Using translational genomics to underpin germplasm improvement for complex traits in crop legumes

Legumes are a group of important plant species that, together with bacteria that live in nodules on the root, can convert nitrogen in the atmosphere to a form that can be used by plants. They include peas and beans as well as crop plants that are used for animal feed. Some legume species have been developed as 'models' that allow us to investigate genome structure, DNA sequence and the control of gene expression in a way that would be more difficult in crops. Model species typically have a small genome size, short generation times and an inbreeding system of reproduction. The barrel medic (Medicago truncatula ) has been developed as a model legume and, for example, is expected to have all its genes sequenced by the end of 2007. Information and resources from model species can be used to understand more about the genetics and genomics of crop plants in a way that will facilitate improved ways of breeding new varieties for the changing needs of agriculture. In this work we will use knowledge of Medicago truncatula to gain understanding of a closely related species, red clover. Red clover (Trifolium pratense L.) is an important crop for feeding animals (sheep, beef and dairy cattle) in the UK and many temperate parts of the world. In this work we will compare the genomes of the model and crop to lay the foundation for new approaches to breeding in the crop. We will do this in several different ways: (i) The sequences of long stretches of DNA will be compared. To do this we will use DNA that has been inserted into bacterial artificial chromosomes (BACs) in a way that allows it to be held together and suitable for sequencing. The extent of similarity in sequence between red clover and M. truncatula will tell us how closely related the two species are and the extent to which we can use information from the model e.g. to clone genes in the crop. (ii) The position of differences in DNA sequence (polymorphisms) will be mapped in the genome of red clover in such as way as to relate these differences to the physical genome as represented by the BACs (iii) A number of bio-informatic approaches will be used to extract information from DNA sequencing, physical and genetic mapping and to place the information found in the wider context of legume genetics. The bioinformatic component of the work will also facilitate the application of the knowledge gained and resources generated to the development of new varieties of red clover and other important crop species.

The objective is to create a robust physical map of diploid clover (Trifolium pratense) that will be anchored to the genome sequence of the legume reference species Medicago truncatula, and aligned to the clover genetic map. The anchored physical map will facilitate dissection of biological traits, future genetic improvement and marker assisted breeding in this important legume crop. The proposal will allow comparative analysis across legume species and create a model for translational genomics in crop legumes. Fingerprinting and end-sequencing of BAC clones from an existing red clover library will be used to obtain 2000 BAC contigs and anchor them to the M. truncatula genome using the closest homologue. Cytogenetics will assess the level of coverage of the clover physical map and resolve issues with misaligned contigs. Approximately 70 gene specific molecular markers previously tested in clover will permit an approximate positioning in the M. truncatula genome to be determined. A web accessible clover information resource with the alignment to M. truncatula, and integrated with the alfalfa resource developed in the US will be established. Integration with other databases will allow us to derive conserved orthologous sequence markers from the clover end-sequence tags that can be integrated with their counterparts in M. truncatula and Lotus japonicus.