Pan grass syntenic gene set based on sugarcane inclusion and the thiamine biosynthesis pathway

• Grant number: 22/16208-9
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• Start date: May 01, 2023
• End date: October 31, 2023
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Marie-Anne Van Sluys
• Grantee: Henrique Moura Dias
• Supervisor: James Carey Schnable
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: University of Nebraska-Lincoln (UNL), United States
• Associated to the scholarship: 19/08239-9 - Functional studies of THI1 in plants, BP.DD

Abstract

The development of a pan-grass synthetic gene set can yield a high-resolution view of the patterns and processes of molecular evolution. However, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems, especially sugarcane, a highly polyploid grass. These challenges range from studying the evolution of chromosome structure to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation, domestication, and adaptation. Here, we present a proposal for a BEPE research internship, which addresses these challenges integrating the orthology of (highly conserved) thiamine genes to define the expected physical position of all genes in various grass genomes and the inclusion of R570 sugarcane in the Pan Grass Syntenic Gene Set developed by the Schnable research group. It is initially proposed the development of such an approach with the sugarcane monoploid reference (R570), where we will seek to dissect the presence-absence, number of copies, and structural variation covering the syntenic set developed by the group abroad. Methods for constructing and visualizing the syntenic orthology as well as the inclusion of sugarcane, can offer a significant addition to the community of sugarcane genomic studies. (AU)