Signaling and regulatory network studies associated to the energy cane

• Grant number: 14/50921-8
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• Start date: September 01, 2016
• End date: November 30, 2022
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Glaucia Mendes Souza
• Grantee: Glaucia Mendes Souza
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• City of the host institution: São Paulo
• Principal investigators: Helaine Carrer
• Associated scholarship(s): 22/00444-5 - Evaluation of GLA02 transgene expression in greenhouse drought experiments, BP.TT; 21/12841-6 - Transgene expression confirmation by the detection of the reporter protein YFP, BP.TT; 21/09063-1 - Development of bioinformatics tools for data integration in the SUCEST-FUN platform, BP.TT; + associated scholarships 20/10876-4 - Bioinformatics tools for data integration on the SUCEST-FUN platform, BP.TT; 20/07851-0 - Gene expression validation of genes related to the development and accumulation of biomass in sugarcane, BP.IC; 19/17104-0 - Cell wall components of contrasting sugarcane progenies for biomass production, BP.IC; 19/05397-2 - Development and management of bioinformatics tools for the SUCEST-FUN platform, BP.TT; 18/17561-9 - Regulatory elements of carbon metabolism in sugar cane, BP.DD; 18/13520-6 - Morphological and agro-technological analyzes of progenies of Saccharum spp, BP.TT; 18/09867-0 - Obtaining the transgenic energy cane, BP.PD; 17/02270-6 - Evaluation of contrasting progenies transcriptome for the accumulation of biomass and identification of regulation networks, BP.PD; 17/02851-9 - Evaluation of biochemical and physiological parameters in contrasting energy cane progenies, BP.IC; 16/21008-8 - Study of sugarcane metabolites along its development in the field, BP.DD - associated scholarships

Abstract

We intend to contribute by analysing physiology, regulatory elements, transcriptome and metabolome of commercial varieties and in crosses with ancestral species in field and greenhouse experiments. The most comprehensive study of sugarcane regulatory networks will be done with the use of Chip-Seq and RNAseq techniques. It will be possible to identify possible regulatory and promoter regions in the sugarcane reference genome sequenced and partially assembled by our group and collaborators. Through the use of Systems Biology and Synthetic Biology approaches, we will define the main targets or networks of genes for the improvement of sugarcane to increase its productivity, to change sucrose fiber and lignin content, and thus pave the way for the development of the Energy-Cane. The large volume of data generated will be stored in the SUCEST- FUN database (http://sucest-fun.org) where it is possible to evaluate and interrogate the data focusing on different aspects. (AU)

Scientific publications

(9)

(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)

ZHANG, JISEN; ZHANG, XINGTAN; TANG, HAIBAO; ZHANG, QING; HUA, XIUTING; MA, XIAOKAI; ZHU, FAN; JONES, TYLER; ZHU, XINGUANG; BOWERS, JOHN; et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.. Nature Genetics, v. 50, n. 11, p. 1565+, NOV 2018. (14/50921-8, 12/51062-3, 08/52146-0)

OLIVEIRA, MAURO DE MEDEIROS; BONADIO, IGOR; DE MELO, ALICIA LIE; SOUZA, GLAUCIA MENDES; DURHAM, ALAN MITCHELL. TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. BRIEFINGS IN BIOINFORMATICS, v. 22, n. 6, NOV 2021. (11/50761-2, 14/50921-8)

DINIZ, AUGUSTO L.; FERREIRA, SAVIO S.; TEN-CATEN, FELIPE; MARGARIDO, GABRIEL R. A.; DOS SANTOS, JOAO M.; BARBOSA, GERALDO V. DE S.; CARNEIRO, MONALISA S.; SOUZA, GLAUCIA M.. Genomic resources for energy cane breeding in the post genomics era. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, v. 17, p. 1404-1414, 2019. (14/50921-8, 16/06917-1, 15/22993-7, 17/02270-6)

FEDERICO, MARIA L.; DINIZ, AUGUSTO L.; SOUZA, GLAUCIA M.; SNOWDON, ROD; ERAZZU, LUIS. Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding. PLANT BREEDING, v. 141, n. 3, p. 10-pg., 2022-04-01. (14/50921-8, 17/02270-6)

NACHTIGALL, PEDRO G.; KASHIWABARA, ANDRE Y.; DURHAM, ALAN M.. CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts. BRIEFINGS IN BIOINFORMATICS, v. 22, n. 3, MAY 2021. (14/50921-8)

SOUZA, GLAUCIA MENDES; VAN SLUYS, MARIE-ANNE; LEMBKE, CAROLINA GIMILIANI; LEE, HAYAN; MARGARIDO, GABRIEL RODRIGUES ALVES; HOTTA, CARLOS TAKESHI; GAIARSA, JONAS WEISSMANN; DINIZ, AUGUSTO LIMA; OLIVEIRA, MAURO DE MEDEIROS; FERREIRA, SAVIO DE SIQUEIRA; et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. GIGASCIENCE, v. 8, n. 12, DEC 2019. (13/07467-1, 08/52074-0, 14/50921-8, 15/22993-7, 12/51062-3, 17/02270-6, 11/50761-2, 16/17545-8, 16/06917-1, 13/23048-9, 08/52146-0)

DINIZ, AUGUSTO LIMA; RODRIGUES DA SILVA, DANIELLE IZILDA; LEMBKE, CAROLINA GIMILIANI; LAMAS COSTA, MAXIMILLER DAL-BIANCO; TEN-CATEN, FELIPE; LI, FORREST; VILELA, ROMEL DUARTE; MENOSSI, MARCELO; WARE, DOREEN; ENDRES, LAURICIO; et al. Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 21, n. 23, DEC 2020. (13/13659-0, 15/01764-0, 17/02270-6, 14/50921-8, 19/15852-9)

SANTINI, LUCIANE; YOSHIDA, LEONARDO; DE OLIVEIRA, KAIQUE DIAS; LEMBKE, CAROLINA GIMILIANI; DINIZ, AUGUSTO LIMA; CANTELLI, GERALDO CESAR; NISHIYAMA-JUNIOR, MILTON YUTAKA; SOUZA, GLAUCIA MENDES. Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, v. 23, n. 19, p. 21-pg., 2022-10-01. (08/52146-0, 20/07851-0, 20/10876-4, 14/50921-8, 18/09867-0, 17/02270-6)

SOUZA, GLAUCIA MENDES; VAN SLUYS, MARIE-ANNE; LEMBKE, CAROLINA GIMILIANI; LEE, HAYAN; MARGARIDO, GABRIEL RODRIGUES ALVES; HOTTA, CARLOS TAKESHI; GAIARSA, JONAS WEISSMANN; DINIZ, AUGUSTO LIMA; OLIVEIRA, MAURO DE MEDEIROS; FERREIRA, SAVIO DE SIQUEIRA; et al. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. GIGASCIENCE, v. 8, n. 12, p. 18-pg., 2019-12-01. (14/50921-8, 08/52074-0, 15/22993-7, 08/52146-0, 12/51062-3, 13/07467-1, 17/02270-6, 11/50761-2, 13/23048-9, 16/06917-1, 16/17545-8)