Genome-wide biomarkers

As plant-breeding is based on the redistribution of genetic information, knowledge of genomic variability of breeding material is pivotal. Although massive-parallel sequencing technologies have allowed for new opportunities to investigate the genomes of plants, the available genotyping-by-sequencing approaches often apply a genome-reductionist approach, thereby knowingly ignoring a large fraction of the interrogated genomes.
Skim- or shallow genome sequencing refers to a next-generation sequencing approach in which the average coverage of the genome by sequencing reads is less than ~2x. Skim-genome sequencing approaches have a major impact on the cost of genotyping-by-sequencing.
We developed a genotyping-by-sequencing method: Genome Lineup, which is based on massive parallel sequencing of complete genomes by employing a shallow-sequencing approach. It encompasses several phases:
In Phase I, genomic differences in a substantial set of different accessions with replication (usually n = 4 x 24) are determined and the genomic variability between the accessions is calculated and visualized, which will result in a “genomic landscape” of the analyzed species. This phase has to be done only once for a species of interest.
In Phase II, new accessions can be placed in this species-specific genomic landscape in singular. This can be of interest for many purposes in plant breeding. For instance, one can quickly see where own or competitors’ new varieties are located in the genomics landscape.
In Phase III, we will try to focus on complex-trait biomarkers by using a genomic-prediction approach.

Visualizing the genomics landscape
All identified genomic differences between the analyzed accessions are used to visualize the accessions in a multidimensional scaling plot for example species X. The same colored dots are the four replicates of one accession.
NB: the axes of the plot indicate the combined genomics differences between accessions.

Point of contact for this research line:

Dr. Martijs Jonker
m.j.jonker at
T 020-525-7939