Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Gene-Associated SNPs For Superior Allele Identification In Applied Breeding Of Outbreeding Pasture Species.

Noel O.I. Cogan^1,3 , Anita C. Vecchies^1,3 , Rebecca C. Ponting^1,3 , Michelle C. Drayton^1,3 , Julie George^1,3 , Jeremy L. Dumsday^1,3,5 , Mark Dobrowolski^2,3 , German C. Spangenberg^1,3 , Tim I. Sawbridge^1,3,4 , Kevin F. Smith^2,3 , John W. Forster^1,3

¹  Primary Industries Research Victoria, Plant Biotechnology Centre, La Trobe University, Bundoora, Victoria 3086, Australia.

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

³  Molecular Plant Breeding Cooperative Research Centre, Australia.

⁴  Present address: Molecular Bioscience Technologies, Department of Primary Industries and Fisheries, Queensland Biosciences Precinct, 306 Carmody Road, The University of Queensland, St. Lucia 4072, Australia.

⁵  Present address: Beckman Coulter, Australia Pty Ltd, 24 College Street, Gladesville, New South Wales 2111, Australia.

Advances in molecular genetic marker technology now permit a targeted approach to the detection of nucleotide diversity in genes controlling key agronomic traits. Large-scale discovery of gene-associated single nucleotide polymorphism (SNP) markers has been performed for the temperate pasture species perennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.). The methodology involves amplicon cloning, high-throughput sequencing, alternate nucleotide identification at multiple locations across transcriptional units of candidate genes, SNP validation by the application of the single nucleotide primer extension (SNuPe) method, and locus assignment to reference genetic maps. Distributions of synonymous and non-synonymous base changes have been determined and the diversity of SNP haplotypic structure has been examined within the species and other closely related taxa. A total of more than 130 perennial ryegrass genes from a range of functional categories have been analysed and c. 1200 SNPs have been identified, with an average incidence of c. 1/60bp in exonic sequences and c. 1/40bp in intronic sequence. The distribution of SNP variation has been determined across several full-length genes involved in herbage quality traits, allowing a preliminary assessment of haplotype structure and stability over gene-length distances. Analysis of haplotype variation provides the basis of associating genotypic variation to phenotypic variation. Successful implementation of this approach requires detailed knowledge of the influence of haplotype on gene expression, as well as the extent and structure of genetic and phenotypic variation in breeders’ germplasm. The most recent resources and strategies for functionally-associated marker-based breeding in forages will be described.