Genetic map

I was in charge for the construction of a sugarcane cultivar genetic map to improve its corresponding genome assembly.

A genetic map is compounded by molecular markers that are separated by relative genetic distances due to crosses between individuals. Genetic maps are used in the assembly of complex genomes such as sugarcane hybrids (Saccharum spp.) because they have highly heterozygous, autopolyploid and aneuploid genomes.

The genome of sugarcane cultivar CC 01-1940 has been used to generate long sequences called scaffolds and a potential genetic map will serve as a guide for the scaffolds in order to depict their linkage groups or chromosomes. This research was focused in the construction of three genetic maps using different strategies whose data came from high-throughput next-generation sequencing (NGS) technologies of a biparental F1 population. 

My contribution to this private project was a methodology for CENICAÑA to build, for the first time ever in the research center, genetic maps from NGS data. A pipeline was delivered to progress in the genome assembly later on, which opens a door for future work on genotype-fenotype association. The three genetic maps presented were able to assemble linkage groups from the cultivar scaffolds. The methodology contributes significantly to CENICAÑA's platform of molecular marker assisted breeding. My work was supervised by Jaime Riascos, Jorge Duitama and Mauricio Quimbaya, and was conducted from February 2019 to September 2020.