Devoloping RAD markers as a resource for plant breeding

  • Blaxter, Mark (Principal Investigator)

Project Details


This proposal addressed the need for large-scale marker development as a resource for plant breeding and genetic mapping. By exploiting the power of next-generation sequencing techniques, RAD sequencing (RADSeq) allows for simultaneous marker discovery and genotyping at a high-throughput level. As additional demands are placed on agriculture due to a growing population and climatic change, plant breeding must adopt new strategies for rapid improvement of crop varieties and exploitation of natural genetic variation. Techniques such as RADSeq will therefore be vital to assisting efforts to maintain global food security, recognized as a key area in its adoption as a BBSRC Strategic Priority. Successful implementation of RADSeq in Lolium will enable future use of the technique in mapping other traits of interest, including those connected to the potential use of Lolium as a bioenergy crop.

Layman's description

Breeding of crop plants to give higher yields of socially useful products (such as biofuels and foodstocks) while reducing the costs of production (in terms of fertiliser input, for example) and reducing waste byproducts is an important goal of modern agricultural science. The way this is done is to track the transmission of a trait of interest, such as high yield, in controlled crosses, and to identify which parts of the plant genome contribute to the desired improvement. However, plant genomes can be very big, and complex, and so traditional methods of developing genetic markers can be slow and error prone. We have been testing a new set of methods that subsample the genome at defined places and generate DNA sequence based genetic markers that can be used for any crop species. We worked on Lolium, the rye grass, a crop that may have future importance as a biofuel crop, aiming to develop methods to assist plant breeders to improve yields.

Key findings

1) Based on data output by this project, in combination with markers identified by Floragenex (Oregon) as part of a commercial partnership with IBERS, over 1000 RAD markers have been developed thus far for Lolium perenne. RAD has been adopted as a major genotyping tool by IBERS and is currently being employed in development of RAD maps in other Lolium populations as well as diploid oats.
2) A skeletal RAD map for L. perenne has been produced and used to map QTL associated with phenotypic traits of interest (self-incompatibility, lipid content and water-soluble carbohydrate).
3) RAD library construction is now routine within the Aberystwyth PI’s lab and RAD sequencing has been optimised for the in-house IBERS Illumina platform, enabling a range of current RAD-based projects across IBERS in both plant and animal species. Analysis of RAD data from this project and the Floragenex partnership has enabled initial development of a RAD bioinformatics pipeline and RAD tag database to facilitate ongoing genotyping.
Effective start/end date1/01/1130/06/12


  • BBSRC: £89,381.00


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