Physical map and shotgun sequence of the Aegilops tauschii genome

Aegilops tauschii is the diploid source of the wheat D genome and an important wheat genetic, genomic, and breeding resource. A shotgun sequence of Ae. tauschii accession AL8/78 was generated with Roche 454, Illumina, and SOliD sequencing platforms and gene sequences are  being assembled. A total of 598,872 BAC clones in nine BAC libraries were fingerprinted with the SNaPshot method and assembled into 3,516 contigs. A high-density genetic map of the Ae. tauschii genome was constructed for anchoring of the contigs. SNPs needed for the construction of the genetic map were discovered with the AGSNP pipeline we had developed. A total of 195,631 gene-based SNPs between the parents of the mapping population (AL8/78 and AS75) were discovered. A 10K Infinium (Illumina) SNP assay was designed and used to genotype an Ae. tauschii mapping population consisting of 1102 F₂ plants. A comparative Ae. tauschii genetic map containing 7,186 loci was constructed and synteny with the rice, B. distachyon, and sorghum pseudomolecules was assessed. Numerous inversion and translocation differences among the compared genomes were detected, most of them in the Ae. tauschii genome. Five-dimensional BAC pools were constructed, genotyped with the 10K Infinium, positive BAC clones were identified with the FPCbrowser software we developed, and BAC contigs were anchored on the genetic map. Contigs equivalent to 78% of the Ae. tauschii genome have been anchored to date. The genetic map was also used for anchoring the Ae. tauschii genome zipper.