Cassava, Manihot esculenta Crantz, is one of the most important crops worldwide, representing the staple security for more than 1 billion people. The development of dense genetic and physical maps, as the basis for implementing genetic and molecular approaches to accelerate the rate of genetic gains in breeding programmes represents a significant challenge. A reference genome sequence for cassava has recently been made available, and community efforts are under way to improve its quality. Cassava is threatened by several pathogens, but the mechanisms of defence are far from understood. Besides, there has been a lack of information about the number of genes related to immunity as well as their distribution and genomic organisation in the cassava genome.

In this study, a high density genetic map of cassava containing 2,141 single nucleotide polymorphisms (SNPs) was constructed. Eighteen linkage groups were resolved with an overall size of 2,571 centimorgans (cM) and an average distance of 1.26 cM between markers. More than half of mapped SNPs (57.4%) are located in coding sequences. Physical mapping of scaffolds of cassava whole genome sequence drafts using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome. One hundred and eighty-nine new scaffolds are anchored to the genetic cassava map leading to an extension of the present cassava physical map by 30.7 Mb. Comparative analysis using anchor markers showed strong co-linearity to previously reported cassava genetic and physical maps. In silico-based searching for conserved domains allowed the annotation of a repertory of 1,061 cassava genes coding for immunity-related proteins (IRPs). Based on a physical map of the corresponding sequencing scaffolds, unambiguous genetic localisation was possible for 569 IRPs.

This is the first study reported so far of an integrated high-density genetic map using SNPs with integrated genetic and physical localisation of newly annotated immunity-related genes in cassava. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits. The enrichment of the physical map with novel scaffolds is in line with the efforts of the cassava genome-sequencing consortium.