Jeffrey Detras
A5070120654- Rice Cultivation and Yield Improvement
- GABA and Rice Research
- Agriculture, Soil, Plant Science
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Research Data Management Practices
- Biomedical Text Mining and Ontologies
- Semantic Web and Ontologies
- Distributed and Parallel Computing Systems
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Genetic diversity and population structure
- Plant Pathogenic Bacteria Studies
- Service-Oriented Architecture and Web Services
- Livestock and Poultry Management
International Rice Research Institute
2008-2020
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with five major groups previously recognized, but also suggest several unreported subpopulations that correlate geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 small indels over 90,000 structural variations contribute to within- between-population variation....
Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture agrifood systems requires quality labeling or annotation in order to be interoperable. As recommended the FAIR principles, data, labels, metadata must use controlled vocabularies ontologies that are popular knowledge domain commonly used community. Despite existence of robust Life Sciences, there is currently no comprehensive full set for across agricultural disciplines. In this paper, we discuss...
A range of resistance loci against different races Xanthomonas oryzae pv. (Xoo), the pathogen causing bacterial blight (BB) disease rice, have been discovered and characterized. Several deployed in modern varieties, however, due to rapid evolution Xoo, a number already become ineffective. The continuous "arms race" between Xoo rice makes it imperative discover new enable durable deployment multiple genes breeding lines. Rice diversity panels can be exploited as reservoirs useful genetic...
The 3000 Rice Genomes Project generated a large dataset of genomic variation to the world's most important crop, Oryza sativa L. Using Burrows-Wheeler Aligner (BWA) and Genome Analysis Toolkit (GATK) variant calling on this dataset, we identified ∼40 M single-nucleotide polymorphisms (SNPs). Five reference genomes rice representing major variety groups were used: Nipponbare (temperate japonica), IR 64 (indica), 93–11 DJ 123 (aus), Kasalath (aus). results are accessible through SNP-Seek...
The Generation Challenge programme (GCP) is a global crop research consortium directed toward improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key activity development GCP bioinformatics platform support research. This includes following: (i) shared, public platform-independent domain models, ontology, data formats enable interoperability analysis flows within platform; (ii) web service registry technologies identify,...
Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture agrifood systems requires quality labelling to be interoperable. As recommended the FAIR principles, data, labels metadata must use controlled vocabularies ontologies that are popular in knowledge domain commonly used community. Despite existence of robust Life Sciences, there is currently no agreed full set for annotation across agricultural disciplines, which may span genetics, environment,...