Evaluating the occurrence of allele-specific expression in the polyploid sugarcane genome

• Grant number: 18/02489-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: April 01, 2018
• End date: March 31, 2019
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Gabriel Rodrigues Alves Margarido
• Grantee: Guilherme Bovi Ambrosano
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil

Abstract

Little is known about the control of gene expression in sugarcane, despite its economic importance to Brazil and to São Paulo. Its complex genomic structure hinders the use of techniques developed for other crops. The genome of sugarcane is polyploid and aneuploid, with evidence of both auto polyploidy and allopolyploid, but most of these techniques were developed for diploid organisms. Differential expression analysis, used in functional genomics research, is one of those techniques. This analysis aims to find differences in the levels of gene expression between samples from contrasting experimental conditions. It can be applied not only to diploids, but also polyploid species, albeit with some particularities. In these organisms, heterozygous loci present several possible allele dosages. In other words, alleles do not necessarily show a 1:1 ratio, as they would in diploid organisms. In addition to activating and repressing specific genes, differential gene expression may promote the expression of a particular allele over the others (preferential allele expression or allele-specific expression). Therefore, the allelic dosage in a given polymorphic site should be considered in the differential expression analysis. This work aims to find evidence of allele-specific expression in leaves of sugarcane infected by Puccinia kuehnii. In addition, it seeks to analyze the associations between the levels of allele expression and the dosage of SNP alleles. We will use RNA-Seq data from samples of the susceptible sugarcane genotype SP89-1115, collected at 0, 12, 24, 48 hours, 5 and 12 days after the inoculation with P. kuehnii. Allele dosage data were obtained through genotyping-by-sequencing of this genotype. (AU)