultura Sylvio Moreira, the Instituto Agronômico de Campinas. Also participate in the NIST as laboratories associated Embrapa (Cassava & Fruits, Cruz das Almas, Bahia and Temperate Clime, Pelotas-RS), Universidade of São Paulo (Institute of Chemistry, Esalq and Cena), Universidade Estadual Paulista (UNESP, Rio Claro), Instituto Biológico, Universidade Federal of Paraná, National Biosciences Laboratory (LNBio), Universidade Estadual de Santa Cruz (Ilhéus, BA), Universidade Federal of Campina Grande, State University of Southwest Bahia (Vitória da Conquista), Universidade Estadual of Maringa, and Instituto Agronomico of Paraná (IAPar). External collaborators include the University of Florida (Citurs Research and Education Center in Lake Alfred), University of California (Berkeley and Davis), John Innes Institute (Norwich, England), Instituto Valencia no de Investigaciones Agricultural (IVIA, Spain), Martin-Luther-Universitat Halle Wintenberg (Halle, Germany), United States Department of Agriculture (USDA, Fort Pierce and Fort Collins), Instituto per Ia Protezione delle Sostenibile Plante (UOS Bari, Italy) and University of Ghent (Bégica). Participate as collaborators the companies Citrosuco SA and Agrolatina Ltda. (AU)

Articles published in Pesquisa FAPESP Magazine about the research grant:
Disease-immune orange trees 
Naranjos inmunes 
Articles published in Agência FAPESP Newsletter about the research grant:
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Scientific publications (34)
(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)
DALIO, RONALDO J. D.; PASCHOAL, DANIELE; ARENA, GABRIELLA D.; MAGALHAES, DIOGO M.; OLIVEIRA, TIAGO S.; MERFA, MARCUS V.; MAXIMO, HEROS J.; MACHADO, MARCOS A. Hypersensitive response: From NLR pathogen recognition to cell death response. Annals of Applied Biology, NOV 2020. Web of Science Citations: 0.
COSTA ARANTES, ANA CAROLINA; COTTA, SIMONE RAPOSO; DA CONCEICAO, PATRICIA MARLUCI; MENEGHIN, SILVANA PERISSATTO; MARTINELLI, RODRIGO; PROSPERO, ALEXANDRE GONCALVES; BOARETTO, RODRIGO MARCELLI; ANDREOTE, FERNANDO DINI; MATTOS-JR, DIRCEU; DE AZEVEDO, FERNANDO ALVES. Implication of Urochloa spp. Intercropping and Conservation Agriculture on Soil Microbiological Quality and Yield of Tahiti Acid Lime in Long Term Orchard Experiment. AGRICULTURE-BASEL, v. 10, n. 11 NOV 2020. Web of Science Citations: 0.
LOURENCO PETTERS-VANDRESEN, DESIRRE ALEXIA; ROSSI, BRUNO JANOSKI; GROENEWALD, JOHANNES Z.; CROUS, PEDRO W.; MACHADO, MARCOS ANTONIO; STUKENBROCK, EVA H.; GLIENKE, CHIRLEI. Mating-type locus rearrangements and shifts in thallism states in Citrus-associated Phyllosticta species. Fungal Genetics and Biology, v. 144, NOV 2020. Web of Science Citations: 0.
PEREIRA, WILLIAN EDUARDO LINO; DE ANDRADE, SHEILA MARIA PEREIRA; DEL PONTE, EMERSON M.; ESTEVES, MARIANA BOSSI; CANALE, MARIA CRISTINA; TAKITA, MARCO AURELIO; COLETTA-FILHO, HELVECIO DELLA; DE SOUZA, ALESSANDRA ALVES. Severity assessment in the Nicotiana tabacum-Xylella fastidiosa subsp. pauca pathosystem: design and interlaboratory validation of a standard area diagram set. TROPICAL PLANT PATHOLOGY, v. 45, n. 6, SI NOV 2020. Web of Science Citations: 0.
DILARRI, GUILHERME; ZAMUNER, CAIO F. C.; MENDES, CAROLINA R.; JUNIOR, JOSE R. M.; MORAO, LUANA G.; MONTAGNOLLI, RENATO N.; BIDOIA, EDERIO D.; FERREIRA, HENRIQUE. Evaluating the potential of electrolysed water for the disinfection of citrus fruit in packinghouses. Journal of the Science of Food and Agriculture, OCT 2020. Web of Science Citations: 0.
ANDRADE, MAXUEL OLIVEIRA; SFORCA, MAURICIO LUIS; HELENO BATISTA, FERNANDA APARECIDA; MIGLIORINI FIGUEIRA, ANA CAROLINA; BENEDETTI, CELSO EDUARDO. The MAF1 Phosphoregulatory Region Controls MAF1 Interaction with the RNA Polymerase III C34 Subunit and Transcriptional Repression in Plants. PLANT CELL, v. 32, n. 9, p. 3019-3035, SEP 2020. Web of Science Citations: 0.
