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Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection

Grant number: 08/52197-4
Support type:Program for Research on Bioenergy (BIOEN) - Thematic Grants
Duration: August 01, 2009 - January 31, 2014
Field of knowledge:Biological Sciences - Genetics
Principal Investigator:Anete Pereira de Souza
Grantee:Anete Pereira de Souza
Home Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Co-Principal Investigators:Antonio Augusto Franco Garcia ; Roland Vencovsky
Associated grant(s):13/27145-9 - SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids, PUB.ART
Associated scholarship(s):12/11109-0 - In silico analysis of transcriptome and genome sequences in sugarcane: SNPs identification, allele specific expression analysis and, development and characterization of microsatellite markers, BP.DD
10/17217-4 - Karyotypic characterization of sugarcane using markers (ribosomal genes and BACs) obtained by molecular methods (FISH), BP.PD
10/06715-3 - Multiple imputation for QTL mapping in outcrossing species, with applications in sugarcane, BP.MS
+ associated scholarships 10/06456-8 - Multiple traits multiple intervals mapping of quantitative trait loci from outbreed crosses, with application in full-sibs sugar-cane, BP.PD
10/03542-0 - Characterization of molecular markers developed from sugarcane genomic sequences, BP.MS
10/00083-5 - Association mapping, linkage disequilibrium and population structure in sugarcane, BP.PD
09/14411-7 - Molecular breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection, BP.TT - associated scholarships

Abstract

Breeding programs have been successfully over the years in the generation of new improved sugarcane varieties (Saccharum spp.), which are more productive and resistant to pests, diseases and abiotic stresses. These varieties are of central importance for sugar and ethanol production. However, breeding process takes about 10 to 15 years to release new varieties, mainly because of the difficulty to correctly identify good genotypes on the fields, since there is strong influence of environmental conditions. This process could be speed up with the development and the use of genetic markers, which are genomic regions that could be observed (evaluated) on each individual. By studying the segregation of those markers, it is possible to estimate the genetic distances between them, resulting in the so called genetic maps. After, linkage studies are performed in order to associate genotype (based on molecular traits) and phenotypes (traits that are evaluated on field conditions, such as sugar and fiber content). If the genomic regions are strongly linked with genes that control agronomic traits, they could be used for help the breeding process. Since most of the traits of agronomic and economic importance are quantitative (controlled by many loci), the major goal is to identify genomic regions associated with such traits, named quantitative trait loci (QTL). The use of markers in genetic studies, including QTL mapping, has allowed important progress in the knowledge of the genomic structure, genetics and evolution of sugarcane. In this project, new markers will be developed and used for QTL mapping. A new class of very useful markers called genic molecular markers (GMMs) will be developed and used. This kind of marker (EST-SSRs and SNPs), also named Functional Markers, will be obtained from expressed sequences from the SUCEST data bank, and sequencing genes from BAC clones. BAC libraries will be constructed using DNA from parental sugarcane varieties employed in the biparental crosses used for genetic mapping. The GMMs developed will be used for: 1) QTL mapping in biparental crosses; 2) association studies using sugarcane genotypes important in breeding programs, using a panel of about 150 genotypes important for Brazilian breeding programs. Once the genomic regions are found, strategies for marker assisted selection will be developed. (AU)

Articles published in Agência FAPESP about the research grant
Research clears the way for genetic sugarcane studies 

Scientific publications (31)
(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)
SFORCA, DANILO AUGUSTO; VAUTRIN, SONIA; CARDOSO-SILVA, CLAUDIO BENICIO; MANCINI, MELINA CRISTINA; ROMERO-DA CRUZ, MARIA VICTORIA; PEREIRA, GUILHERME DA SILVA; CONTE, MONICA; BELLEC, ARNAUD; DAHMER, NAIR; FOURMENT, JOELLE; RODDE, NATHALIE; VAN SLUYS, MARIE-ANNE; VICENTINI, RENATO; FRANCO GARCIA, ANTONIO AUGUSTO; FORNI-MARTINS, ELIANA REGINA; CARNEIRO, MONALISA SAMPAIO; HOFFMANN, HERMANN PAULO; PINTO, LUCIANA ROSSINI; DE ANDRADE LANDELL, MARCOS GUIMARAES; VINCENTZ, MICHEL; BERGES, HELENE; DE SOUZA, ANETE PEREIRA. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. FRONTIERS IN PLANT SCIENCE, v. 10, MAY 7 2019. Web of Science Citations: 0.
