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Genomic resources of manioc (Manihot esculenta) for the evolutionary study of cultivated varieties and in the search of important genes for breeding

Grant number: 18/00036-9
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): November 01, 2018
Effective date (End): October 31, 2021
Field of knowledge:Agronomical Sciences - Agronomy - Crop Science
Principal Investigator:Anete Pereira de Souza
Grantee:Alessandro Alves Pereira
Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

Manioc (Manihot esculenta Crantz) is the staple food crop that originated in Amazonia that reached the biggest importance in the world, and is currently the eight most cultivated crop. Cultivated manioc (ssp. esculenta) was domesticated from M. esculenta ssp. flabellifolia, and currently two major groups of varieties (sweet and bitter manioc) are cultivated. The objective of this proposal is generating novel genomic resources for manioc through the whole genome re-sequencing of accessions of wild manioc using next-generation sequencing (NGS) technologies. Additionally, we intend to evaluate the molecular variation of genes with signatures of selection among cultivated manioc and the wild ancestor. Using target-sequencing, SNP markers will be identified in coding and non-coding portions of these genes to characterize functional genetic variation. New allelic and structural variants may be detected increasing the knowledge about the species' biology. The functional characterization these genes may evidence which cellular processes may have been affected during the evolution of the crop. Furthermore, whole genome re-sequencing will facilitate molecular marker discovery that may be used in genetic mapping applied to the crop's breeding.