ARENA, GABRIELLA D.; RAMOS-GONZALEZ, PEDRO LUIS; FALK, BRYCE W.; CASTEEL, CLARE L.; FREITAS-ASTUA, JULIANA; MACHADO, MARCOS A. Plant Immune System Activation Upon Citrus Leprosis Virus C Infection Is Mimicked by the Ectopic Expression of the P61 Viral Protein. FRONTIERS IN PLANT SCIENCE, v. 11, AUG 7 2020. Web of Science Citations: 0.
CAVALCA, LUCIA B.; ZAMUNER, CAIO F. C.; SALDANHA, LUIZ L.; POLAQUINI, CARLOS R.; REGASINI, LUIS O.; BEHLAU, FRANKLIN; FERREIRA, HENRIQUE. Hexyl gallate for the control of citrus canker caused byXanthomonas citrisubspcitri. MICROBIOLOGYOPEN, v. 9, n. 9 AUG 2020. Web of Science Citations: 0.
PACHECO, INAIARA DE SOUZA; GALDEANO, DIOGO MANZANO; SPOTTI LOPES, JOAO ROBERTO; MACHADO, MARCOS ANTONIO. Development on Infected Citrus over Generations Increases Vector Infection by `CandidatusLiberibacter Asiaticus inDiaphorina citri'. INSECTS, v. 11, n. 8 AUG 2020. Web of Science Citations: 0.
GRANATO, LAIS MOREIRA; OLIVEIRA, TIAGO S.; BOSCARIOL-CAMARGO, RAQUEL L.; GALDEANO, DIOGO M.; SILVA, V, NICHOLAS; MAXIMO, HEROS J.; DALIO, RONALDO J. D.; MACHADO, MARCOS A. `CandidatusLiberibacter asiaticus' putative effectors:in silicoanalysis and gene expression in citrus leaves displaying distinct huanglongbing symptoms. TROPICAL PLANT PATHOLOGY, v. 45, n. 6, SI JUL 2020. Web of Science Citations: 0.
MOREIRA MARTINS, PAULA MARIA; ANDRADE, MAXUEL DE OLIVEIRA; BENEDETTI, CELSO EDUARDO; DE SOUZA, ALESSANDRA ALVES. Xanthomonas citri subsp. citri: host interaction and control strategies. TROPICAL PLANT PATHOLOGY, v. 45, n. 3, SI JUN 2020. Web of Science Citations: 0.
SORATTO, TATIANY APARECIDA TEIXEIRA; CURTOLO, MAIARA; MARENGO, SAMANTA; DEZOTTI, ANA LUCIA; LIMA, ROMULO PEDRO MACEDO; GAZAFFI, RODRIGO; MACHADO, MARCOS ANTONIO; CRISTOFANI-YALY, MARIANGELA. QTL and eQTL mapping associated with host response toCandidatusLiberibacter asiaticus in citrandarins. TROPICAL PLANT PATHOLOGY, v. 45, n. 6, SI MAY 2020. Web of Science Citations: 0.
MAIARA CURTOLO; LAÍS MOREIRA GRANATO; TATIANY APARECIDA TEIXEIRA SORATTO; MAISA CURTOLO; RODRIGO GAZAFFI; MARCO AURÉLIO TAKITA; MARIÂNGELA CRISTOFANI-YALY; MARCOS ANTONIO MACHADO. Expression Quantitative Trait Loci (eQTL) mapping for callose synthases in intergeneric hybrids of Citrus challenged with the bacteria Candidatus Liberibacter asiaticus. GENETICS AND MOLECULAR BIOLOGY, v. 43, n. 2, p. -, 2020. Web of Science Citations: 0.
GRANATO, LAIS MOREIRA; PICCHI, SIMONE CRISTINA; ANDRADE, MAXUEL DE OLIVEIRA; MARTINS, PAULA MARIA MOREIRA; TAKITA, MARCO AURELIO; MACHADO, MARCOS ANTONIO; DE SOUZA, ALESSANDRA ALVES. The ecnA Antitoxin Is Important Not Only for Human Pathogens: Evidence of Its Role in the Plant Pathogen Xanthomonas citri subsp. citri. Journal of Bacteriology, v. 201, n. 20 OCT 2019. Web of Science Citations: 0.
