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Mock reference assembly and SNPs identification for Megathyrsus maximus

Grant number: 19/10747-2
Support type:Scholarships in Brazil - Scientific Initiation
Effective date (Start): July 01, 2019
Effective date (End): November 30, 2019
Field of knowledge:Agronomical Sciences - Agronomy
Principal Investigator:Anete Pereira de Souza
Grantee:Lucas Leme Pinheiro
Home Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

Megathyrsus maximus (sin. Panicum maximum) is the second most commercialized tropical forage in Brazil and presents high productivity and adaptability to different types of soil. Few genetic information is available due to the complex autotetraploid genome of this species. Plants phylogenetically close have been used as reference in the SNPs (single nucleotide polymorphisms) discovery for genomic studies of M. maximus. However, apomorphic characters of economic interest of the species are not included in these approaches. In this context, the project aims to assemble a Mock Reference for M. maximus from previously obtained GBS (Genotyping By Sequencing) data and the SNPs identification based on the alignment of genome Mock with GBS data. Assembly of this genome and SNPs discovery will be performed by the pipeline GBS-SNP-CROP, once that has a strategy for SNP calling into scenarios where there is no available genome. Markers identified can be complemented to the linkage map constructed by our group and may also be used in later genomic studies, therefore will contribute to greater knowledge of the species and other forages.