The big wheat genome in the big data era

Wheat is one of the most important crops worldwide, providing food for ~30% of the world population. While significant advances have been made since the Green Revolution, today’s agriculture is facing unprecedented challenges: to keep pace with the growing human demand in an environmentally and socially sustainable manner and in a context of climate change. It has long been argued that a better knowledge of the wheat genome should help to face this challenge. However, because of its size, allohexaploid nature, and high repeat content, the wheat genome has long been perceived as too complex for molecular studies. The advent of high-throughput genotyping and sequencing technologies have opened new perspectives and led to a paradigm change. As a result, the International Wheat Genome Sequencing Consortium (IWGSC) has recently achieved a high-quality reference sequence of the wheat genome that has been analyzed in details through the integration of several genomics data. These analyses revealed the wheat genome peculiarities, such as an uneven distribution of recombination events, a strong structural and functional partitioning, a higher proportion of non-syntenic and duplicated genes compared to other crops, a correlation between gene and genome structure and expression as well as the existence of chromosomal domains enriched in co-expressed genes. These characteristics are the result of wheat evolution. However, compared to wild species, wheat has a complex history of evolution that also includes domestication and breeding. Results on the wheat genome structure, function and evolution will be presented, together with examples illustrating the intricate links between the wheat genome organization and wheat breeding, and showing how one can impact the other.