About Breedbase
The Breedbase system has evolved from the Sol Genomics Network (SGN) and Cassavabase and related sites (see RTBbase.org).
Breedbase is striving to be a complete breeding management system, including field management, data collection, crossing utilities, and advanced trial analysis.
Please refer to the Breedbase manual for detailed information about available features.
Lab members |
Staff |
Interns |
Emeritus Staff |
Bioinformatics Analysts
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Interns
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Selected Publications |
- 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. The Sol Genomics Network (SGN)âfrom genotype to phenotype to breeding. (2015) Nucleic Acids Res. Volume 43 (Database issue):D1036-41.
- Fernandez-Pozo N, Rosli H.G., Martin G.B., Mueller L.A. The SGN VIGS Tool: User-Friendly Software to Design Virus-Induced Gene Silencing (VIGS) Constructs for Functional Genomics (2015) Molecular Plant, Volume 8, Issue 3, 486-488
- The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution (2012) Nature 485, 635-641.
- Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S, Fischer-York T, Pujar A, Leto J, Gosselin J, Mueller LA (2010). The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucl. Acids Res. Oct 08, 2010. doi: 10.1093/nar/gkq866.
- Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA (2010). solQTL: A Tool for QTL analysis, Visualization and Linking to Genomes at SGN Database. BMC Bioinformatics 2010, 11:525.
- Mueller LA, et al., (2009). A snapshot of the emerging tomato genome sequence. Plant Gen. March 2009 2:78-92; doi:10.3835/plantgenome2008.08.0005.
- Menda N, Buels RM, Tecle I, Mueller LA (2008). A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol. 2008 Aug;147(4):1788-99 (PMID: 18539779).
- Mueller LA, Mills AA, Skwarecki B, Buels RM, Menda N, Tanksley SD (2008). The SGN comparative map viewer. Bioinformatics. 2008 Feb 1;24(3):422-3.
- Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD (2005). The Sol Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond. Plant Physiol 138(3):1310-7.
- Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006). Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics. 2006 Nov;174(3):1407-20.
- Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Petiard V, Tanksley SD (2005). Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet. 2005 Dec;112(1):114-30.
Funding |
SGN gratefully acknowledges funding from the following funding sources:
National Science Foundation (USA)
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USDA
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Nestle Corporation
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BARD
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Acknowledgments |
Special thanks to the Cornell Biological Services Unit for making their compute clusters available for some of our analyses.
Some data on SGN was obtained from EU-SOL projects. Special thanks to our colleagues at EU-SOL.