ex situ genetic resources

diversity sets


Species Number of lines Founder Accession list Availability
B. napus 188 download xls WHRI
B. oleracea 376 (to be confirmed)    

Development of Diversity Sets for long-term community-wide molecular and trait exploration of Brassica gene-pools

Graham King, Graham Teakle, Dave Astley, Dave Pink. HRI, March 2004

Modern crops contain a surprisingly narrow genetic base, despite the existence of extensive allelic variation within germplasm collections. Although breeders exploit the existing natural variation for particular target traits within crop species, there has been considerable reduction in biodiversity through canalisation of alleles. Introduction Core Collections have been developed for Brassica spp in the past, within EU GenRes and other programmes. These were based on accessions held within public genetic resource collections (see 1; 2; 3;) . Seed were multiplied and accessions screened for a number of fungal and other resistance traits. Whilst valuable in identifying 'hotspots' of variation within the relevant gene-pools, these collections consisted of heterogeneous and heterozygous materlal. This limits their long-term use for correlating detailed genetic studies.

"Diversity Fixed Foundation Set" (DFFS) definition:

"an informative set of genetically fixed lines representing a structured sampling of diversity across a genepool"

dffs

The Concept


In the course of recent molecular analysis we have found considerable genotypic variation within individual extant genetic resource accessions. This is present both as within-line heterogeneity and within-plant heterozygosity. As such, any co-ordinated trait and genetic studies will be very difficult to interpret unless material with acceptable levels of homozygosity is produced and made publicly available. To address this issue and provide researchers with relevant resources, 'Diversity Fixed Foundation Sets' (DFFS) will be constructed. These are designed to represent the majority of allelic variation within respective gene pools in a form suitable for long term exploitation by researchers and end users. Theoretical studies (Lawrence MJ, et al (1995) Euphytica 82:89-99; 101-107) indicate that 400 homozygous accessions, collected from throughout the world, should contain 99% of the allelic polymorphism (i.e for alleles with frequencies >2%) present in the species. see also 4

DFFS Stucture

HRI first initiated the establishment of a DFFS for B. oleracea, which is comprised of a structured sample of 386 accessions representing the diversity within the gene-pool. These have been selected as nested subsets of 94 (so DNA samples fit on a 96-well microtitre plate, with 2 controls). Each subset has been selected to represent diversity within species subtaxa and crop type, as well as variation in eco-geographic origin. The sets are being fixed through generation of doubled haploids and inbreeding to establish 'immortal' lines which may be used by a wide range of researchers and breeders for trait and molecular assessment. The approach of generating fixed lines is particularly powerful as the data obtained are cumulative, allowing long-term comparative analysis. In addition, fixed lines enable experimental trials to be established with replicate plants. As such they may be interpreted to provide insights into contribution and interaction of genetic, environmental and developmental components of variation. Details of the composition of the founder sets will be presented in the near future.

Development of the sets


Survey available genetic resources and related information Identify and source accessions to represent diversity Grow sample of plants and select representative 'founder plant' Extract DNA of founder plant - prepare GenomiPhiTM sample Bulk seed of founder plant Preliminary assessment of variation in founder line Fix founder line by microspore (doubled haploids) or single seed descent selfing (inbred line) Extract DNA from fixed lines and make available Bulk up seed of fixed lines and make available The timeline for the work varies according to the genertion time of the selected lines and responsiveness to microspore culture.

Uses


Availability and distribution

HRI will make the DFFS available through the HRI Genomics Resource Centre (contact) Seed For B. oleracea, seed of S1 of the primary subset of 94 accessions will be made available as a public resource by June 2005. For the B. napus set, seed will be made available via the OREGIN project. The availability of the seed for the fixed lines will be dependent upon progress in the 'fixing' process. DNA We are currently evaluating the suitability of GenomiPhiTM to generate suitable quantity and quality of DNA for distribution. This will be particularly useful in ensuring that DNA of founder-plant DNA is available in the intervening period during which lines are being fixed. The research community will thus have access to a verified source of uniform DNA for comparative studies. For B. oleracea, DNA of founder plants will be available later in 2004 For B. napus, DNA of founder plants will be available later in 2004

Data collation

WHRI will collate genotype and phenotypic data into a structured database (a module of the CropStore family of databases), and make available over the web through online interfaces, XML etc. The genotype data will become integrated into other online Brassica genome and genetic databases.

Current status