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Sugarcane signaling and regulatory networks

Abstract

We aim to study signaling and regulatory networks in sugarcane and to develop tools for a systems biology approach in this grass. As a starting point we intend to characterize three agronomical traits of interest: drought, brix and lignin content. We will study gene categories with a well known regulatory role (Transcription Factors, Protein Kinases and Phosphatases), conduct studies on the Transcriptome, produce transgenics, develop a database and computacional tools to integrate the several levels of information and we will initiate the whole genome sequencing of a Brazilian sugarcane cultivar. In parallel, we intend to implement ChIP-Seq technology in sugarcane, to identify TF targets and gene promoters. The results will have multiple direct consequences on breeding programs that frequently select for CREs and TF changes in search for genotypes better adapted to the environment and with increased agronomical performance. PKs activate signaling cascades in response to environmental stimuli and our studies point to a predominant role of PKs in the regulation of sucrose content and drought responses. To identify new genes associated to brix, drought and lignin content we will characterize the transcriptome of genotypes and cultivars that contrast for these traits using olinonucleotide arrays. Genes of interest will be functionally evaluated by generating transgenics altered for their expression. To integrate the immense amount of public data and that generated by this project a robust computational infrastructure and database will be developed. The SUCEST-FUN database will integrate the SUCEST sequences, promoters, CREs, expression data, agronomical, physiological and biochemical characterization of sugarcane cultivars. We will also participate in the development of the GRASSIUS database to establish sugarcane, rice, maize and sorghum regulatory networks. (AU)

Articles published in Agência FAPESP Newsletter about the research grant:
Genes-alvos para o melhoramento da cana-energia são identificados 
Target genes for breeding of energy sugarcane are identified 
Identifican genes blancos para el mejoramiento de la caña energía 
Articles published in Pesquisa FAPESP Magazine about the research grant:
La caña de azúcar mapeada 
Sugarcane mapped 
Entre azúcares y genes 
Between sugars and genes 
Articles published in other media outlets (1 total):
Brasil Amazônia Agora: A cana mapeada » Brasil Amazônia Agora (11/Jun/2021)