POLAQUINI, CARLOS R.; MORAO, LUANA G.; NAZARE, ANA C.; TORREZAN, GUILHERME S.; DILARRI, GUILHERME; CAVALCA, LUCIA B.; CAMPOS, DEBORA L.; SILVA, ISABEL C.; PEREIRA, JESSE A.; SCHEFFERS, DIRK-JAN; DUQUE, CRISTIANE; PAVAN, FERNANDO R.; FERREIRA, HENRIQUE; REGASINI, LUIS O. Antibacterial activity of 3,3 `-dihydroxycurcumin (DHC) is associated with membrane perturbation. BIOORGANIC CHEMISTRY, v. 90, n. SI SEP 2019. Web of Science Citations: 0.
PETRY, FABIANE C.; DE NADAI, FABIO B.; CRISTOFANI-YALY, MARIANGELA; LATADO, RODRIGO R.; MERCADANTE, ADRIANA Z. Carotenoid biosynthesis and quality characteristics of new hybrids between tangor (Citrus reticulata x C. sinensis) cv. `Murcott' and sweet orange (C. sinensis) cv. `Pera'. Food Research International, v. 122, p. 461-470, AUG 2019. Web of Science Citations: 5.
SHIMO, HUGO MASSAYOSHI; TERASSI, CAROLINA; SILVA, CAIO CESAR LIMA; ZANELLA, JACKELINE DE LIMA; MERCALDI, GUSTAVO FERNANDO; ROCCO, SILVANA APARECIDA; BENEDETTI, CELSO EDUARDO. Role of the Citrus sinensis RNA deadenylase CsCAF1 in citrus canker resistance. MOLECULAR PLANT PATHOLOGY, v. 20, n. 8, p. 1105-1118, AUG 2019. Web of Science Citations: 1.
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, JUL 5 2019. Web of Science Citations: 2.
SILVA, MATHEUS C.; SOUSA, ANDRESSA R. O.; CRUZ, ELAINE S.; SCHLICHTING, ALESSANA F.; SOARES FILHO, WALTER S.; GESTEIRA, ABELMON S.; COELHO FILHO, MAURICIO A.; COSTA, MARCIO G. C. Phenotyping of new hybrid citrus rootstocks under water deficit reveals conserved and novel physiological attributes of drought tolerance. ACTA PHYSIOLOGIAE PLANTARUM, v. 41, n. 6 JUN 2019. Web of Science Citations: 0.
ROGERIO, LUANA APARECIDA; GALDEANO, DIOGO MANZANO; ARENA, GABRIELLA DIAS; NUNES, MARIA ANDREIA; MACHADO, MARCOS ANTONIO; NOVELLI, VALDENICE MOREIRA. Reference genes for gene expression studies by RT-qPCR in Brevipalpus yothersi (Acari: Tenuipalpidae), the mite vector of citrus leprosis virus. SCIENTIFIC REPORTS, v. 9, APR 25 2019. Web of Science Citations: 0.
MORAO, LUANA G.; POLAQUINI, CARLOS R.; KOPACZ, MALGORZATA; TORREZAN, GUILHERME S.; AYUSSO, GABRIELA M.; DILARRI, GUILHERME; CAVALCA, LUCIA B.; ZIELINSKA, ALEKSANDRA; SCHEFFERS, DIRK-JAN; REGASINI, LUIS O.; FERREIRA, HENRIQUE. A simplified curcumin targets the membrane of Bacillus subtilis. MICROBIOLOGYOPEN, v. 8, n. 4 APR 2019. Web of Science Citations: 2.
GONCALVES, LUANA P.; BOSCARIOL CAMARGO, RAQUEL L.; TAKITA, MARCO AURELIO; MACHADO, MARCOS A.; DOS SOARES FILHO, WALTER S.; COSTA, MARCIO G. C. Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq. BMC Genomics, v. 20, FEB 6 2019. Web of Science Citations: 3.
MAURICIO, F. N.; SORATTO, T. A. T.; DIOGO, J. A.; BOSCARIOL-CAMARGO, R. L.; DE SOUZA, A. A.; COLETTA-FILHO, H. D.; SILVA, J. A. A.; MEDEIROS, A. H.; MACHADO, M. A.; CRISTOFANI-YALY, M. Analysis of Defense-Related Gene Expression in Citrus Hybrids Infected by Xylella fastidiosa. PHYTOPATHOLOGY, v. 109, n. 2, p. 301-306, FEB 2019. Web of Science Citations: 1.
NAVIA, DENISE; NOVELLI, VALDENICE M.; ROMBAUTS, STEPHANE; FREITAS-ASTUA, JULIANA; DE MENDONCA, RENATA SANTOS; NUNES, MARIA ANDREIA; MACHADO, MARCOS A.; LIN, YAO-CHENG; LE, PHUONG; ZHANG, ZAICHAO; GRBIC, MIODRAG; WYBOUW, NICKY; BREEUWER, JOHANNES A. J.; VAN LEEUWEN, THOMAS; VAN DE PEER, YVES. Draft Genome Assembly of the False Spider Mite Brevipalpus yothersi. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, v. 8, n. 6 FEB 2019. Web of Science Citations: 2.
GUIMARAES, RONEY FONTES; CAMILLO, LUCIANA RODRIGUES; SOUSA, AURIZANGELA OLIVEIRA; GONCALVES, LUANA PEREIRA; CARDOSO MACEDO, JAMILLY COSTA; SIQUEIRA, GIOVANO SOUSA; MAGALHAES BARBOSA, ANTONIA MARLENE; ALVIM, FATIMA CERQUEIRA; CARDOSO COSTA, MARCIO GILBERTO; PIROVANI, CARLOS PRIMINHO. Genome-wide identification and expression analysis of the molecular chaperone binding protein BiP genes in Citrus. Tree Genetics & Genomes, v. 14, n. 6 DEC 2018. Web of Science Citations: 0.
ARENA, GABRIELLA D.; RAMOS-GONZALEZ, PEDRO L.; ROGERIO, LUANA A.; RIBEIRO-ALVES, MARCELO; CASTEEL, CLARE L.; FREITAS-ASTUA, JULIANA; MACHADO, MARCOS A. Making a Better Home: Modulation of Plant Defensive Response by Brevipalpus Mites. FRONTIERS IN PLANT SCIENCE, v. 9, AUG 15 2018. Web of Science Citations: 4.
SAVIETTO, ABIGAIL; POLAQUINI, CARLOS ROBERTO; KOPACZ, MALGORZATA; SCHEFFERS, DIRK-JAN; MARQUES, BEATRIZ CARVALHO; REGASINI, LUIS OCTAVIO; FERREIRA, HENRIQUE. Antibacterial activity of monoacetylated alkyl gallates against Xanthomonas citri subsp citri. Archives of Microbiology, v. 200, n. 6, p. 929-937, AUG 2018. Web of Science Citations: 6.
LIMA, ROMULO P. M.; CURTOLO, MAIARA; MERFA, MARCUS V.; CRISTOFANI-YALY, MARIANGELA; MACHADO, MARCOS A. QTLs and eQTLs mapping related to citrandarins' resistance to citrus gummosis disease. BMC Genomics, v. 19, JUL 3 2018. Web of Science Citations: 0.
PEREIRA, SUZAM L. S.; MARTINS, CRISTINA P. S.; SOUSA, AURIZANGELA O.; CAMILLO, LUCIANA R.; ARAUJO, CAROLINE P.; ALCANTARA, GRAZIELLE M.; CAMARGO, DANIELLE S.; CIDADE, LUCIANA C.; DE ALMEIDA, ALEX-ALAN F.; COSTA, MARCIO G. C. Genome-wide characterization and expression analysis of citrus NUCLEAR FACTOR-Y (NF-Y) transcription factors identified a novel NF-YA gene involved in drought-stress response and tolerance. PLoS One, v. 13, n. 6 JUN 15 2018. Web of Science Citations: 4.
MARTINS, PAULA M. M.; MERFA, MARCUS V.; TAKITA, MARCO A.; DE SOUZA, ALESSANDRA A. Persistence in Phytopathogenic Bacteria: Do We Know Enough?. FRONTIERS IN MICROBIOLOGY, v. 9, MAY 25 2018. Web of Science Citations: 13.
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, MAR 2018. Web of Science Citations: 4.
CURTOLO, MAIARA; TEIXEIRA SORATTO, TATIANY APARECIDA; GAZAFFI, RODRIGO; TAKITA, MARCO AURELIO; MACHADO, MARCOS ANTONIO; CRISTOFANI-YALY, MARIANGELA. High-density linkage maps for Citrus sunki and Poncirus trifoliata using DArTseq markers. Tree Genetics & Genomes, v. 14, n. 1 FEB 2018. Web of Science Citations: 3.
DALIO, RONALDO J. D.; HERLIHY, JOHN; OLIVEIRA, TIAGO S.; MCDOWELL, JOHN M.; MACHADO, MARCOS. Effector Biology in Focus: A Primer for Computational Prediction and Functional Characterization. MOLECULAR PLANT-MICROBE INTERACTIONS, v. 31, n. 1, p. 22-33, JAN 2018. Web of Science Citations: 5.
FERNANDES DE CAMPOS, KELLY APARECIDA; DE AZEVEDO, FERNANDO ALVES; BASTIANEL, MARINES; CRISTOFANI-YALY, MARIANGELA. RESISTANCE TO ALTERNARIA BROWN SPOT OF NEW CITRUS HYBRIDS. Revista Brasileira de Fruticultura, v. 39, n. 5, p. 1-10, 2017. Web of Science Citations: 0.

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