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

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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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    ABSTRACT: Abstract The widespread availability of nano-enabled products in the global market may lead to the release of a substantial amount of engineered nanoparticles in the environment, which frequently display drastically different physiochemical properties than their bulk counterparts. The purpose of the study was to evaluate the impact of citrate-stabilised silver nanoparticles (AgNPs) on the plant Arabidopsis thaliana at three levels, physiological phytotoxicity, cellular accumulation and subcellular transport of AgNPs. The monodisperse AgNPs of three different sizes (20, 40 and 80 nm) aggregated into much larger sizes after mixing with quarter-strength Hoagland solution and became polydisperse. Immersion in AgNP suspension inhibited seedling root elongation and demonstrated a linear dose-response relationship within the tested concentration range. The phytotoxic effect of AgNPs could not be fully explained by the released silver ions. Plants exposed to AgNP suspensions bioaccumulated higher silver content than plants exposed to AgNO(3) solutions (Ag(+) representative), indicating AgNP uptake by plants. AgNP toxicity was size and concentration dependent. AgNPs accumulated progressively in this sequence: border cells, root cap, columella and columella initials. AgNPs were apoplastically transported in the cell wall and found aggregated at plasmodesmata. In all the three levels studied, AgNP impacts differed from equivalent dosages of AgNO(3).
    Nanotoxicology 01/2012; 7(3). DOI:10.3109/17435390.2012.658094 · 7.34 Impact Factor
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    • "In 2010, the soybean genome was sequenced and assembled by the Soybean Genome Sequencing Consortium in the USA (Schmutz et al. 2010). The genome data are available via databases, phytozome ( and Soybase (Grant et al. 2010) ( Other soybean genomes were sequenced by a next generation sequencer (Kim et al. 2010, Lam et al. 2010). "
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    ABSTRACT: Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and genome sequencing are the most effective approaches towards understanding the structure and function of the soybean genome. We constructed bacterial artificial chromosome (BAC) libraries from the Japanese soybean cultivar, Enrei. The end-sequences of approximately 100,000 BAC clones were analyzed and used for construction of a BAC-based physical map of the genome. BLAST analysis between Enrei BAC-end sequences and the Williams82 genome was carried out to increase the saturation of the map. This physical map will be used to characterize the genome structure of Japanese soybean cultivars, to develop methods for the isolation of agronomically important genes and to facilitate comparative soybean genome research. The current status of physical mapping of the soybean genome and construction of database are presented.
    Breeding Science 01/2012; 61(5):661-4. DOI:10.1270/jsbbs.61.661 · 1.34 Impact Factor
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    • "The soybean SSR markers used in this study were developed by the Beltsville Agricultural Research Center (Cregan et al. 1999; Song et al. 2004). Primer sequence information for all SSR markers is available at the SoyBase website (Grant et al. 2010). The EST-SSR marker used in this study was developed by Hwang et al. (2009). "
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    ABSTRACT: Asian rust, caused by the fungus Phakopsora pachyrhizi, is the most severe disease currently threatening soybean crops in Brazil. The development of resistant cultivars is a top priority. Genetic characterization of resistance genes is important for estimating the improvement when these genes are introduced into soybean plants and for planning breeding strategies against this disease. Here, we infected an F2 population of 140 plants derived from a cross between ‘An-76’, a line carrying two resistance genes (Rpp2 and Rpp4), and ‘Kinoshita’, a cultivar carrying Rpp5, with a Brazilian rust population. We scored six characters of rust resistance (lesion color [LC], frequency of lesions having uredinia [%LU], number of uredinia per lesion [NoU], frequency of open uredinia [%OU], sporulation level [SL], and incubation period [IP]) to identify the genetic contributions of the three genes to these characters. Furthermore, we selected genotypes carrying these three loci in homozygosis by marker-assisted selection and evaluated their genetic effect in comparison with their ancestors, An-76, PI230970, PI459025, Kinoshita and BRS184. All three genes contributed to the phenotypes of these characters in F2 population and when pyramided, they significantly contributed to increase the resistance in comparison to their ancestors. Rpp2, previously reported as being defeated by the same rust population, showed a large contribution to resistance, and its resistance allele seemed to be recessive. Rpp5 had the largest contribution among the three genes, especially to SL and NoU. Only Rpp5 showed a significant contribution to LC. No QTLs for IP were detected in the regions of the three genes. We consider that these genes could contribute differently to resistance to soybean rust, and that genetic background plays an important role in Rpp2 activity. All three loci together worked additively to increase resistance when they were pyramided in a single genotype indicating that the pyramiding strategy is one good breeding strategy to increase soybean rust resistance. KeywordsAsian rust– Phakopsora pachyrhizi –Resistance genes–Composite interval mapping
    Euphytica 11/2011; 182(1):53-64. DOI:10.1007/s10681-011-0465-3 · 1.69 Impact Factor
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