Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

Joshi, Trupti; Patil, Kapil; Fitzpatrick, Michael R.; Franklin, L. D.; Yao, Qiuming; Cook, Jacob; Wang, Zheng; Libault, Marc; Brechenmacher, Laurent; Valliyodan, Babu; Wu, Xiaolei; Cheng, Jianlin; Stacey, Gary; Nguyen, Henry T.; Xu, Dong

doi:10.1186/1471-2164-13-s1-s15

Cited by 97 publications

(80 citation statements)

References 28 publications

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“…The 425 genes unique to G. max were further analysed to look for overlap with transcription factor predictions from SoyDB [13], functional annotations and the different pathways available in SoyKB [9]. Out of the 425 unique genes, 313 have Pfam domain annotations and 132 can be mapped to various pathways.…”

Section: Methodsmentioning

confidence: 99%

“…We have also developed graphical tools to simplify the analysis of QTLs and traits, and overlay insertion and deletion regions of one over the other to highlight the genomic differences. This graphical chromosome visualizer is part of Breeding Program tools in SoyKB [9] web resources and provides extensive analysis and visualization capacity with genomics variation data such as SNPs, GWAS, insertions and deletions being overlaid on different QTL regions from multiple traits.…”

Section: Introductionmentioning

confidence: 99%

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Genomic differences between cultivated soybean, G. max and its wild relative G. soja

Joshi

Valliyodan

Wu³

et al. 2013

BMC Genomics

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BackgroundGlycine max is an economically important crop and many different varieties of soybean exist around the world. The first draft sequences and gene models of G. max (domesticated soybean) as well as G. soja (wild soybean), both became available in 2010. This opened the door for comprehensive comparative genomics studies between the two varieties.ResultsWe have further analysed the sequences and identified the 425 genes that are unique to G. max and unavailable in G. soja. We further studied the genes with significant number of non-synonymous SNPs in their upstream regions. 12 genes involved in seed development, 3 in oil and 6 in protein concentration are unique to G. max. A significant number of unique genes are seen to overlap with the QTL regions of the three traits including seed, oil and protein. We have also developed a graphical chromosome visualizer as part of the Soybean Knowledge Base (SoyKB) tools for molecular breeding, which was used in the analysis and visualization of overlapping QTL regions for multiple traits with the deletions and SNPs in G. soja.ConclusionsThe comparisons between genome sequences of G. max and G. soja show significant differences between the genomic compositions of the two. The differences also highlight the phenotypic differences between the two in terms of seed development, oil and protein traits. These significant results have been integrated into the SoyKB resource and are publicly available for users to browse at http://soykb.org/GSoja.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic differences between cultivated soybean, G. max and its wild relative G. soja

Joshi

Valliyodan

Wu³

et al. 2013

BMC Genomics

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“…Websites such as SoyBase (Cannon et al 2012), SoyKB (Joshi et al 2012), and Phytozome (Goodstein et al 2011) allow users to access data by sequence, gene names, markers and traits of interest, expression patterns, or homology to known genes in other species. For a full description of these databases, we refer readers to the corresponding publications and websites.…”

Section: Genome-based Resources For Soybean Improvementmentioning

confidence: 99%

Soybean Functional Genomics: Bridging the Genotype-to-Phenotype Gap

O’Rourke

Graham

Whitham

2017

Compendium of Plant Genomes

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Technological advances coupled with the economic importance of soybean have led to increased efforts to understand gene function and associate genes with phenotypes of agronomic and fundamental interest. Functional genomics approaches aim to develop sufficient understanding needed to bridge the genotype-tophenotype gap. In general terms, functional genomics approaches begin by using highly parallelized methods to analyze genomes, transcriptomes, proteomes, and metabolomes to generate hypotheses about genes that control phenotypes. Candidate genes are then tested for their contributions to phenotypes through various methods such as RNA silencing, genetic mutation, or overexpression. In this chapter, we review the current approaches, tools, and resources that are being applied for functional genomics research in soybean. RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. Technological advances coupled with the economic importance of soybean have led to increased efforts to understand gene function and associate genes with phenotypes of agronomic and fundamental interest. Functional genomics approaches aim to develop sufficient understanding needed to bridge the genotype-to-phenotype gap. In general terms, functional genomics approaches begin by using highly parallelized methods to analyze genomes, transcriptomes, proteomes, and metabolomes to generate hypotheses about genes that control phenotypes. Candidate genes are then tested for their contributions to phenotypes through various methods such as RNA silencing, genetic mutation, or overexpression. In this chapter, we review the current approaches, tools, and resources that are being applied for functional genomics research in soybean.

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“…The tissue-specific expression patterns of these genes were then extracted from the soybean gene expression transcriptomics atlas (Libault et al 2010). These publicly available transcriptomics data (soyKB database, http://www.soykb.org) were produced by Solexa sequencing of three replicates of each tissue (Joshi et al 2012).…”

Section: Comparison Of Cell Wall-related Gene Expressionmentioning

confidence: 99%

Xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I do not have identical structures in soybean root and root hair cell walls

Muszyński

O’Neill

Ramasamy

et al. 2015

Planta

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Chemical analyses and glycome profiling demonstrate differences in the structures of the xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I isolated from soybean ( Glycine max ) roots and root hair cell walls. The root hair is a plant cell that extends only at its tip. All other root cells have the ability to grow in different directions (diffuse growth). Although both growth modes require controlled expansion of the cell wall, the types and structures of polysaccharides in the walls of diffuse and tip-growing cells from the same plant have not been determined. Soybean (Glycine max) is one of the few plants whose root hairs can be isolated in amounts sufficient for cell wall chemical characterization. Here, we describe the structural features of rhamnogalacturonan I, rhamnogalacturonan II, xyloglucan, glucomannan, and 4-O-methyl glucuronoxylan present in the cell walls of soybean root hairs and roots stripped of root hairs. Irrespective of cell type, rhamnogalacturonan II exists as a dimer that is cross-linked by a borate ester. Root hair rhamnogalacturonan I contains more neutral oligosaccharide side chains than its root counterpart. At least 90% of the glucuronic acid is 4-O-methylated in root glucuronoxylan. Only 50% of this glycose is 4-O-methylated in the root hair counterpart. Mono O-acetylated fucose-containing subunits account for at least 60% of the neutral xyloglucan from root and root hair walls. By contrast, a galacturonic acid-containing xyloglucan was detected only in root hair cell walls. Soybean homologs of the Arabidopsis xyloglucan-specific galacturonosyltransferase are highly expressed only in root hairs. A mannose-rich polysaccharide was also detected only in root hair cell walls. Our data demonstrate that the walls of tip-growing root hairs cells have structural features that distinguish them from the walls of other roots cells.

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Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

Cited by 97 publications

References 28 publications

Genomic differences between cultivated soybean, G. max and its wild relative G. soja

Genomic differences between cultivated soybean, G. max and its wild relative G. soja

Soybean Functional Genomics: Bridging the Genotype-to-Phenotype Gap

Xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I do not have identical structures in soybean root and root hair cell walls

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