ULBRICHT FERREIRA, REBECCA CAROLINE; DE CASTRO LARA, LETICIA APARECIDA; CHIARI, LUCIMARA; LIMA BARRIOS, SANZIO CARVALHO; DO VALLE, CACILDA BORGES; VALERIO, JOSE RAUL; VILELA TORRES, FABRICIA ZIMERMANN; FRANCO GARCIA, ANTONIO AUGUSTO; DE SOUZA, ANETE PEREIRA. Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance. FRONTIERS IN PLANT SCIENCE, v. 10, FEB 21 2019. Web of Science Citations: 0.
PEREIRA, GUILHERME S.; GARCIA, ANTONIO AUGUSTO F.; MARGARIDO, GABRIEL R. A. A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids. BMC Bioinformatics, v. 19, NOV 1 2018. Web of Science Citations: 1.
DURIGAN, MAURICIO; CARDOSO-SILVA, CLAUDIO BENICIO; CIAMPI-GUILLARDI, MAISA; TOLEDO-SILVA, GUILHERME; MORI, GUSTAVO M.; FRANCO, REGINA M. B.; SOUZA, ANETE P. Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis. PLoS Neglected Tropical Diseases, v. 12, n. 11 NOV 2018. Web of Science Citations: 0.
ALVES, FABIO M.; SARTORI, ANGELA L. B.; ZUCCHI, MARIA I.; AZEVEDO-TOZZI, ANA M. G.; TAMBARUSSI, EVANDRO V.; ALVES-PEREIRA, ALESSANDRO; DE SOUZA, ANETE P. Genetic structure of two Prosopis species in Chaco areas: A lack of allelic diversity diagnosis and insights into the allelic conservation of the affected species. ECOLOGY AND EVOLUTION, v. 8, n. 13, p. 6558-6574, JUL 2018. Web of Science Citations: 1.
MANCINI, MELINA C.; CARDOSO-SILVA, CLAUDIO B.; SFORCA, DANILO A.; DE SOUZA, ANETE PEREIRA. ``Targeted Sequencing by Gene Synteny,{''} a New Strategy for Polyploid Species: Sequencing and Physical Structure of a Complex Sugarcane Region. FRONTIERS IN PLANT SCIENCE, v. 9, MAR 28 2018. Web of Science Citations: 0.
ALVES, FABIO M.; SARTORI, ANGELA L. B.; ZUCCHI, MARIA I.; AZEVEDO-TOZZI, ANA M. G.; TAMBARUSSI, EVANDRO V.; DE SOUZA, ANETE P. A high level of outcrossing in the vulnerable species Prosopis rubriflora in a Chaco remnant. Australian Journal of Botany, v. 66, n. 4, p. 360-368, 2018. Web of Science Citations: 0.
FONSECA, EMANUELLA MARIA BARRETO; SCORSATO, VALERIA; DOS SANTOS, MARCELO LEITE; TOMAZINI, ATILIO; TADA, SUSELY FERRAZ SIQUEIRA; DOS SANTOS, CLELTON APARECIDO; DE TOLEDO, MARCELO AUGUSTO SZYMANSKI; DE SOUZA, ANETE PEREIRA; POLIKARPOV, IGOR; APARICIO, RICARDO. Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 73, n. 4, p. 222-227, APR 1 2017. Web of Science Citations: 1.
DURIGAN, MAURICIO; CIAMPI-GUILLARDI, MAISA; RODRIGUES, RICARDO C. A.; GREINERT-GOULART, JULIANE A.; SIQUEIRA-CASTRO, ISABEL C. V.; LEAL, DIEGO A. G.; YAMASHIRO, SANDRA; BONATTI, TAIS R.; ZUCCHI, MARIA I.; FRANCO, REGINA M. B.; DE SOUZA, ANETE P. Population genetic analysis of Giardia duodenalis: genetic diversity and haplotype sharing between clinical and environmental sources. MICROBIOLOGYOPEN, v. 6, n. 2 APR 2017. Web of Science Citations: 5.
