Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Development Of Functionally-Associated Genetic Markers For Genetic Improvement Of White Clover (Trifolium repens L.)

John W. Forster^1,3 , Nathaniel R. Bannan^2,3 , Noel O.I. Cogan^1,3 , Michelle C. Drayton^1,3 , Julie George^1,3 , Kahlil Lawless^1,3 , Rebecca C. Ponting^1,3 , Kevin F. Smith^2,3 , German C. Spangenberg^1,3 , Anita C. Vecchies^1,3 , Tania C. Wilkinson^2,3

¹  Primary Industries Research Victoria, Victorian AgriBiosciences Centre, La Trobe University, Bundoora, Victoria 3083, Australia.

²  Primary Industries Research Victoria, Hamilton Centre, Mount Napier Road, Hamilton, Victoria 3300, Australia

³  Molecular Plant Breeding Cooperative Research Centre, Australia.

First-generation genetic markers and associated linkage maps for white clover have been based on SSR variation. The second generation of genetic markers will be based on SNPs in genes whose function is putatively correlated with target biochemical and physiological characters. Two-way pseudo-test cross trait-specific genetic mapping families have been developed for the analysis of multiple agronomic traits, providing an important resource for in vitro SNP development and genetic map construction. In silico SNP identification was performed in over 1400 white clover EST contigs, followed by validation in the parents of the mapping families. Polymorphic SNP loci are present in close to 100 genes across a range of functional categories. SNPs have also been identified in vitro from cDNA sequences of annotated genes of interest by amplicon cloning and sequencing, including those encoding enzymes involved in condensed tannin biosynthesis, organic acid biosynthesis, cyanogenesis, nodulation function, floral development and other functions. Complex haplotypic structures were revealed, associated with both within- and between-genome sequence duplication events. Genetic linkage maps have been constructed to combine pre-existing genomic DNA-derived SSR and EST-SSR data, and to incorporate gene-associated SNP loci. The functionally-associated markers will be used to assess co-location with QTLs for correlated traits, supported by translational genomics with model legume species such as Medicago truncatula and Lotus japonicus. The comparative analysis of T. repens with other Fabaceae genomes provides a rationalised basis for linkage group nomenclature. The gene-associated SNP markers provide a valuable resource supporting marker-assisted breeding for key agronomic traits.