The next generation of molecular markers in plant sciences

Genotyping-by-sequencing (GBS) is a technique to generate genome-wide sets of molecular markers. Briefly, DNA is extracted from an individual (or a pool of individuals) and digested using one or more restriction enzymes. Indexed adapters are ligated to the resulting fragments which are then amplified, purified and sequenced using Illumina technology. At ILVO we apply this method in several species to answer diverse research questions in plant science. Here, we present a few case studies. In the first project GBS is used to construct a genetic map of the rose species Rosa wichurana. GBS-based molecular markers are used to validate integrated physical, cytogenetic and contact probability maps in order to obtain a high-quality genome assembly, useful in breeding programs. In the second project, GBS is applied to a range of strains of the oomycete Phytophthora, known to cause severe disease in a variety of plant hosts. GBS-based markers are called in a reference-free approach and are used to identify Phytophthora hybrid strains (which may be more aggressive) and their potential ancestral species, based on presence/absence of genomic loci as well as SNP profiles. Finally, GBS is applied to pools of perennial ryegrass plants (Lolium perenne), an important feed crop. Changes in genome wide allele frequency fingerprints (GWAFFs) are used to identify signatures of selection and adaptation for landscape genomics on wild accessions on the one hand and in controlled long term field trials under different conditions on the other hand. In conclusion, by adopting and applying GBS in different fields of plant sciences, we enable plant breeders, plant pathologists and evolutionary biologists to elevate their research to a new level.