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PMID: 25428362 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.

Nucleic acids research ·Vol. 43 ·No. Database issue ·2015-01-00 ·Pages D1036-41

Fernandez-Pozo N, Menda N, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA

Abstract

The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana. The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases.

MeSH Terms
Breeding Crosses, Genetic Databases, Nucleic Acid Genome, Plant Genomics Genotype Internet Phenotype Solanaceae/genetics,metabolism
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Fernandez-Pozo Noe
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Menda Naama
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Edwards Jeremy D
Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
Saha Surya
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA.
Tecle Isaak Y
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Strickler Susan R
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Bombarely Aureliano
Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA.
Fisher-York Thomas
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Pujar Anuradha
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Foerster Hartmut
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Yan Aimin
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
Mueller Lukas A
Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA lam87@cornell.edu.
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gku1195
Email
lam87@cornell.edu
Published
2015-01-00
Epub
2014-00-26
Pages
D1036-41
Language
English
Region
England
NLM ID
0411011
PMCID
PMC4383978
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gku1195 PMC Full Text View journal details
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