ALMEIDA BALSALOBRE, THIAGO WILLIAN; PEREIRA, GUILHERME DA SILVA; ALVES MARGARIDO, GABRIEL RODRIGUES; GAZAFFI, RODRIGO; BARRETO, FERNANDA ZATTI; ANONI, CARINA OLIVEIRA; CARDOSO-SILVA, CLAUDIO BENICIO; COSTA, ESTELA ARAUJO; MANCINI, MELINA CRISTINA; HOFFMANN, HERMANN PAULO; DE SOUZA, ANETE PEREIRA; FRANCO GARCIA, ANTONIO AUGUSTO; CARNEIRO, MONALISA SAMPAIO. GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane. BMC Genomics, v. 18, JAN 11 2017. Web of Science Citations: 16.
BRITO, VINICIUS L. G.; MORI, GUSTAVO M.; VIGNA, BIANCA B. Z.; AZEVEDO-SILVA, MARIANNE; SOUZA, ANETE P.; SAZIMA, MARLIES. Genetic structure and diversity of populations of polyploid Tibouchina pulchra Cogn. (Melastomataceae) under different environmental conditions in extremes of an elevational gradient. Tree Genetics & Genomes, v. 12, n. 6 DEC 2016. Web of Science Citations: 3.
ZANOTTO VIGNA, BIANCA BACCILI; DE OLIVEIRA, FERNANDA ANCELMO; DE TOLEDO-SILVA, GUILHERME; DA SILVA, CARLA CRISTINA; DO VALLE, CACILDA BORGES; DE SOUZA, ANETE PEREIRA. Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. BMC Genomics, v. 17, NOV 11 2016. Web of Science Citations: 2.
BALSALOBRE, THIAGO W. A.; MANCINI, MELINA C.; PEREIRA, GUILHERME DA S.; ANONI, CARINA O.; BARRETO, FERNANDA Z.; HOFFMANN, HERMANN P.; DE SOUZA, ANETE P.; GARCIA, ANTONIO A. F.; CARNEIRO, MONALISA S. Mixed Modeling of Yield Components and Brown Rust Resistance in Sugarcane Families. AGRONOMY JOURNAL, v. 108, n. 5, p. 1824-1837, SEP-OCT 2016. Web of Science Citations: 5.
COSTA, E. A.; ANONI, C. O.; MANCINI, M. C.; SANTOS, F. R. C.; MARCONI, T. G.; GAZAFFI, R.; PASTINA, M. M.; PERECIN, D.; MOLLINARI, M.; XAVIER, M. A.; PINTO, L. R.; SOUZA, A. P.; GARCIA, A. A. F. QTL mapping including codominant SNP markers with ploidy level information in a sugarcane progeny. EUPHYTICA, v. 211, n. 1, p. 1-16, SEP 2016. Web of Science Citations: 6.
SERAPHIM, N.; BARRETO, M. A.; ALMEIDA, G. S. S.; ESPERANCO, A. P.; MONTEIRO, R. F.; SOUZA, A. P.; FREITAS, A. V. L.; SILVA-BRANDAO, K. L. Genetic diversity of Parides ascanius (Lepidoptera: Papilionidae: Troidini): implications for the conservation of Brazil's most iconic endangered invertebrate species. CONSERVATION GENETICS, v. 17, n. 3, p. 533-546, JUN 2016. Web of Science Citations: 3.
VIGNA, BIANCA B. Z.; SANTOS, JEAN C. S.; JUNGMANN, LETICIA; DO VALLE, CACILDA B.; MOLLINARI, MARCELO; PASTINA, MARIA M.; PAGLIARINI, MARIA SUELY; GARCIA, ANTONIO A. F.; SOUZA, ANETE P. Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping. PLoS One, v. 11, n. 4 APR 22 2016. Web of Science Citations: 6.
