CGN has compiled a lettuce collection for users who are specifically interested in variation in genes existing within gene bank material. So far, the DNA sequence of 100 samples has been determined.
The special collection lettuce, currently consisting of 442 samples, has largely been selected from the regular CGN collection. It represents all lettuce crop types and its most important crop wild relatives. It includes samples with ample trait information, in particular on disease resistances. Wild species are an important source of new traits for lettuce and therefore are well represented in the special collection.
The selection was compiled in the framework of the TKI project International Lactuca Genomics Consortium (ILGC), in which 17 breeding companies from the Netherlands and abroad participate. TKI stands for Topconsortia for Knowledge and Innovation, a programme in which companies and scientists search for sustainable solutions for food security and food safety.
Genes and traits
The identification and utilization of suitable genetic resources for breeding is greatly facilitated when more is known about the genes and their function, and the existing variation therein. To investigate how the variation in genes influences the variation in traits, genetic and phenotypic data need to be collected from the same materials.
For each of 442 gene bank accessions a single plant was cultivated, of which DNA was isolated for sequence analysis and seed was produced by self-fertilisation to obtain single seed descent (SSD) lines. Through the use of SSD lines of a sequenced plant new phenotypic information can be linked to existing genotypic information. This makes this special collection important for breeding purposes as it provides a basis for ‘marker-assisted breeding’. The DNA sequence of the first 100 samples has been established by the ILGC. All genotypic data, generated within the project, will become publically available in due time. This will make the special collection interesting to a broad user community.
Hundred and fifty lines of the special collection have also been used to investigate phytochemical variation. Results from this metabolomics research will provide an extra set of phenotypic data to which the genotypic data will be linked. This information will also become publically available in due time.
The distinction between regular and special CGN collections
The regular CGN collections are developed for conservation and use, and are being maintained under a mandate from the Dutch government. The management of these collections follows strict procedures, which are recorded in a quality management system. The collections can be searched online and accessions can be requested for research, breeding and education, under the terms and conditions of the ‘standard material transfer agreement’ (SMTA).
Special collections are not primarily aimed at conservation in perpetuity, but at specific user communities and purposes. The range of user groups and purposes can be wide, and hence special collections may widely differ in nature. For example, special collections may consist of specific research populations, genetically homogenous lines for breeding or heritage varieties aimed at a more general public. An important difference with the regular collections is that special collections are not maintained according to strict procedures, cannot be online searched or requested, and are not necessarily distributed under SMTA conditions. In addition, users might be charged for providing the special services.
Currently, CGN has developed special collections of lettuce and tomato. Materials from both collections have been distributed several times.