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

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.

MYB107 and MYB9 Homologs Regulate Suberin Deposition in Angiosperms

“…Data were acquired for the various species from the following databases, making use of the gene IDs curated by these databases: SOL Genomics Network database (Fernandez-Pozo et al, 2015), Grape Genome Database (Vitulo et al, 2014), Spud DB (Hirsch et al, 2014), The Arabidopsis Information Resource (Lamesch et al, 2012), Rice Genome Annotation Project (Kawahara et al, 2013), and Genome Database for Rosaceae (Jung et al, 2014). Orthology between species was determined via alignment of relevant protein sequences with the ortholog database from the PLAZA Comparative Genomics Platform (Proost et al, 2015).…”

“…Library preparation was performed according to previously described methods (Zhong et al, 2011) and samples run on the Illumina HiSeq 2000 under default parameters generating 50-bp single end reads. Reads were mapped to either the apple (Malus x domestica; Jung et al, 2014), tomato (Fernandez-Pozo et al, 2015), or Arabidopsis (Lamesch et al, 2012) predicted transcriptome according to methods described previously (Itkin et al, 2013), generating normalized RPKM values for each gene.…”

In-Silico Identification of Novel Resistant Genes for Fungal Pathogen Fusarium oxysporum f. sp. cubense Race 4: Causative Agent of Banana Vascular Wilt Disease

“…The protein sequences of resistant I, and I-2 genes were retrieved through UniprotKb and I-1 and I-3 were retrieved through Sol Genomics Network database [23].…”

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

“…The remaining clones are also evaluated in clonal evaluation yield trials for variety development as well as for re-training the GS prediction model. Cassavabase (www.cassavabase.org): A bioinformatics infrastructure that integrates phenotypic data from field trials, genotypic data, as well as statistical tools in a single, user-friendly, web-based, and reliable database [130]. Breeders can use the intuitive web-based interphase to calculate genomic-estimated breeding values (GEBVs) of individuals by selecting a training population for modeling and estimating genomic-estimated breeding values of selection candidates (http://cassavabase.org/solgs).…”

“…Table 2 provides a partial list of deployed or planned breedingrelevant technology and tools currently in use. The Kazusa marker database [150] features genomics and genetics information for 10 plant species, whereas SolGenomics is a portal for several solanaceous plant species [130]. These and other breeders' toolboxes such as Soybase and MaizeGDB can serve as a starting point for comparative analysis of orphan crops with limited genomic resources.…”