AquaFunc Public
Integrated knowledge on functional genomics in sustainable aquaculture

Trout existing Genomics resources



Type Exist Available Tissue Description Project Biblio Producer Contact
Complete genome sequence To be planned


cGRASP http://www.cgrasp.org/whitepaper050905.pdf
William Davidson,Yann Guiguen,Caird Rexroad III
BAC library Yes

10x, Swanson clonal line, 184000 clones USDA Anim Genet. 2004 Apr;35(2):130-133 Amplicon express Yniv Palti
BAC library Yes

4.5x, OSU, 100000 clones USDA
Amplicon express Ruth Phillips,John Hansen
BAC library Yes

6.7x and 3x
Anim Genet. 2001 Aug;32(4):200-4

cDNA library Yes
testis
AGENAE BMC Genomics. 2006 Aug 3;7:196 CRB GADIE Yann Guiguen
cDNA library Yes
ovary
AGENAE BMC Genomics. 2006 Aug 3;7:196 CRB GADIE Yann Guiguen
cDNA library Yes
pooled
AGENAE BMC Genomics. 2006 Aug 3;7:196 CRB GADIE Yann Guiguen
cDNA library Yes
kidney or intestine or gill or brain or liver or spleen or skin or muscle 36 SSH libraries | 2820 contigs | used by Aquafirst STRESSGENES

Patrick Prunet
cDNA library Yes

14544 EST GENOME CANADA Genome Res. 2004 Mar;14(3):478-90
Ben Koop
cDNA library Yes

Information available through Unigene website USDA Cytogenet Genome Res. 2003;102(1-4):347-54
Caird Rexroad III
cDNA library in progress

20000 ESTs


Ben Koop
Radiation Hybrid Panel Not successfull






SNP marker Yes


AGENAE

Edwige Quillet,Francine Krieg
SNP marker Yes


USDA

Caird Rexroad III
Microsatellite marker Yes Published

AGENAE BMC Genomics 2006,7:302 INRA René Guyomard
Microsatellite marker Yes


USDA

Caird Rexroad III
AFLP marker Yes






candidate genes marker Yes Informations available from contact

USDA

Yniv Palti
candidate genes marker Yes

SNPs AQUAFIRST
INRA Edwige Quillet,Francine Krieg
candidate genes marker Yes





Roy Danzmann
candidate genes marker Yes Informations available from contact

USDA

Caird Rexroad III
candidate genes marker Yes Informations available from contact

Aquanet,APC,INRA
INRA Muriel Mambrini
Microarray gene expression Yes available from contact pangenomic membrane AGENAE
CRB GADIE Yann Guiguen
Microarray gene expression Yes available from contact stress genes 3400 oligos(3400 contigs) AQUAFIRST

Patrick Prunet
Microarray gene expression Yes available from contact

USDA

Scott Gahr
Microarray gene expression Yes available from contact pangenomic 16K Salmonid GRASP BMC Genomics. 2005 Sep 15;6:126
Ben Koop
Microarray gene expression Yes available from contact pangenomic 5000 oligos (contigs) cGRASP

Ben Koop
Microarray genotyping (SNIP) No





NULL
special genetic background Yes

Divergent line INRA Aquaculture, vol 245, Issues 1-4, 4March 2005, Pages 49-61
Edwige Quillet
special genetic background Yes

selected line INRA J Hered. 2002 Mar-Apr;93(2):91-9
Edwige Quillet
special genetic background Yes

selected line INRA

Edwige Quillet
special genetic background Yes

Reference lines INRA

Edwige Quillet
special genetic background Yes

~15 homozygous lines INRA Fish Shellfish Immunol. 2007 may; 22(5):510-9. Epub 2006 jul 31
Edwige Quillet
special genetic background Yes

Genetic monosex pop | Special YY and XX male breeders


Yann Guiguen
special genetic background Yes





Jeffrey Silverstein
special genetic background Yes





Gary Thorgaard
special genetic background Yes

Divergent line NERC Gen Comp Endocrinol. 1999 Oct;116(1):122-32
Tom Pottinger
Transgenic line Yes No
3 hemizygous lines with labelled thymus cells INRA,FAIR5
INRA Muriel Mambrini
Transgenic line Yes No
6 hemizygous and 2 homozygous lines harbouring antisense constructs INRA
INRA Muriel Mambrini,Michel Bremont









Type Exist Available Tissue Description Project Biblio Producer Contact
physical map in progress information available from contact
Finger Printing USDA

Yniv Palti
physical map in progress

BAC End Sequence INRA,GENOSCOPE
Genoscope/INRA Carine Genet
genetic, linkage map Yes

2780 cM | 31 linkage groups | 1000 markers including 300 microsats within EST AGENAE,INRA BMC Genomics 2006, 7:302 INRA Carine Genet,René Guyomard
genetic, linkage map Yes

1400 markers including 220 microsat | WSU
Genetics, 1998 Feb;148:839-50 | Anim Genet. 2003 Apr;34(2):102-15
Gary Thorgaard
genetic, linkage map Yes

400 microsat, 800 AFLP | Guelph SALMAP Genetics 2000 Jul;155(3):1331-45 | Geneome 2005 Dec;48(6):1037-51
Roy Danzmann
genetic, linkage map Yes


USDA

Caird Rexroad III
physical/genetic maps integration To be planned


cGRASP


Radiation hybrid map No


NULL


QTL detection in progress


USDA

Caird Rexroad III,Yniv Palti
QTL detection in progress


AQUAFIRST

Edwige Quillet
QTL detection in progress


INRA

Edwige Quillet
QTL detection Yes



Genetics 2007 Janv;175(1):335-47
Gary Thorgaard
QTL detection Yes



Heredity 80(1998) 143-151
Moira Ferguson,Roy Danzmann
QTL detection Yes



Mol Genet Genomics.2001 Mar;265(1):23-31
Nobuaki Okamoto
QTL detection Yes



J Hered.2003 Jul-Aug;94(4):273-84
Moira Ferguson,Roy Danzmann
QTL detection Yes



J Hered.2005 Mar-Apr;96(2):97-107
Guy Perry,Roy Danzmann









Type Exist Available Tissue Description Project Biblio Producer Contact
Bioinformatics database Yes http://www.sigenae.org/
74734 contigs and singlets(oct 2006) AGENAE
INRA Christophe Klopp
Bioinformatics database Yes http://www.ncbi.nlm.nih.gov/UniGene/lbrowse2.cgi?TAXID=8022

UNIGENE


Bioinformatics database Yes http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=r_trout
83863 contigs, ESTs and Tc(jun 2006) GENE INDEX Nucleic Acids Res. 2005 janv 1,33 (Database issue):D71-4
John Quackenbush
Bioinformatics database Yes http://www.cgrasp.org/

cGRASP

William Davidson
Bioinformatics database Yes http://web.uvic.ca/cbr/grasp/
51199 contigs and singlets (Nov. 2006) cGRASP
cGRASP Ben Koop
Bioinformatic service Yes http://www.sigenae.org/
ESTs sequence cleaning and clustering, library statistics, microarray data storage and processing AGENAE

Christophe Klopp
Bioinformatics tool Yes http://www.sigenae.org/
computer programs for comparative genomic studies AGENAE

Christophe Klopp