To meet the challenge they used "next-generation" sequencing techniques, in which the DNA is broken up randomly into numerous small segments and assembled into longer sequence reads by identifying the overlapping ends. The sequence "reads" generated for bread wheat were then compared to those from the known sequences of a diverse range of grasses, including rice and barley.
"We wanted to know whether we could use next-gen' sequencing on large complex genomes in what was almost a worst-case scenario for challenging the technology," said McCombie about his approach, "and we wanted to do it using an agriculturally important crop."
Sequencing the diploid ancestors of wheat, some of which was done in the McCombie lab, enabled the team to computationally dissect out which sequences were gene copies and which were repeats. This data was then used to further the understanding of the hexaploid ancestral genome and the temporal relationship between it and the diploid ancestor.
Ancient origins, evolution, and the future of bread wheat agriculture
Originally formed during the spread of agriculture among settled societies, bread wheat came about from the hybridization between cultivated wheat (T. dicoccoides) and goat grass (Aegilops tauschii) about 8,000 years ago. One aim of the sequencing project was to learn from the genome's current features how bread wheat has evolved since its domestication.
In this effort the investigators identified 94,000 to 96,000 genes. They also noted an abundance of gene fragments -- ancestral genes that had been chopped up during the cross-breeding process used by farmers over the centuries.
In addition they were able to assemble a catalog of 132,000 SNPs (single-nucleotide polymorphisms, or "snips") positions along the full genome where a single unit, or "letter," of DNA varied from the sequence of closely related plants.
|Contact: Edward Brydon Ph.D.|
Cold Spring Harbor Laboratory