Introduction

Traditional plant breeding is an empirical skill in selecting plants and populations that meet the requirements set by the craftsman. In principle, breeders can draw from two sources of genetic variation: natural variation present in the germplasm and induced variation (mutagenesis or transgenesis). It is expected that there is still a large reservoir of useful alleles (= a sequence variant of a gene) both in ‘old’ breeding material as in related and wild/exotic germplasm that has been disregarded up to now.

Due to rapid developments in genomics research, the breeding approach is changing quickly. In the last 3 decades, all kinds of molecular markers have been used, eventually resulting in the ultimate detection platform for “single nucleotide polymorphisms” (SNPs). Until now, the development of such markers was quite cumbersome. In the last 2 years, DNA sequencing technology and development of bioinformatics tools and methodologies have soared. For several crops a complete core genome sequence is available (maize, rice, tomato, potato, cucumber, watermelon, melon, cabbage…) and many more species are on the verge of being sequenced. Massive re-sequencing of new lines or varieties has solved the old bottleneck of marker development, but new limitations and challenges immediately arose regarding the hardware and software needed to handle and analyse these new whole-genome data.
The challenge is not so much data production, but storage, access, retrieval, update, correction, security, (re-)usage of data and ultimately of course the analysis, manipulation and application of data. This demands the creation of suitable data infrastructures and e-science environments and their maintenance.

Virtual breeding

Contemporary plant breeding is evolving into applied genomics. Innovative traditional breeding is mostly based on crosses between crop species and related wild species. The wild species are represented in germplasm collections and within every species a large number of so-called “accessions” is stored. Accessions are very often “weedy looking plants” that seem to be devoid of agronomical properties, except for the trait of interest, for which a direct screen is already available.
Germplasm collections have been proven to be especially valuable for resistance breeding. The desired resistance loci are transferred by crosses and repeated backcrosses to existing parental lines. In many cases, no genes are added by the inter-specific cross, but exchange of a better allele is actually taking place.
At the genome level, that is what breeders do; massively working on allele replacement. One drawback of this is that the replacement does not only introduce the desired allele, but also adjacent chromosome fragments.

One of the earliest accomplishments by man in classical breeding is the domestication of wild plants. By analysing “old” and “recent” domesticated plant material it will be possible to find ontology and descend of lines and varieties. Only in the very last years, the so called “pan-genome concept” has been proposed and confirmed. Originally, biologists assumed that within every species the DNA content would be similar, if not identical. Surprisingly this seems not to be the case, not for humans but also not for plants. Individual plants may although, phenotypically normal looking, contain more, or less “genes”. Depending on the environment, the presence or absence of such genes may be beneficial. High-throughput sequencing will without doubt help to shed light on this unexpected phenomenon.

We envision that high-throughput sequencing of public germplasm collections of stock centres, combined with appropriate bioinformatics tools, can become very important in the process of finding new elite alleles “in silico”. In this way, it will be possible to forecast which genotype from which accession from which related species will be promising for a specific breeding project. This sequence information can be used for “in silico” mining of interesting genes/alleles in these accessions. In essence, this reverses the original workflow: first “virtual” analysis and on the basis of the outcome, dedicated crosses.

All of the VLPB activities will render plant breeding into a very modern art and science whereby variety making by craftsmanship is integrated with rational “in silico” design.