Help on Database Terminology


Contig Nomenclature:
The contig assemblies are numbered after the Harvest Barley Assembly #21 consensi they are derived from. The prefix 'ABC' stands for Affymetrix Barley Contig. The HarvEST Barley database created by Steve Wanamaker and Timothy Close (University of California, Riverside) is available from http://harvest.ucr.edu.


Mutation Nomenclature:
The polymorphisms are named after the Affymetrix Barley Contig they are derived from, plus a version number, plus their position within the consensus sequence produced by Consed. The prefix 'scsnp' denotes the Scottish Crop Research Institute as the source of the data, plus "snp" as the type of polymorphism.


Primer Nomenclature:
Primers are stored in terms of a primer pair ID, describing the left and right hand primers designed to the original Harvest Barley Assembly #21 consensus sequence. The primer pairs and primers are again numbered after the contig they were designed from.


Subcontig ID:
Some of the Consed assemblies were split into two (or more) parts during the contigging process, therefore the database stores these "subcontigs" as separate items, each with their own subcontig ID number.


Consed Contig Consensus:
Please note that the consensi produced by Consed represent the best quality base calls at each sequence position, rather than the most common base that appears at each position.


Mutation Location on Consensus:
The positions in the Consed consensus do not include gaps that may appear in the consensus.




Project Outline


Choice of Candidate Genes:
The genes investigated in the project were chosen from the Harvest Barley Assembly #21. These contigs were selected for homology to known abiotic stress response genes in other plant species. Other candidate genes were identified from gene expression experiments using the Barley1 GeneChip. In total a list of 3370 candidate genes was created.


Choice of Barley Genotypes:
Fragments of the genes in the candidate list were sequenced from parents of the three major mapping populations (Oregon Wolfe Barley Dominant, Oregon Wolfe Barley Recessive, Steptoe, Morex, Lina and Hordeum vulgare ssp. sponaneum (HS92). To make the project more relevant to barley breeding, a subset of the genes were sequenced in a wider selection of cultivated barley germplasm.


Mutation Detection and Confirmation:
DNA sequences generated from the chosen barley genotypes were analysed using Mutation Surveyor Software, and latterly with Consed/Polyphred. Both of these programs detect polymorphisms for each candidate contig using aligned DNA sequences from the different genotypes. Mutations were then confirmed by manual inspection of chromatograms.


Polymorphism Database:
The polymorphism and alignment data from Mutation Surveyor and Consed/Polyphred was extracted using custom Perl5 scripts and input into a mySQL database. The web interface to the database was also written in Perl5/CGI.