Balance between dosage and allelic expression to map the global gene expression profile in sugarcane

• Grant number: 15/16399-5
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Effective date (Start): January 01, 2016
• Effective date (End): December 31, 2019
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Anete Pereira de Souza
• Grantee: Cláudio Benício Cardoso da Silva
• Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated scholarship(s): 17/26781-0 - Transcriptome survey of sugarcane hybrids (Saccharum spp.) and ancestral species (S. officinarum and S. spontaneum) for gene expression pattern and homoeologous interaction studies, BE.EP.PD

Abstract

Polyploidy is an inheritable condition where more than two chromosome sets occur in the cell nucleus, thus increasing the allelic dosage amounts more than two sets (diploid). Several studies have shown that allelic expression is sensitive to dosage effects and various regulation mechanisms may influence it. Modern cultivars of sugarcane (Saccharum spp.) are polyploids complex of great economic interest, which have multiple copies of chromosomes homoeologous. However, the composition and dosage impacts in the allelic expression are poorly understood in this species. The literature reports that allelic expression may be dosage dependent, when the allele expression levels to be correlated with allelic dosage in the genome; or dosage independent, when the expression is not correlated with genome dosage. Genetic mechanisms such as cis and trans regulation, epigenetic effects, dosage compensation and gene or genomic dominance can be responsible for these events. Scientific and technological advances have made available new tools and information that allow phenomena investigations like these, even in complex organisms such as sugarcane. In this project, we discuss the study of global gene expression in sugarcane, through identification of the allele frequency and dosage by genotyping of SNP (Single Nucleotide Polymorphism) markers present at different gene sequences associated with the expression profile of these genes present in the global transcriptome of sugarcane, as well as completion of the sequencing of genomic fragments containing the genes under study. This study aims to investigate the possible mechanisms related to the effect of dosage on the allelic expression from different genes in sugarcane and to investigate your expression level. The individuals chosen for execution of this project are six parents of three genetic mapping populations with research in progress, and S. officinarum and S. spontaneum species, which were the first parents of the sugarcane hybrids. This approach is unprecedented study about the gene expression control in complex polyploid plants. It is expected that this project has a great impact about the knowledge about the molecular mechanisms related to allelic expression, mainly in sugarcane, and motivate others experiments covering specific target genes in specific tissues, to complement the studies. (AU)

Scientific publications

(5)

(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)

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. (17/05014-0, 15/16399-5, 14/11482-9, 08/52197-4)

AONO, ALEXANDRE HILD; GONZAGA PIMENTA, RICARDO JOSE; BASSO GARCIA, ANA LETYCIA; CORRER, FERNANDO HENRIQUE; HOSAKA, GUILHERME KENICHI; CARRASCO, MARISHANI MARIN; CARDOSO-SILVA, CLAUDIO BENICIO; MANCINI, MELINA CRISTINA; SFORCA, DANILO AUGUSTO; DOS SANTOS, LUCAS BORGES; et al. The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. FRONTIERS IN PLANT SCIENCE, v. 12, JUL 7 2021. (14/11482-9, 18/18588-8, 19/03232-6, 15/22993-7, 15/16399-5, 08/52197-4, 19/21682-9, 05/55258-6, 19/19340-2)

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; et al. 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. (15/16399-5, 08/52197-4, 14/11482-9)

CARDOSO-SILVA, CLAUDIO BENICIO; AONO, ALEXANDRE HILD; MANCINI, MELINA CRISTINA; SFORCA, DANILO AUGUSTO; DA SILVA, CARLA CRISTINA; PINTO, LUCIANA ROSSINI; ADAMS, KEITH L.; DE SOUZA, ANETE PEREIRA. Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.). FRONTIERS IN PLANT SCIENCE, v. 13, p. 13-pg., 2022-06-30. (14/11482-9, 15/16399-5, 19/03232-6, 15/24346-9, 17/26781-0, 08/52197-4)

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, p. 8-pg., 2018-03-28. (17/05014-0, 14/11482-9, 15/16399-5, 08/52197-4)