Gramene: A Resource for Comparative Grass Genomics
The rice genome is more than a resource for understanding the biology of a single species. It is a window into the structure and function of genes in other crop grasses as well. Using rice as the sequenced reference genome, researchers can identify and understand the relationships among genes, pathways and phenotypes in a wide range of grass species.Extensive work over the past two decades has shown remarkably consistent conservation of gene order within large segments of linkage groups in rice, maize, sorghum, barley, wheat, rye, sugarcane and other agriculturally important grasses. A substantial body of data supports the notion that the rice genome is substantially colinear at both large and short scales with other crop grasses, opening the possibility of using rice synteny relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum. As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the rice genome and leverage the rice genomic sequence for identifying and understanding corresponding genes, pathways and phenotypes in other crop grasses. This is achieved by building automated and curated relationships between rice and other cereals for both sequence and biology. The automated and curated relationships are queried and displayed using controlled vocabularies and web-based displays. The controlled vocabularies (Ontologies), currently being utilized include Gene ontology, Plant ontology, Trait ontology, Environment ontology and Gramene Taxonomy ontology. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database.
Specific Aims:
“What are the functionally shared elements of plant genomes and how does diversity in these elements relate to agronomically valuable traits?”
Three research aims of the project are designed to answer this question: (1) Using comparative genomics to identify functional elements and sequence variants that may have phenotypic consequences; (2) Annotating biological pathways in order to provide the infrastructure to understand how those sequence variants lead to phenotypes; (3) Collecting and uniformly reanalyzing QTL and diversity data in order to connect genetic diversity to phenotypic variation. These three aims form a tripod which cannot stand up if any leg is removed. The comparative maps and genome builds are essential to allow for the transfer of information from one species to the next, for the integration of QTL and diversity data, and for the dissemination of the third party functional data sets listed in specific aim 1. The pathway collection and annotation of specific aim 2 is essential for the biological interpretation of QTL and diversity data. The collection, integration and reanalysis of QTL and diversity data is necessary to identify the relationship between genotypic and phenotypic variation.
Deliverables for Aim 1 (Dr. Ware):
- Comparative genetic, physical and sequence maps of /O. sativa/ and 11 wild /Oryza/ species (/alta, rufipogon, glaberrima, nivara, minuta, officinalis, australiensis, brachyantha, granulata, ridleyi, coarcta/), /Z. mays, S. bicolor/, and /Arabidopsis./
- Nucleotide-level genome annotation views of these species, including the functional consequence of SNPs, using Ensembl framework.
- Physical (contig) map views of these species, using Ensembl framework.
- Protein comparisons among these species.
- Detailed gene and protein level views of the annotations of these species.
- Incorporation of roughly 9 functional genomics data sets in various species generated by NSF and USDA-funded groups listed in the main text.
- Whole genome alignments of rice, maize, sorghum, /brachypodium,/ poplar and /arabidopsis/, refreshed annually.
- Twice-yearly releases via web browser, FTP bulk downloads, GrameneMart data warehouse queries, DAS and SSWAP.
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