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Towards identification of beneficial alleles controlling traits for sustainable production: SNP discovery in Brassica oleracea - IF0152

Description
The Genetic Resources Unit (GRU) at Warwick HRI has been extremely successful at conserving plant genetic resources of field vegetables important to the UK and the GRU has responsibility for the international collections of carrot, alliums and brassica. There are over 6000 accession in the brassica collection representing the diversity within the genepool. However, this causes researchers and breeders logistical problems when it comes to screening the collection for a particular trait since generally, it is not possible to assess all of the accessions in the collection; there is therfore the question of "where to start?". This problem has been alleviated by the construction of diversity sets which are samples of the diversity maintained in the collection which are structured in such a way as to optimize both the geographical and genetic variation. These diversity sets are therefore ‘gateways’ into the collections.

Currently three Brassica Diversity sets (known as Diversity fixed foundation sets or DFFS) are being produced at Warwick; a Brassica oleracea (cabages, cauliflowe DFFS, a wild C genome species (wild species related to B oleracea) DFFS and a B. napus DFFS. These are important strategic resources for brassica crop improvement (both for vegetable brassica and for OSR). It is anticipated they will be sources of new beneficial alleles for a number of important traits for sustainable production (e.g. water use and nutrient use efficiency) as well as potential sources of alleles for. reducing waste during production (e.g. pest and disease resistance) or post harvest (e.g. improved shelf life) as well as alleles for improved nutrient status. However, in order to improve our ability to exploit the natural allelic variation captured in these DFFS we need to put in place the technology and tools to characterise them better to allow us to identify beneficial alleles more rapidly. To do this we need to increase the number of molecular markers available to us to
a) Understand the genetic diversity we have captured and thereby provide information to end users (researchers and breeders) about how to find beneficial alleles.
b) Be able to use techniques such as association mapping to identify such beneficial alleles.
c) Provide breeders with markers to allow them to introduce beneficial alleles into elite adapted germplasm more rapidly.
This will facilitate a more rapid response to meet the demands of drivers such as adapting to climate change more efficiently and effectively and policy.

To date, the BolDFFS has been screened for the uptake of a range of minerals and water use efficiency, and the BnaDFFS has been screened for nitrogen assimilation and is currently being used to study phosphate use efficiency. To use this trait data for association mapping requires the lines of the DFFSs to be screened with a large number of markers. The markers of choice for this are called Single Nucleotide Polymorphisms (SNPs)

The use of SNPs compared offers a higher throughput, better resolution and cheaper methodology. In humans over 2 million SNPs have been identified in the International HapMap Project and extensive subsets of these are being used to screen large numbers of individuals. Associations with the traits and specific SNPs, known as linkage disequilibrium (LD), result in fine scale mapping of the genes and gene identification. A similar resource is being developed in the model plant species Arabidopsis. Brassicas are closely related to Arabidopsis, the first plant for which the complete genome sequence was determined. The diploid Brassica genome is, however, far more complex having undergone a triplication of the genome. This means that Arabidopsis markers can not readily be used with Brassica’s. Consequently there is a pressing need to develop a large number of SNPs within the brassica’s for use in the development of high throughput genotype screening assays that will form the basis for the identification and mapping of loci underlying traits of interest, particularly the quantitative traits which impact upon sustainable production etc. Currently there are very few public SNP markers available for any Brassica crop types.

In this project we propose to carry out a pilot scale experiment of Brassica oleracea SNP discovery which will provide the necessary information to form the basis of an approach to identify and map sufficient SNPs to provide the tools for rapid identification and introgression of beneficial alleles from the DFFS.
Objective
Objective:
The objective of this project is to carry out a pilot scale Brassica oleracea SNP discovery experiment to identify 2000 SNPs.
We will also provide information for the design of a strategy to identify and map sufficient SNPs for the rapid identification of beneficial alleles from the brassica diversity sets through techniques such as association mapping.
Project Documents
• Abstract : Towards identification of beneficial alleles controlling traits for sustainable production. SNP discovery in Brassica oleracea   (166k)
Time-Scale and Cost
From: 2009

To: 2009

Cost: £49,900
Contractor / Funded Organisations
Warwick - HRI
Keywords
Allocated - WHRI              
Brassicas              
Genetics              
Horticulture              
Integrated Farming Systems              
Oilseed Rape              
Sustainable Farming and Food Science              
Sustainable Farming Systems