SANTOS, CLELTON A.; ZANPHORLIN, LET-CIA M.; CRUCELLO, ALINE; TONOLI, CELISA C. C.; RULLER, ROBERTO; HORTA, MARIA A. C.; MURAKAMI, MARIO T.; DE SOUZA, ANETE PEREIRA. Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 beta-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions. BIOTECHNOLOGY FOR BIOFUELS, v. 9, MAR 22 2016. Web of Science Citations: 9.
RONQUE, MARIANE U. V.; AZEVEDO-SILVA, MARIANNE; MORI, GUSTAVO M.; SOUZA, ANETE P.; OLIVEIRA, PAULO S. Three ways to distinguish species: using behavioural, ecological, and molecular data to tell apart two closely related ants, Camponotus renggeri and Camponotus rufipes (Hymenoptera: Formicidae). Zoological Journal of the Linnean Society, v. 176, n. 1, p. 170-181, JAN 2016. Web of Science Citations: 11.
SANTOS, ELISA S. L.; CERQUEIRA-SILVA, CARLOS BERNARD M.; MORI, GUSTAVO M.; AHNERT, DARIO; MELLO, DURVAL L. N.; PIRES, JOSE LUIS; CORREA, RONAN X.; DE SOUZA, ANETE P. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil. PLoS One, v. 10, n. 12 DEC 16 2015. Web of Science Citations: 6.
BARRETO, M. A.; SANTOS, J. C. S.; CORREA, R. X.; LUZ, E. D. M. N.; MARELLI, J.; SOUZA, A. P. Detection of genetic resistance to cocoa black pod disease caused by three Phytophthora species. EUPHYTICA, v. 206, n. 3, p. 677-687, DEC 2015. Web of Science Citations: 4.
MARGARIDO, G. R. A.; PASTINA, M. M.; SOUZA, A. P.; GARCIA, A. A. F. Multi-trait multi-environment quantitative trait loci mapping for a sugarcane commercial cross provides insights on the inheritance of important traits. MOLECULAR BREEDING, v. 35, n. 8 AUG 2015. Web of Science Citations: 3.
AZEVEDO-SILVA, MARIANNE; MORI, GUSTAVO M.; SOUZA, ANETE P.; OLIVEIRA, PAULO S. Microsatellites for two Neotropical dominant ant species, Camponotus renggeri and C-rufipes (Hymenoptera: Formicidae). CONSERVATION GENETICS RESOURCES, v. 7, n. 2, p. 459-462, JUN 2015. Web of Science Citations: 1.
CERQUEIRA-SILVA, C. B. M.; JESUS, O. N.; OLIVEIRA, E. J.; SANTOS, E. S. L.; SOUZA, A. P. Characterization and selection of passion fruit (yellow and purple) accessions based on molecular markers and disease reactions for use in breeding programs. EUPHYTICA, v. 202, n. 3, p. 345-359, APR 2015. Web of Science Citations: 9.
DURIGAN, MAURICIO; ABREU, ALUANA GONCALVES; ZUCCHI, MARIA IMACULADA; BUENO FRANCO, REGINA MAURA; DE SOUZA, ANETE PEREIRA. Genetic Diversity of Giardia duodenalis: Multilocus Genotyping Reveals Zoonotic Potential between Clinical and Environmental Sources in a Metropolitan Region of Brazil. PLoS One, v. 9, n. 12 DEC 23 2014. Web of Science Citations: 21.
CERQUEIRA-SILVA, CARLOS BERNARD M.; SANTOS, ELISA S. L.; JESUS, ONILDO N.; VIEIRA, JOAO G. P.; MORI, GUSTAVO M.; CORREA, RONAN X.; SOUZA, ANETE P. Molecular Genetic Variability of Commercial and Wild Accessions of Passion Fruit (Passiflora spp.) Targeting ex Situ Conservation and Breeding. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 15, n. 12, p. 22933-22959, DEC 2014. Web of Science Citations: 3.
CERQUEIRA-SILVA, CARLOS BERNARD M.; JESUS, ONILDO N.; SANTOS, ELISA S. L.; CORREA, RONAN X.; SOUZA, ANETE P. Genetic Breeding and Diversity of the Genus Passiflora: Progress and Perspectives in Molecular and Genetic Studies. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 15, n. 8, p. 14122-14152, AUG 2014. Web of Science Citations: 17.
