Biotechnological and genomic strategies for quality, productivity and sustainable management of citrus, coffee and sugar cane in the State of São Paulo

• Grant number: 20/07045-3
• Support Opportunities: Research Grants - Problem-Oriented Research Centers in São Paulo
• Start date: October 01, 2021
• End date: September 30, 2026
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Mariângela Cristofani-Yaly
• Grantee: Mariângela Cristofani-Yaly
• Host Institution: Instituto Agronômico (IAC). Agência Paulista de Tecnologia dos Agronegócios (APTA). Secretaria de Agricultura e Abastecimento (São Paulo - Estado). Campinas , SP, Brazil
• Pesquisadores principais: Alessandra Alves de Souza ; Marinês Bastianel ; Oliveiro Guerreiro Filho ; Silvana Aparecida Creste Dias de Souza
• Associated researchers: Alessandra Ferreira Ribas ; Celso Luis Rodrigues Vegro ; Claudia Barros Monteiro Vitorello ; Dirceu de Mattos Junior ; Evandro Henrique Schinor ; Fernando Alves de Azevedo ; Francisco de Assis Alves Mourão Filho ; Graciela da Rocha Sobierajski ; Helvecio Della Coletta Filho ; Hugo Bruno Correa Molinari ; Ivan de Godoy Maia ; Jorge Maurício Costa Mondego ; Julieta Andrea Silva de Almeida ; Júlio César Mistro ; Katia Nachiluk ; Lilian Padilha ; Luiz Filipe Protasio Pereira ; Marco Aurélio Takita ; Marcos Antonio Machado ; Marcos Guimarães de Andrade Landell ; Maria Helena de Souza Goldman ; Michael dos Santos Brito ; Mirian Perez Maluf ; Patrícia Cia ; Paulo Mazzafera ; Raquel Luciana Boscariol Camargo ; Roberto Fritsche Neto ; Rodrigo Gazaffi ; Terezinha de Jesus Garcia Salva ; Tiago Campos Pereira ; Valdenice Moreira Novelli
• Associated scholarship(s): 25/07338-4 - Assessments of development and disease tolerance in genetically modified plants maintained in field and greenhouse conditions., BP.TT; 25/02473-0 - Callogenesis from leaf explants of Coffea arabica L. for application of gene editing technology, BP.TT; 24/19703-6 - Genetic transformation of citrus mediated by Agrobacterium rhizogenes, BP.TT; + associated scholarships 24/19329-7 - CRISPR DNA-free gene editing through protoplasts for the development of new HLB-resistant or tolerant citrus plants, BP.TT; 24/17330-8 - Production of sugarcane and energy cane in scale, BP.TT; 24/17963-0 - Obtaining commercial HLB-tolerant sweet orange varieties via CRISPR genome editing., BP.PD; 24/18198-6 - Prospecting for Candidate Genes related to the response to HLB, BP.TT; 24/16590-6 - Production of sugarcane and energy cane embryogenic calli for genetic transformation, BP.TT; 24/13403-0 - Fenotyping and obtention of genetically modified plants: A Cisgenic approach to control the HLB, BP.PD; 24/00646-2 - Ciência a MesaCast - application of plant breeding biotechnology of citrus, coffee and sugar cane., BP.JC; 24/00640-4 - Ciência a MesaCast - application of plant breeding biotechnology of citrus, coffee and sugar cane., BP.JC; 24/00742-1 - Production of transgenic sugarcane and energy cane plant in scale, BP.TT; 23/06114-0 - Antisense oligonucleotide and CRISPR/CAS strategy for caffeine reduction in Coffea arabica, BP.PD; 23/10997-4 - Production of embryogenic callus of sugarcane and energy cane for genetic transformation, BP.TT; 23/04788-3 - Transcriptional characterization of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene in sugarcane and energy cane genotypes in response to infection by the smut fungus (Sporisorium scitamineum), BP.MS; 22/12483-5 - CRISPR/Cas9 system in Sieve Element Occlusion c (SEOc) gene editing, aiming at obtaining citrus plants tolerant to Huanglongbing (HLB), BP.MS; 22/12720-7 - Large scale production of transgenic sugarcane and energy cane, BP.TT; 22/10505-1 - Genetic Engineering and Synthetic Biology approaches applied to the development of novel resistant or tolerant sweet orange (Citrus sinensis) varieties against Huanglongbing (HLB), BP.PD; 22/02147-8 - Production of embryogenic calli from sugarcane and energy cane for genetic transformation, BP.TT; 22/02177-4 - Production of transgenic sugarcane and energy cane plants in scale, BP.TT; 22/02228-8 - Production of embryogenic calli for genetic transformation of rice and energy cane, BP.TT; 21/10123-9 - Physiology and specialized metabolism of Citrandarins under different cultural management, BP.DR; 21/13478-2 - Genome editing of grass species via CRISPR/Cas9, BP.DR; 21/03466-7 - Editing Citrus sinensis genes to attenuate the accumulation of callose associated with HLB Huanglongbing (HLB) symptoms, BP.DR; 21/03989-0 - Homologous recombination mediated by the CRISPR/Cas system and insertion of a resistance gene in the development of Huanglongbing-resistant sweet orange varieties, BP.PD - associated scholarships

