Scripts, documentation and tools to construct a sugarcane genetic map. Code was implemented to tailor the genome assembly of a commercial sugarcane cultivar. Here is an abstract of the work done where all the scripts and tools were used.
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 sugarcane cultivar CC 01-1940 has been used to generate long sequences called scaffolds and a potential genetic map will serve as a guide of the scaffolds in order to depict the linkage groups or chromosomes. This research shows the construction of three genetic maps using different strategies whose data comes from high-throughput next-generation sequencing (NGS) technologies of a biparental F1 population. The progeny is a result of the crossing between sugarcane cultivars CC 01-746 and CC 01-1940. The 93 individuals plus both parents were sequenced using Whole Genome Sequencing (WGS). This set of reads per individual were aligned to the scaffolds with outcomes higher than 85%. The alignments were used for variants detection and selection of high quality SNPs that enable linkage map construction. A total of 3,739 loci, 4,096 loci and 7,816 loci were obtained respectively for each SNP calling strategy. Strategy A yielded a map size of 9,679.50 cM with an average density of 6.05 cM/loci. Strategy B yielded a map of 1,191.30 cM with an average density of 1.96 cM/loci and strategy C yielded a map of 1,198.74 cM with an average density of 2.19 cM/loci. This is the first time that CENICAÑA builds genetic maps from NGS data, which releases an important pipeline to advance in the genome assembly and unveils a tool for future work on genotype-phenotype association. The three genetic maps presented here are able to assemble linkage groups from the cultivar scaffolds. This methodology contributes significantly to CENICAÑA's platform of molecular marker assisted breeding.