DE SETTA, NATHALIA; MONTEIRO-VITORELLO, CLAUDIA BARROS; METCALFE, CUSHLA JANE; QUEIROGA CRUZ, GUILHERME MARCELO; DEL BEM, LUIZ EDUARDO; VICENTINI, RENATO; SILVEIRA NOGUEIRA, FABIO TEBALDI; CAMPOS, ROBERTA ALVARES; NUNES, SIDENY LIMA; GASPERAZZO TURRINI, PAULA CRISTINA; VIEIRA, ANDREIA PRATA; OCHOA CRUZ, EDGAR ANDRES; SILVEIRA CORREA, TATIANA CAROLINE; HOTTA, CARLOS TAKESHI; VARANI, ALESSANDRO DE MELLO; VAUTRIN, SONIA; DA TRINDADE, ADILSON SILVA; VILELA, MARIANE DE MENDONCA; LEMBKE, CAROLINA GIMILIANI; SATO, PALOMA MIEKO; DE ANDRADE, RODRIGO FANDINO; NISHIYAMA, JR., MILTON YUTAKA; CARDOSO-SILVA, CLAUDIO BENICIO; SCORTECCI, KATIA CASTANHO; FRANCO GARCIA, ANTONIO AUGUSTO; CARNEIRO, MONALISA SAMPAIO; KIM, CHANGSOO; PATERSON, ANDREW H.; BERGES, HELENE; D'HONT, ANGELIQUE; DE SOUZA, ANETE PEREIRA; SOUZA, GLAUCIA MENDES; VINCENTZ, MICHEL; KITAJIMA, JOAO PAULO; VAN SLUYS, MARIE-ANNE. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics, v. 15, JUN 30 2014. Web of Science Citations: 47.
CARDOSO-SILVA, CLAUDIO BENICIO; COSTA, ESTELA ARAUJO; MANCINI, MELINA CRISTINA; ALMEIDA BALSALOBRE, THIAGO WILLIAN; COSTA CANESIN, LUCAS EDUARDO; PINTO, LUCIANA ROSSINI; CARNEIRO, MONALISA SAMPAIO; FRANCO GARCIA, ANTONIO AUGUSTO; DE SOUZA, ANETE PEREIRA; VICENTINI, RENATO. De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties. PLoS One, v. 9, n. 2 FEB 11 2014. Web of Science Citations: 37.
GARCIA, ANTONIO A. F.; MOLLINARI, MARCELO; MARCONI, THIAGO G.; SERANG, OLIVER R.; SILVA, RENATO R.; VIEIRA, MARIA L. C.; VICENTINI, RENATO; COSTA, ESTELA A.; MANCINI, MELINA C.; GARCIA, MELISSA O. S.; PASTINA, MARIA M.; GAZAFFI, RODRIGO; MARTINS, ELIANA R. F.; DAHMER, NAIR; SFORCA, DANILO A.; SILVA, CLAUDIO B. C.; BUNDOCK, PETER; HENRY, ROBERT J.; SOUZA, GLAUCIA M.; VAN SLUYS, MARIE-ANNE; LANDELL, MARCOS G. A.; CARNEIRO, MONALISA S.; VINCENTZ, MICHEL A. G.; PINTO, LUCIANA R.; VENCOVSKY, ROLAND; SOUZA, ANETE P. SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids. SCIENTIFIC REPORTS, v. 3, DEC 2 2013. Web of Science Citations: 38.
PASTINA, M. M.; MALOSETTI, M.; GAZAFFI, R.; MOLLINARI, M.; MARGARIDO, G. R. A.; OLIVEIRA, K. M.; PINTO, L. R.; SOUZA, A. P.; VAN EEUWIJK, F. A.; GARCIA, A. A. F. A mixed model QTL analysis for sugarcane multiple-harvest-location trial data. THEORETICAL AND APPLIED GENETICS, v. 124, n. 5, p. 835-849, MAR 2012. Web of Science Citations: 36.
SERANG, OLIVER; MOLLINARI, MARCELO; FRANCO GARCIA, ANTONIO AUGUSTO. Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids. PLoS One, v. 7, n. 2 FEB 17 2012. Web of Science Citations: 37.

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