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)
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; NISHIYAMA, MILTON YUTAKA; TEN-CATEN, FELIPE; RAGAGNIN, GEOVANI TOLFO; ANDRADE, PABLO DE MORAIS; DE SOUZA, ROBSON FRANCISCO; NICASTRO, GIANLUCCA GONCALVES; PANDYA, RAVI; KIM, CHANGSOO; GUO, HUI; DURHAM, ALAN MITCHELL; CARNEIRO, MONALISA SAMPAIO; ZHANG, JISEN; ZHANG, XINGTAN; ZHANG, QING; MING, RAY; SCHATZ, MICHAEL C.; DAVIDSON, BOB; PATERSON, ANDREW H.; HECKERMAN, DAVID. 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. Web of Science Citations: 3.
ZHANG, JISEN; ZHANG, XINGTAN; TANG, HAIBAO; ZHANG, QING; HUA, XIUTING; MA, XIAOKAI; ZHU, FAN; JONES, TYLER; ZHU, XINGUANG; BOWERS, JOHN; WAI, CHING MAN; ZHENG, CHUNFANG; SHIL, YAN; CHEN, SHUAI; XU, XIUMING; YUE, JINGJING; NELSONS, DAVID R.; HUANG, LIXIAN; LI, ZHEN; XU, HUIMIN; ZHOU, DONG; WANG, YONGJUN; HU, WEICHANG; LIN, JISHAN; DENG, YOUJIN; PANDEY, NEHA; MANCINI, MELINA; ZERPA, DESSIREE; NGUYEN, JULIE K.; WANG, LIMING; YU, LIANG; XIN, YINGHUI; GE, LIANGFA; ARRO, JIE; HAN, JENNIFER O.; CHAKRABARTY, SETU; PUSHKO, MARIJA; ZHANG, WENPING; MA, YANHONG; MA, PANPAN; LV, MINGJU; CHEN, FAMING; ZHENG, GUANGYONG; XU, JINGSHENG; YANG, ZHENHUI; DENG, FANG; CHEN, XUEQUN; LIAO, ZHENYANG; ZHANG, XUNXIAO; LIN, ZHICONG; LIN, HAI; YAN, HANSONG; KUANG, ZHENG; ZHONG, WEIMIN; LIANG, PINGPING; WANG, GUOFENG; YUAN, YUAN; SHI, JIAXIAN; HOU, JINXIANG; LIN, JINGXIAN; JIN, JINGJING; CAO, PEIJIAN; SHEN, QIAOCHU; JIANG, QING; ZHOU, PING; MA, YAYING; ZHANG, XIAODAN; XU, RONGRONG; LIU, JUAN; ZHOU, YONGMEI; JIA, HAIFENG; MA, QING; QI, RUI; ZHANG, ZHILIANG; FANG, JINGPING; FANG, HONGKUN; SONG, JINJIN; WANG, MENGJUAN; DONG, GUANGRUI; WANG, GANG; CHEN, ZHENG; MA, TENG; LIU, HONG; DHUNGANA, SINGHA R.; HUSS, SARAH E.; YANG, XIPING; SHARMA, ANUPMA; TRUJILLO, JHON H.; MARTINEZ, MARIA C.; HUDSON, MATTHEW; RIASCOS, JOHN J.; SCHULER, MARY; CHEN, LI-QING; BRAUN, DAVID M.; LI, LEI; YU, QINGYI; WANG, JIANPING; WANG, KAI; SCHATZ, MICHAEL C.; HECKERMAN, DAVID; VAN SLUYS, MARIE-ANNE; SOUZA, GLAUCIA MENDES; MOORE, PAUL H.; SANKOFF, DAVID; VANBUREN, ROBERT; PATERSON, ANDREW H.; NAGAI, CHIFUMI; MING, RAY. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.. Nature Genetics, v. 50, n. 11, p. 1565+, NOV 2018. Web of Science Citations: 37.
DOS SANTOS, FERNANDA R. C.; ZUCCHI, MARIA I.; PARK, JONG-WON; BENATTI, THIAGO R.; DA SILVA, JORGE A.; SOUZA, GLAUCIA M.; LANDELL, MARCOS G. A.; PINTO, LUCIANA R. New Sugarcane Microsatellites and Target Region Amplification Polymorphism Primers Designed from Candidate Genes Related to Disease Resistance. SUGAR TECH, v. 19, n. 2, p. 219-224, APR 2017. Web of Science Citations: 0.
CUNHA, CAMILA P.; ROBERTO, GUILHERME G.; VICENTINI, RENATO; LEMBKE, CAROLINA G.; SOUZA, GLAUCIA M.; RIBEIRO, RAFAEL V.; MACHADO, EDUARDO C.; LAGOA, ANA M. M. A.; MENOSSI, MARCELO. Ethylene-induced transcriptional and hormonal responses at the onset of sugarcane ripening. SCIENTIFIC REPORTS, v. 7, MAR 7 2017. Web of Science Citations: 14.
FERREIRA, SAVIO SIQUEIRA; HOTTA, CARLOS TAKESHI; DE CARLI POELKING, VIVIANE GUZZO; COELHO LEITE, DEBORA CHAVES; BUCKERIDGE, MARCOS SILVEIRA; LOUREIRO, MARCELO EHLERS; PEREIRA BARBOSA, MARCIO HENRIQUE; CARNEIRO, MONALISA SAMPAIO; SOUZA, GLAUCIA MENDES. Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane. Plant Molecular Biology, v. 91, n. 1-2, p. 15-35, MAY 2016. Web of Science Citations: 21.
NISHIYAMA, JR., MILTON YUTAKA; FERREIRA, SAVIO SIQUEIRA; TANG, PEI-ZHONG; BECKER, SCOTT; POERTNER-TALIANA, ANTJE; SOUZA, GLAUCIA MENDES. Full-Length Enriched cDNA Libraries and ORFeome Analysis of Sugarcane Hybrid and Ancestor Genotypes. PLoS One, v. 9, n. 9 SEP 15 2014. Web of Science Citations: 7.
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: 50.
WACLAWOVSKY, ALESSANDRO J.; SATO, PALOMA M.; LEMBKE, CAROLINA G.; MOORE, PAUL H.; SOUZA, GLAUCIA M. Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content. Plant Biotechnology Journal, v. 8, n. 3, p. 263-276, Apr. 2010. Web of Science Citations: 163.
YILMAZ, ALPER; NISHIYAMA, JR., MILTON Y.; FUENTES, BERNARDO GARCIA; SOUZA, GLAUCIA MENDES; JANIES, DANIEL; GRAY, JOHN; GROTEWOLD, ERICH. GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses. Plant Physiology, v. 149, n. 1, p. 171-180, Jan. 2009. Web of Science Citations: 138.

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