KV 1605-118 Building the green HapMap (BO-50-002-030, BO-26.03-009-005)

In plant breeding, accurate haplotyping will have a major impact on genetic insight of many plant genomes including major food, ornamental and energy crops (e.g. potato, wheat) and thus finally on crop quality.

‘Building the Green Hapmap’ project opens new avenues for unlocking genetic diversity at the haplotype level and for facilitating optimal parent selection, to boost breeding in the Netherlands for efficient development of new global competitive varieties.

This will not only address the ploidy challenge, but also decipher other unsolved issues with complex genomes: heterozygosity, structural variation, repeats and genome duplications.

The Green Hapmap project applies and adapts the newest DNA sequencing technology ‘10XGenomics’ to obtain long range information from highest quality short read sequence data. The resulting ‘linked-reads’ span 10s to over 100 kilobases and are used for alignment, variant analysis and reconstruction of phase blocks all at unprecedented levels. Within this project this technology will be specifically applied to and adapted for polyploid plant genome analysis. The project will focus on three plant species with increasing genome size, complexity and ploidy levels: diploid carrot, auto-tetraploid potato and auto-hexaploid chrysanthemum.