Building the Green Hapmap

Projectnummer: 1605-118
Thema: Duurzame Plantaardige Productie
Looptijd: 2017 - 2020
Budget publiek: € - 
Budget privaat:  € - 
Projectleider: Elio Schijlen /
Kennisinstelling: WUR Bioscience

Marker-assisted breeding strategies, feasible in diploids inbreeding crop species, cannot be applied in outbreeding heterozygous diploid and polyploid crops because the existing genotyping technology does not provide enough resolution for pursuing the associated marker. The major reason is that currently markers can only be associated with traits at the SNP level and not at the level of an individual haplotype. This makes it impossible to determine whether a trait-linked SNP is on the beneficialhaplotype, or also on another negative contributing haplotype linked by chance due to the structure of the population. In the latter case, further breeding often results in a loss of predictive power for the trait-linked SNP, and failure of breeding for the aimed target. As a consequence, only a limited number (8-10) of selection markers are routinely used, only for qualitative traits where one allele is sufficient for expression of a dominant trait such as disease resistance, while no markers for quantitative traits, such as yield and quality traits, are used. Although the obvious solution is breeding on the level of individual haplotypes, the technology to do so is currently lacking.

A promising technology to deal with haplotype assembly in a cost-effective manner is 10x Genomics. At the beginning of 2016, the company launched their Chromium platform. The core technology is a Gel bead inside Emulsion (GEM) and uses droplet microfluidic technology prior to standard (Illumina) sequencing to generate “linked reads” that can be used to piece together haplotypes. Examples of success currently focus on the diploid human genome ( propose to early adopt 10x Genomics technology to plant genomes and to developmethods for haplotyping and improving genome assembly customized for this technology in valuable polyploid crops.

Bekijk hier de voortgangsrapportage 2017 van Building the Green Hapmap.

Bekijk hier de voortgangsrapportage 2018 van Building the Green Hapmap.

Bekijk hier de voortgangsrapportage 2019 van Building the Green Hapmap.