Abstract

NPOP-IAC, headquartered at IAC in Campinas, has the main strategic objective of expanding the scientific and technological aiming to solve well-defined problems in three different and economically important cultures of Brazilian agribusiness, citrus, sugar cane and coffee. The adoption of the genomic and biotechnology themes is justified by the current state of the art of breeding programs under development at Agronomic Institute (IAC) regarding the three cultures with a strong insertion of biotechnology. Supported by projects with agencies (State and Federal) and / or partnerships with companies, these programs, in addition to a significant genetic base, represented by the germplasms bank, accumulated databases of genomes, transcriptomes, genetically transformed genotypes and genetic-molecular knowledge of biotic and abiotic interactions processes, as well as biochemical processes which are important in the expression of phenotypic and agronomic characteristics. By focusing on the three most important agribusiness chains in São Paulo, the NPOP-IAC is aligned with the need to seek solutions that can have a high impact on the respective sector and the State economy. Together the three chains have gross production values in the order of 55 (citrus), 97 (coffee) and 255 (cane) billions of Reais (R$), with the State of São Paulo representing 52, 12 and 48% of national production, respectively. Despite the social and economic importance of these production chains, they have scientific and technological challenges that need to be addressed. Such challenges limit its maintenance, reduce competitiveness, increase costs and impact the environment with its current solutions. In each of the three cultures covered in the NPOP-IAC, specific problems are addressed with proposed solutions as bellow describe. In citrus, the focus will be the disease known as huanglongbing (HLB), considered the most devastating citrus disease in the world. The proposal will focus on three in progress lines of action: I. evaluation of genetically modified (GM) citrus in field trials; II. gene editing by CRISPR to reduce the hypersensitivity (HR) response of plants infected by the HLB bacteria and genotyping; and III. to use of rootstocks tolerant to HLB and that induce smaller size of the canopy variety aiming improve disease management and mechanic harvest. By leveraging genetic information from the coffee breeding program at the IAC, NPOP-IAC will focus its efforts on the generation of commercial low-caffeine arabica coffee genotypes. Such genotypes are being produced by traditional breeding but will also be obtained by silencing genes by CRISPR from the previously selected caffeine synthesis pathway. There is worldwide demand for specialty coffees, especially with a low caffeine content. (AU)

Scientific publications

(11)

(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)

CONTILIANI, DANYEL FERNANDES; SRETENOVIC, SIMON; DAILEY, MICAH; ZHOU, MAN; CHENG, YANHAO; CRESTE, SILVANA; XIAO, SHUNYUAN; QI, YIPING. Harnessing novel cytidine deaminases from the animal kingdom for robust multiplexed base editing in rice. Plant Biotechnology Journal, v. N/A, p. 11-pg., 2025-02-14. (20/07045-3, 21/13478-2, 22/11738-0)

BASTIANEL, MARINES; MARTINELLI, RODRIGO; DEVITE, FERNANDO TREVIZAN; CRISTOFANI-YALY, MARIANGELA; FERREIRA, RODRIGO DO VALE; STUCHI, EDUARDO SANCHES; DE AZEVEDO, FERNANDO ALVES. Reaction of Mandarins to the Alternaria Brown Spot and Huanglongbing: Identification of Potential Varieties for These Diseases to Be Managed in the Field. HORTICULTURAE, v. 9, n. 6, p. 12-pg., 2023-06-01. (17/24564-1, 20/07045-3, 14/50880-0)

PRADO, GUILHERME SOUZA; ROCHA, DHIOVANNA CORREIA; DOS SANTOS, LUCAS NASCIMENTO; CONTILIANI, DANYEL FERNANDES; NOBILE, PAULA MACEDO; MARTINATI-SCHENK, JULIANA CAMARGO; PADILHA, LILIAN; MALUF, MIRIAN PEREZ; LUBINI, GREICE; PEREIRA, TIAGO CAMPOS; et al. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE, v. 14, p. 27-pg., 2024-01-08. (20/07045-3, 21/13478-2, 22/10505-1, 22/11738-0)

