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 gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and 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 genome that 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 Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context 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 value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in 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 developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at 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 genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 - Meeting Abstracts - Antwerp, Belgium. 15–20 July 2017

This work was produced as part of the activities of FAPESP Research,\ud Disseminations and Innovation Center for Neuromathematics (grant\ud 2013/07699-0, S. Paulo Research Foundation). NLK is supported by a\ud FAPESP postdoctoral fellowship (grant 2016/03855-5). ACR is partially\ud supported by a CNPq fellowship (grant 306251/2014-0)

Geospatial and Temporal Semantic Analytics

The amount of digital data available to researchers and knowledge workers has grown tremendously in recent years. This is especially true in the geography domain. As the amount of data grows, problems of data relevance and information overload become more severe. The use of semantics has been proposed to combat these problems (Berners-Lee et al., 2001; Egenhofer, 2002). Semantics refer to the meaning of data rather than its syntax or structure. Systems which can understand and process data at a semantic level can achieve a higher level of automation, integration, and interoperability. Applications generally use semantic technology for three basic purposes: (1) semantic integration, (2) semantic search and contextual browsing, and (3) semantic analytics and knowledge discovery (Sheth & Ramakrishnan, 2003)

Semantic Analytics in Intelligence: Applying Semantic Association Discovery to Determine Relevance of Heterogeneous Documents

We describe an ontological approach for determining the relevance of documents based on the underlying concept of exploiting complex semantic relationships among real-world entities. This research builds upon semantic metadata extraction and annotation, practical domain-specific ontology creation, main-memory query processing, and the notion of semantic association. A prototype application illustrates the approach by supporting the identification of insider threats for document access. In this scenario, we describe how investigative assignments performed by intelligence analysts are captured into a context of investigation by including concepts and relationships from the ontology. A relevance measure for documents is computed using semantic analytics techniques. Additionally, a graph-based visualization component allows exploration of potential document access beyond the ‘need to know’. We also discuss how a commercial product using Semantic Web technology, Semagix Freedom, is used for metadata extraction when designing and populating an ontology from heterogeneous sources

Peer-to-Peer Discovery of Semantic Associations

Abstract. The Semantic Web vision promises an extension of the current Web in which all data is annotated with machine understandable metadata. The relationship-centric nature of this data has led to the definition of Semantic Associations, which are complex relationships between resources. Semantic Associations attempt to answer queries of the form “how are resource A and resource B related? ” Knowing how two entities are related is a crucial question in knowledge discovery applications. Much the same way humans collaborate and interact to form new knowledge, discovery of Semantic Associations across repositories on a peer-to-peer network can allow peers to share their local knowledge to collectively make new discoveries. In this paper we propose a method for computing Semantic Associations over distributed RDF data stores in a peer-to-peer setting. We follow a hierarchical peer / super-peer network topology, and we propose a novel query planning algorithm based on a notion of knowledgebase borders and minimum distances between borders.