Bread wheat (Triticum aestivum) accounts for 20% of the calories consumed by the entire world and is one of the Big Three globally important crops, along with rice and corn.
A few months after we got barley deciphered, an international effort has completed the technically daunting task of sequencing the bread wheat genome - its constituent number of paired DNA bases, or nucleotides, totals 17,000,000,000 base-pairs (17 Gb), about five times the amount of DNA in the human genome, and it is a hexaploid genome, which means it has six copies of each of its seven chromosomes, the complete set numbering 42 chromosomes. The human genome is diploid, with 23 pairs of chromosomes and a total of 46 chromosomes.
Up to 80% of the bread wheat genome consists of repetitive sequences and because of the way genomes are usually sequenced – by stitching together hundreds of millions or billions of tiny fractions of a full genome -- the bread wheat genome's size makes it very hard to determine which part of the genome any particular sequence readout has come from, and whether it is a unique or repeat sequence. By comparison, the barley genome revealed in October was about one third the size.
That complexity required "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.
The potential payoff is huge: developing new strategies for breeding and improving wheat crops.
"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 Professor W. Richard McCombie
of Cold Spring Harbor Laboratory about the approach, "and we wanted to do it using an agriculturally important crop."
Sequencing the diploid ancestors of wheat enabled the international 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 because the study revealed the evolution of bread wheat from ancestral strains through to its current domesticated form.
The ancient origins of bread wheat
Even the most fervent organic food proponent is not eating the wheat our ancestors did. Bread wheat came about from genetic modification combining 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.
The investigators identified 94,000 to 96,000 genes and 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 single-nucleotide polymorphisms (SNPs, pronounced "snips" for the 5 non-biologists who have read this far and didn't know how to pronounce it) – positions along the full genome where a single unit, or "letter," of DNA varied from the sequence of closely related plants.
The bread wheat genome has undergone rapid and significant changes, including loss of gene family members during the time it was being domesticated. Bread wheat moved from having two sets of chromosomes to multiples of that number -- the 6 sets seen today. This chromosomal multiplication is deemed desirable, as selecting for them is a way to overcome the sterility that occurs when breeding hybrid crops.
The investigators also found many expanded gene families within the bread wheat genome. The majority of these are associated with crop productivity and include ones involved in defense, nutritional content, energy harvesting, metabolism, and growth.
Current breeding practices and knowledge have been exploited to the point that yield increases have slowed. The sequencing and analysis in this study provides a framework with which this crop can now be improved.
"While we and our collaborators continue to work to enhance the resolution of our knowledge of the wheat genome, these results should have an significant impact on breeding efforts and further research studies of the wheat genomes and its those of its wild relatives," said McCombie, summing up the project's technical and biological impact.