Subterranean Clover(Trifolium subterraneum L.) Genomic Resources: Building a Comprhensive Platform for Molecular Breeding

Subterranean clover (Trifolium subterraneum L.) is the key forage pasture legume species in Australia and is also an ideal reference species for comparative mapping within the Leguminosae. It is a diploid (2n =16), predominantly inbreeding annual species that can be readily hybridised. It also has a wide range of diversity for both qualitative and quantitative agronomic and morphological characters. A draft genome sequence of size ~480Mb has been described for subterranean clover (based on cv. Daliak). This represents 86% of the estimated 556.6 Mb subterranean clover genome. We used an Illumina next-generation sequencing platform to generate 277.1 Gb (HiSeq) + 23.6 Gb (MiSeq) of genome sequence, which along with sequences derived from a Roche 454 machine (2.72 Gb) enabled us to assemble the pseudo-chromosomes anchored to a high density linkage map based on a custom designed Affymetrix Axiom SNPchip. A total number of 65,295 genes were predicted using Augustus and 18,023 of these were homologous with Medicago truncatula (4.0v1).

This reference genome will serve as a genomic resource of subterranean clover and facilitate identification of the genetic basis of agronomically important traits, which are vital for the future genetic improvement of pasture legumes. Having a fully sequenced genome has profound implications for the pre-breeding and molecular marker development of subterranean clover. Presently, a panel of 97 world core collection accessions and 28 elite Australian cultivars, has been extensively phenotyped and genotyped to construct a haplotype map (HapMap) which will serve as a powerful tool enabling identification of the genes and genetic variations for important economic and morphological traits.