Project Summaries

11-109  Project Manager: D. C. Jones

COTTONGEN DATABASE DEVELOPMENT AND MAINTENANCE

Doreen Main, Washington State University

CottonGen is a comprehensive database that will benefit all cotton researchers and ultimately growers across the 17 states where cotton is grown.  Highlighted below is the progress to date in the initial start-up and development of CottonGen.

CottonGen v0.9 released and presented at ICGI 2012.

New data added to GBrowse:
The Chinese BGI D-genome sequence assembly v1.0 and annotations
The Chinese BGI D-genome sequence annotations
CottonGen unigene v1.0 aligned to the BGI D-genome
PlantGDB unigenes aligned to the BGI D-genome
J. Udall 2012 Unigene contigs aligned to the BGI D-genome
NCBI cotton dbest sequences aligned to the BGI D-genome
Cacao theobroma v0.9 proteins aligned to the BGI D-genome
Arabidopsis thaliana TAIR10 proteins aligned to the BGI D-genome
CottonGen markers aligned to the BGI D-genome

New data added to both NCBI and Batch BLAST servers:
The Chinese BGI D-genome 13 chromosomes and 4434 scaffolds sequences
The Chinese BGI D-genome 40976 CDS sequences
The Chinese BGI D-genome 40976 protein sequences
GenBank cotton dbSNP 39862 sequences
CottonGen 3451 RFLP marker sequences
CottonGen 1278 SNP marker sequences
CottonGen 12330 SSR marker sequences

New data added to CMap:
TM-1 x Hai-7124, BC1 (2012)
CIRAD High Density Consensus (2012)

New or corrected data have been made ready in templates for loading to chado:
736 CICR EST-SSR markers with marker source data
3414 loci and 3047 markers of TM-1 x Hai-7124, BC1 (2012)
8253 loci and 6617 markers of CIRAD High Density Consensus (2012)
27633 Sample_ID information from Du_2005 dataset added into genotype sheet
16 new and 362 corrections for stock_id_in_collection sheet
Corrections of species for map sheet
22 image files of 2 accessions from USDA-ARS germplasm characterization Project
52 trait scores of 2 accessions from USDA-ARS germplasm characterization Project

New web pages developed:
Search Overview page
Marker individual details page (http://dev.cottongen.org/node/6624)
Polymorphism individual details page (http://dev.cottongen.org/polymorphism/5876)
Germplasm individual details page (http://dev.cottongen.org/node/61126)
Species individual details page (http://dev.cottongen.org/node/503)
Downloads page (http://dev.cottongen.org/node/458237)
Data Contributors page (http://dev.cottongen.org/node/458238)

ICGI website
Cleaned up ICGI 2012 site after conference completed.
Released 2012 ICGI Research Conference Proceedings at http://www.cottongen.org/ejournal/current/1.

CottonGen for upcoming research conferences:
CottonGen oral presentation request for PAG 2012 ICGI Workshop has been accepted.
CottonGen abstract prepared, submitted and has been accepted as oral presentation at Beltwide 2013 conference.
CottonGen abstract prepared, submitted and has been accepted as computer demo at PAG 2013.

Work in Progress

Organizing next steering committee meeting
Preparing presentation for Beltwide conference in 2013
Preparing presentations for PAG 2013 ICGI Workshop
Preparing presentation for PAG 2013 Computer Demo Program
Preparing poster presentation for PAG 2013
Preparing CottonGen flyers for PAG 2012 Plant Genome Databases Booth
Adding in missing marker information (source sequences, species, germplasm, library, etc.).
Completing upload of germplasm passport data, QTL data, and germplasm evaluation data from China and US.
Continue to develop details pages for individual data.
Continue to develop search pages
Working on advanced searches
Set up templates for users to submit data

 

Project Year: 2012
 

Search 2012 Projects:


STATE PROGRAM
▸ Alabama
▸ Arizona
▸ Arkansas
▸ California
▸ Florida
▸ Georgia
▸ Louisiana
▸ Mississippi
▸ Missouri
▸ New Mexico
▸ North Carolina
▸ Oklahoma
▸ South Carolina
▸ Tennessee
▸ Texas
▸ Virginia

CORE PROGRAM
▸ Cotton Incorporated Fellow
▸ Cottonseed
▸ Crop Improvement
▸ Farm-to-Mill
▸ Production Efficiency
▸ Sustainable Cotton
▸ Variety Improvement

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