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Scientific publications (12)
(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)
MOURA, Y. A.; ALVES-PEREIRA, A.; DA SILVA, C. C.; SOUZA, L. M.; DE SOUZA, A. P.; KOEHLER, S.. Secondary origin, hybridization and sexual reproduction in a diploid-tetraploid contact zone of the facultatively apomictic orchid Zygopetalum mackayi. Plant Biology, v. 22, n. 5, p. 939-948, . (18/00036-9, 14/04426-5)
OLIVEIRA, S. D. S.; GOIS, I. B.; BLANK, A. F.; ARRIGONI-BLANK, M. F.; ZUCCHI, M., I; PINHEIRO, J. B.; BATISTA, C. E.; ALVES-PEREIRA, A.. Genome-wide diversity in native populations of Croton grewioides Baill., a future crop with fungicidal and antioxidant activity, using SNP markers. Genetic Resources and Crop Evolution, v. 69, n. 5, p. 14-pg., . (18/00036-9)
ALVES-PEREIRA, ALESSANDRO; CLEMENT, CHARLES R.; PICANCO-RODRIGUES, DORIANE; VEASEY, ELIZABETH ANN; DEQUIGIOVANNI, GABRIEL; FERREYRA RAMOS, SANTIAGO LINORIO; PINHEIRO, JOSE BALDIN; DE SOUZA, ANETE PEREIRA; ZUCCHI, MARIA IMACULADA. A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. EVOLUTIONARY APPLICATIONS, v. 13, n. 2, . (12/08307-5, 18/00036-9, 13/08884-5, 13/00003-0)
DIAZ, LEILA M.; ALVES-PEREIRA, ALESSANDRO; ZUCCHI, MARIA, I; MACHADO DE CARVALHO, MARIA A.; GASPAR, MARILIA. Chrysolaena obovata (Less.) Dematt., a species native of Brazilian Cerrado: genetic diversity and structure of natural populations and potential for inulin production. Genetic Resources and Crop Evolution, v. N/A, p. 16-pg., . (18/00036-9)
GERIBELLO PRIOLLI, REGINA HELENA; BAJAY, MIKLOS MAXIMILIANO; ALVES-PEREIRA, ALESSANDRO; LIMA TRIBST, ALLINE ARTIGIANI; MATIAS SILVANO, RENATO AZEVEDO; MACEDO LOPES, PRISCILA FABIANA; BEGOSSI, ALPINA. Genome-wide diversity of the reef fish Epinephelus marginatus (Lowe, 1834): contributions to the conservation of groupers. CAHIERS DE BIOLOGIE MARINE, v. 63, n. 3, p. 14-pg., . (14/16939-7, 18/00036-9)
ISHIZUKA, TAMYLIN KAORI; CORDEIRO, ERICK MAURICIO GOES; ALVES-PEREIRA, ALESSANDRO; BATISTA, CARLOS EDUARDO DE ARAUJO; MURUA, MARIA GABRIELA; PINHEIRO, JOSE BALDIN; SETHI, AMIT; NAGOSHI, RODNEY N.; FORESTI, JOSEMAR; ZUCCHI, MARIA IMACULADA. Population genomics of fall armyworm by genotyping-by-sequencing: Implications for pest management. PLoS One, v. 18, n. 4, p. 16-pg., . (18/00036-9)
BRITO, FABIANY DE ANDRADE; ZUCCHI, MARIA IMACULADA; PINHEIRO, JOSE BALDIN; ARRIGONI-BLANK, MARIA DE FATIMA; DEQUIGIOVANNI, GABRIEL; GRANDO, CAROLINA; BATISTA, CARLOS EDUARDO; ALVES-PEREIRA, ALESSANDRO; BLANK, ARIE FITZGERALD. Low diversity in the native populations of Croton tetradenius Baill. when using SNP markers: a future crop with an insecticidal activity. Genetic Resources and Crop Evolution, . (18/00036-9)
SANTOS, ALESANDRO SOUZA; CAZETTA, ELIANA; FARIA, DEBORAH; LIMA, THAMARA MOURA; GOMES LOPES, MARIA TERESA; CARVALHO, CAROLINA DA SILVA; ALVES-PEREIRA, ALESSANDRO; MORANTE-FILHO, JOSE CARLOS; GAIOTTO, FERNANDA AMATO. Tropical forest loss and geographic location drive the functional genomic diversity of an endangered palm tree. EVOLUTIONARY APPLICATIONS, v. 16, n. 7, p. 17-pg., . (18/00036-9, 14/01029-5)
FRANCISCONI, ANA FLAVIA; CAUZ-SANTOS, LUIZ AUGUSTO; MORALES MARROQUIN, JONATHAN ANDRE; VAN DEN BERG, CASSIO; ALVES-PEREIRA, ALESSANDRO; DE ALENCAR, LUCIANO DELMONDES; PICANCO-RODRIGUES, DORIANE; ZANELLO, CESAR AUGUSTO; COSTA, MARCONES FERREIRA; GOMES LOPES, MARIA TERESA; et al. Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes. PLoS One, v. 17, n. 7, p. 26-pg., . (19/04100-6, 18/00036-9)
ALVES-PEREIRA, ALESSANDRO; NOVELLO, MARIANA; DEQUIGIOVANNI, GABRIEL; PINHEIRO, JOSE BALDIN; BRANCALION, PEDRO H. S.; VEASEY, ELIZABETH ANN; CLEMENT, CHARLES R.; DE SOUZA, ANETE PEREIRA; ZUCCHI, MARIA IMACULADA. Genomic Diversity of Three Brazilian Native Food Crops Based on Double-Digest Restriction Site-Associated DNA Sequencing. TROPICAL PLANT BIOLOGY, v. 12, n. 4, p. 268-281, . (12/08307-5, 18/00036-9, 13/17354-0, 13/08884-5, 13/00003-0)
BRITO, FABIANY DE ANDRADE; ZUCCHI, MARIA IMACULADA; PINHEIRO, JOSE BALDIN; ARRIGONI-BLANK, MARIA DE FATIMA; DEQUIGIOVANNI, GABRIEL; GRANDO, CAROLINA; BATISTA, CARLOS EDUARDO; ALVES-PEREIRA, ALESSANDRO; BLANK, ARIE FITZGERALD. Low diversity in the native populations of Croton tetradenius Baill. when using SNP markers: a future crop with an insecticidal activity. Genetic Resources and Crop Evolution, v. 68, n. 8, p. 3145-3159, . (18/00036-9)
ALVES-PEREIRA, ALESSANDRO; ZUCCHI, MARIA IMACULADA; CLEMENT, CHARLES R.; GOMES VIANA, JOAO PAULO; PINHEIRO, JOSE BALDIN; VEASEY, ELIZABETH ANN; DE SOUZA, ANETE PEREIRA. elective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varietie. SCIENTIFIC REPORTS, v. 12, n. 1, . (12/08307-5, 13/00003-0, 18/00036-9)

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