Article

SoyBase, the USDA-ARS soybean genetics and genomics database

USDA-ARS-CICGRU, Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
Nucleic Acids Research (Impact Factor: 9.11). 12/2009; 38(Database issue):D843-6. DOI: 10.1093/nar/gkp798
Source: PubMed

ABSTRACT

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics
and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated
with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of
more than 90 unique traits. SoyBase also contains the well-annotated ‘Williams 82’ genomic sequence and associated data mining
tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively
interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols,
soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development
and trait terms, which are also linked to the more general plant ontologies. SoyBase can be accessed at http://soybase.org.

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    • "In addition, most of the research findings from Arabidopsis can be applied to crop plant species, which either have much larger genome sizes, such as soybean (1000 Mb) (Grant et al. 2010; Shultz et al. 2006) and maize (2500 Mb) (Schnable et al. 2009), or have no genomic information, such as zucchini and cucumber. Moreover, the developmental stages, vegetative and reproductive, in the life cycle of Arabidopsis are well defined and quantitatively characterised (SI. Figure 1 for example) (Boyes et al. 2001; Kjemtrup et al. 2003). "
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    • "Transposable element annotation was obtained from SoyBase (http://www.soybase.org; Grant et al. 2010). Conserved domain annotation was obtained from the NCBI Conserved Domain Database (CDD; version 3.14; http:// www.ncbi.nlm.nih.gov/cdd/; "
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    ABSTRACT: Key message: Discovery of new germplasm sources and identification of haplotypes for the durable Soybean mosaic virus resistance gene, Rsv 4, provide novel resources for map-based cloning and genetic improvement efforts in soybean. The Soybean mosaic virus (SMV) resistance locus Rsv4 is of interest because it provides a durable type of resistance in soybean [Glycine max (L.) Merr.]. To better understand its molecular basis, we used a population of 309 BC3F2 individuals to fine-map Rsv4 to a ~120 kb interval and leveraged this genetic information in a second study to identify accessions 'Haman' and 'Ilpumgeomjeong' as new sources of Rsv4. These two accessions along with three other Rsv4 and 14 rsv4 accessions were used to examine the patterns of nucleotide diversity at the Rsv4 region based on high-depth resequencing data. Through a targeted association analysis of these 19 accessions within the ~120 kb interval, a cluster of four intergenic single-nucleotide polymorphisms (SNPs) was found to perfectly associate with SMV resistance. Interestingly, this ~120 kb interval did not contain any genes similar to previously characterized dominant disease resistance genes. Therefore, a haplotype analysis was used to further resolve the association signal to a ~94 kb region, which also resulted in the identification of at least two Rsv4 haplotypes. A haplotype phylogenetic analysis of this region suggests that the Rsv4 locus in G. max is recently introgressed from G. soja. This integrated study provides a strong foundation for efforts focused on the cloning of this durable virus resistance gene and marker-assisted selection of Rsv4-mediated SMV resistance in soybean breeding programs.
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    • "Transcripts for 152 annotated WRKY genes were detected on SoyBase EST database (http://soybase.org/) and/or on five global expression experiments: SuperSAGE of soybean leaves 12, 24 and 48 hours after inoculation (hai) of P. pachyrhizi [46], RNA-Seq of microdissected lesions 10 days after inoculation of P. pachyrhizi, two different microarrays of leaves 12 and 120 hai of P. pachyrhizi (available in the current literature) and RNA-Seq expression data of healthy plants in different developmental stages [47], available at SoyBase [48]. The GmWRKY genes were distributed over the 20 soybean chromosomes with protein sequences ranging from 121 to 1,356 amino acids in length (Table 1 and Additional file 1). "
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