Shifting the limits in wheat research and breeding using a fully annotated reference genome

INTRODUCTION Wheat ( Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. RATIONALE Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gainas well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genomesequence, including regulatory sequencesand genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genomethat is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat GenomeSequencing Consortium set out to deliver a high-quality annotated reference genomesequence of bread wheat. RESULTS An annotated reference sequence representing the hexaploid bread wheat genomein the form of 21 chromosome-like sequence assemblieshas now been delivered, giving access to 107,891 high-confidence genes, including their genomiccontext of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future valueof the annotated assembly for molecular breedingand research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locusconferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editingof the flowering-time trait. CONCLUSION This annotated reference sequence of wheat is a resource that can now drive disruptive innovationin wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developedfor model-organism genomeswill facilitate a better understanding of the wheat genomeas a result of the high-quality chromosome-based genomeassembly. By necessity, breeders work with the genomeat the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genomesequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomesfor breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing.