Slicing the wheat genome

This year celebrates the 100th anniversary of the birth of Norman Borlaug, the Nobel Prize-winning plant geneticist who, through his contribution to the “green revolution,” reminds us of the importance of applying scientific knowledge to develop crop varieties. This is even more important today as we face a rapidly expanding global population, climate change, and the need to keep agricultural efforts sustainable while minimizing environmental impacts. Accessing the fundamental information of crop genomes aids in accelerating breeding pipelines and improves our understanding of the molecular basis of agronomically important traits, such as yield and tolerance to abiotic and biotic stresses.

Obtaining a reference sequence of the genome of bread wheat (Triticum aestivum), the staple food for 30% of the world's population, is a scientific challenge. Wheat's hexaploid genome was formed from multiple hybridization events between three different progenitor species (comprising three individual subgenomes: A, B, and D). This resulted in a large—five times that of humans—and highly redundant genome with more than 80% of the genome consisting of repeated sequences. For these reasons, a reference sequence—a contiguous sequence ordered along the chromosomes—cannot be generated by using whole-genome shotgun sequencing approaches with current high-throughput short read technologies. To overcome this complexity, the International Wheat Genome Sequencing Consortium (IWGSC) developed a strategy of physical mapping and sequencing the individual chromosomes and chromosome arms of the bread wheat genome. In this special issue of Science, four Research Articles are presented in full online (www.sciencemag.org/extra/wheatgenome), with abstracts in print on p. 286 and a News story on p. 251. These papers present major advances toward obtaining a reference sequence and enhancing our understanding of the bread wheat genome.

The IWGSC produced a survey of the gene content and composition of all 21 chromosomes and identified 124,201 gene loci, with more than 75,000 positioned along the chromosomes. Comparing the bread wheat gene sequences with gene repertoires from its closest extant relatives (representing the species that donated the A, B, and D progenitor genomes) showed limited gene loss during the evolution of the hexaploid wheat genome but frequent gene duplications after these genomes came together. Gene expression patterns revealed that none of the subgenomes dominated gene expression.

Choulet et al. describe the sequencing, assembly, annotation, and analysis of the reference sequence of the largest wheat chromosome, 3B, which at nearly 1 gigabase is more than seven times larger than the entire sequence of the model plant Arabidopsis thaliana. Relying on a physical map derived from the chromosome 3B–specific bacterial artificial chromosome (BAC) library (1), more than 8000 BAC clones were sequenced and assembled into a pseudomolecule—a nearly complete representation of the entire chromosome. This high-quality, ordered sequence revealed a partitioning into distinct regions along the chromosome, including distal segments that are preferential targets for recombination, adaptation, and genomic plasticity. Many inter- and intrachromosomal duplications were also observed, illuminating the structural and functional redundancy of the wheat genome. This sequence, which can be anchored to the genetic and phenotypic maps, will aid breeders by increasing the pace and simplifying the process of identifying and cloning genes underlying agronomic traits.

Marcussen et al. used the IWGSC chromosome survey sequences to analyze the timing and phylogenetic origin of the diploid genomes that have come together to form the A, B, and D subgenomes of bread wheat. They unravel ancient hybridization events in the wheat lineage and reveal that the ancestral A and B genomes diverged from a common ancestor ∼7 million years ago. They also show that the D genome was formed through homoploid hybrid speciation—hybridization that does not result in a genome duplication event—between relatives of the A and B genomes 1 million to 2 million years later.

Pfeifer et al. address inter- and intragenomic gene expression regulation within a polyploid genome by providing an in-depth analysis of the transcriptional landscape of the developing wheat grain. They show that the transcriptional network delineates a complex and highly orchestrated interplay of the individual wheat subgenomes and identify transcriptional active or inactive domains along the chromosomes that might indicate epigenetic control of grain development.

Together, these Research Articles explore multiple dimensions of the 17-gigabase wheat genome and pave the way toward achieving a full reference sequence to underpin wheat research and breeding.