An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of 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. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1491-4) contains supplementary material, which is available to authorized users.

The sustainability of agro-ecosystems depends on their ability to deliver an entire package of multiple ecosystem services, rather than provisioning services alone. New social and ecological dimensions of agricultural management must be explored in agricultural landscapes, to foster this ability. We propose a social–ecological framework for the service-based management of agro-ecosystems, specified through an explicit and symmetric representation of the ecosystem and the social system, and the dynamic links between them. It highlights how management practices, with their multiple effects, could drive the provision of multiple services. Based on this framework, we have identified the design of collective multiservice management as a key research issue. It requires innovations in stakeholder organizations and tools to foster synergy between ecosystem functioning and social dynamics, given the complexity and uncertainties of ecological systems

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