DE SOUZA, ANA JULIA BORIM; CRISTOFANI-YALY, MARIANGELA; DA CONCEICAO, PATRICIA MARLUCI; DEVITE, FERNANDO TREVIZAN; BASTIANEL, MARINES; ROMERO, PAULO VITOR SANCHES; PADILHA, PEDRO HENRIQUE BARRIO; DE AZEVEDO, FERNANDO ALVES. Physiological and productivity responses of Tahiti acid lime grafted onto dwarfing rootstocks under different planting and mulching practices. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS, v. 9, p. 16-pg., 2025-02-05. (20/07045-3)

CAVICHIOLI, THAIS MAGNI; CURTOLO, MAIARA; CRISTOFANI-YALY, MARIANGELA; RODRIGUES, JOSIANE; DELLA COLETTA-FILHO, HELVECIO. Temporal Analysis of Candidatus Liberibacter asiaticus in Citrandarin Genotypes Indicates Unstable Infection. AGRONOMY-BASEL, v. 12, n. 10, p. 11-pg., 2022-10-01. (20/07045-3, 21/03989-0, 19/06412-5)

DEVITE, FERNANDO TREVIZAN; BASTIANEL, MARINES; CRISTOFANI-YALY, MARIANGELA; DE SOUZA, ANA JULIA BORIM; GADANHOTO, BIANA PELISSARI; ARANTES, ANA CAROLINA COSTA; DE AZEVEDO, FERNANDO ALVES. Performance of Valencia sweet orange grafted onto dwarfing citrandarins. FRONTIERS IN PLANT SCIENCE, v. 16, p. 15-pg., 2025-03-06. (20/07045-3)

PICCHI, SIMONE C.; REBELATTO, DANIELE; MARTINS, PAULA M. M.; BLUMER, SILVIA; MESQUITA, GEISA L.; HIPPLER, FRANZ W. R.; MATTOS JR, DIRCEU; BOARETTO, RODRIGO M.; MACHADO, MARCO A.; TAKITA, MARCO A.; et al. N-acetylcysteine absorption and its potential dual effect improve fitness and fruit yield in Xylella fastidiosa infected plants. Pest Management Science, v. 80, n. 9, p. 11-pg., 2024-05-02. (15/22144-0, 17/02733-6, 20/07045-3, 13/10957-0, 19/11566-1, 14/50880-0)

MARTINS, PAULA MARIA MOREIRA; GRANATO, LAIS MOREIRA; MORGAN, TULIO; NALIN, JULIA LOPES; TAKITA, MARCO AURELIO; ALFENAS-ZERBINI, POLIANE; DE SOUZA, ALESSANDRA ALVES. Analysis of CRISPR-Cas loci distribution in Xanthomonas citri and its possible control by the quorum sensing system. FEMS Microbiology Letters, v. 371, p. 10-pg., 2024-02-14. (20/07045-3, 16/01273-9, 13/10957-0, 14/50880-0, 19/01901-8)

CRISTOFANI-YALY, MARIANGELA; DEZOTTI, ANA LUCIA; CAVICHIOLI, THAIS MAGNI; ROVERSSI, FERNANDA; NOVELLI, VALDENICE MOREIRA; BASTIANEL, MARINES. Genetic Characterization and Fruit Quality Analysis of New Mandarin Hybrids. AGRONOMY-BASEL, v. 14, n. 11, p. 13-pg., 2024-11-01. (14/50880-0, 20/07045-3, 17/24564-1, 15/23839-1)

CAVICHIOLI, THAIS MAGNI; CURTOLO, MAIARA; CRISTOFANI-YALY, MARIANGELA; RODRIGUES, JOSIANE; COLETTA-FILHO, HELVECIO DELLA. Effects of 'Candidatus' Liberibacter Asiaticus on the Root System of Poncirus trifoliata Hybrids as a Rootstock for 'Valencia' Scion. HORTICULTURAE, v. 10, n. 9, p. 7-pg., 2024-09-01. (20/07045-3, 19/06412-5, 21/03989-0)

DEVITE, FERNANDO TREVIZAN; DE AZEVEDO, FERNANDO ALVES; BASTIANEL, MARINES; SCHINOR, EVANDRO HENRIQUE; DA CONCEICAO, PATRICIA MARLUCI. Mandarin Essential Oils as an Alternative Method of Controlling the Fungus Alternaria alternata (Fr.: Fr.) Keissler. HORTICULTURAE, v. 9, n. 6, p. 13-pg., 2023-06-01. (17/24564-1, 20/07045-3)