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1.  Cytotoxic and antioxidant properties of active principals isolated from water hyacinth against four cancer cells lines 
Eichhornia crassipes (Mart) solms is an invasive macrophyte causing serious problems to the network of irrigation and drainage canals in the Nile Delta region. The present study aim to evaluate the potential anticancer and antioxidant activities of Eichhornia crassipes crude extract and its pure compounds.
The macrophyte was collected from El-Zomor canal, River Nile (Egypt), cleaned, air dried, grinded then extracted with methanol (crude extract). The extract was fractionated using pre-coated silica gel plates (TLC F254) with hexane/ethyl acetate (8.5: 1.5 v/v) as mobile phase. Nine fractions were separated (A-I) then scratched, eluted with the same mobile phase, filtered and the separated fractions were determined and identified using spectroscopic methods (Mass spectrum (MS), Infra red (IR) and Proton H-Nuclear magnetic resonance (H-NMR). Both the crude extract and its nine identified compounds were tested for their antioxidant (using 2, 2 diphenyl-1-picrylhydrazyl (DPPH), 2, 2′- azino-bis {ethylbenzthiazoline-6-sulfonic acid (ABTS.)} methods) and anticancer activity (using MCF-7, HeLa, Hep.G2 and EACC cell lines).
The antioxidant and anticancer activities of the crude extract exhibited the highest effect while the compounds showed variable effects which depend on the type of compound and cancer cell line. The antioxidant activity of the crude extract exhibited the highest followed in descending order by compounds D, E, G and H respectively. Concerning the anticancer potency, the crude extract showed also the highest effect while the identified compounds (A, B, C, D, E, F, G, H and I) showed variable anticancer activities against the four different cell lines. In addition, Compound I exhibited the most potent anticancer activity against HepG2 cell line while compound D exhibited high anticancer activity against HeLa cells and EACC. The results revealed the presence of different compounds (Alkaloids and terpenoids) with variable antioxidant and anticancer activities which elicited an auto-augmentation in the crude extract leading to its greatest activities. The action of the identified anticancer compounds on DNA fragmentation was studied.
The study illustrated the potential of Eichhornia as a valuable resource for natural compounds of desirable medicinal properties (e.g. antioxidants and anticancer).
PMCID: PMC4213547  PMID: 25315352
Eichhornia crassipes; Cytotoxicity; Anticancer; Antioxidant; Active ingredients
2.  A phylogenetic review of the North American band-winged grasshopper genus, Encoptolophus Scudder with description of Nebulatettix gen.n. (Orthoptera: Acrididae: Oedipodinae) 
Insect systematics & evolution  2012;43(2):117-145.
A taxonomic review of the North American band-winged grasshopper genus Encoptolophus Scudder (Orthoptera: Acrididae: Oedipodinae) was conducted. This genus is hypothesized to be non-monophyletic following a cladistic analysis of the genera in the Chortophaga genus group. We examined all species currently classified in this genus group for morphological characters and one behavioral character. The phenotypic character data were combined with three mitochondrial genes: cytochrome c oxidase subunit II, 16S rRNA and 12S rRNA. A parsimony analysis was performed on the combined data resulting in two equally parsimonious trees. Encoptolophus, as historically defined, is resolved in three separate clades. The results support erection of a new genus, Nebulatettix Gómez, Lightfoot & Miller gen.n. to comprise one of the groups historically classified in Encoptolophus. In addition, we transfer the species Encoptolophus californicus Bruner to Chimarocephala Scudder, comb.n., a combination used historically. The evolution of certain characters in the Chortophaga group is discussed, and a key to the genera is provided.
PMCID: PMC3941475  PMID: 24605044
Systematics; taxonomy; character evolution; morphology; Chimarocephala; Chortophaga; Shotwellia
3.  Hand hygiene monitoring technology: protocol for a systematic review 
Systematic Reviews  2013;2:101.
Healthcare worker hand hygiene is thought to be one of the most important strategies to prevent healthcare-associated infections, but compliance is generally poor. Hand hygiene improvement interventions must include audits of compliance (almost always with feedback), which are most often done by direct observation - a method that is expensive, subjective, and prone to bias. New technologies, including electronic and video hand hygiene monitoring systems, have the potential to provide continuous and objective monitoring of hand hygiene, regular feedback, and for some systems, real-time reminders. We propose a systematic review of the evidence supporting the effectiveness of these systems. The primary objective is to determine whether hand hygiene monitoring systems yield sustainable improvements in hand hygiene compliance when compared to usual care.
MEDLINE, EMBASE, CINAHL, and other relevant databases will be searched for randomized control studies and quasi-experimental studies evaluating a video or electronic hand hygiene monitoring system. A standard data collection form will be used to abstract relevant information from included studies. Bias will be assessed using the Cochrane Effective Practice and Organization of Care Group Risk of Bias Assessment Tool. Studies will be reviewed independently by two reviewers, with disputes resolved by a third reviewer. The primary outcome is directly observed hand hygiene compliance. Secondary outcomes include healthcare-associated infection incidence and improvements in hand hygiene compliance as measured by alternative metrics. Results will be qualitatively summarized with comparisons made between study quality, the measured outcome, and study-specific factors that may be expected to affect outcome (for example, study duration, frequency of feedback, use of real-time reminders). Meta-analysis will be performed if there is more than one study of similar systems with comparable outcome definitions.
Electronic and video monitoring systems have the potential to improve hand hygiene compliance and prevent healthcare-associated infection, but are expensive, difficult to install and maintain, and may not be accepted by all healthcare workers. This review will assess the current evidence of effectiveness of these systems before their widespread adoption.
Study registration
PROSPERO registration number: CRD42013004519
PMCID: PMC3874644  PMID: 24219817
4.  Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens 
BMC Plant Biology  2013;13:43.
The protein encoded by GmRLK18-1 (Glyma_18_02680 on chromosome 18) was a receptor like kinase (RLK) encoded within the soybean (Glycine max L. Merr.) Rhg1/Rfs2 locus. The locus underlies resistance to the soybean cyst nematode (SCN) Heterodera glycines (I.) and causal agent of sudden death syndrome (SDS) Fusarium virguliforme (Aoki). Previously the leucine rich repeat (LRR) domain was expressed in Escherichia coli.
The aims here were to evaluate the LRRs ability to; homo-dimerize; bind larger proteins; and bind to small peptides. Western analysis suggested homo-dimers could form after protein extraction from roots. The purified LRR domain, from residue 131–485, was seen to form a mixture of monomers and homo-dimers in vitro. Cross-linking experiments in vitro showed the H274N region was close (<11.1 A) to the highly conserved cysteine residue C196 on the second homo-dimer subunit. Binding constants of 20–142 nM for peptides found in plant and nematode secretions were found. Effects on plant phenotypes including wilting, stem bending and resistance to infection by SCN were observed when roots were treated with 50 pM of the peptides. Far-Western analyses followed by MS showed methionine synthase and cyclophilin bound strongly to the LRR domain. A second LRR from GmRLK08-1 (Glyma_08_g11350) did not show these strong interactions.
The LRR domain of the GmRLK18-1 protein formed both a monomer and a homo-dimer. The LRR domain bound avidly to 4 different CLE peptides, a cyclophilin and a methionine synthase. The CLE peptides GmTGIF, GmCLE34, GmCLE3 and HgCLE were previously reported to be involved in root growth inhibition but here GmTGIF and HgCLE were shown to alter stem morphology and resistance to SCN. One of several models from homology and ab-initio modeling was partially validated by cross-linking. The effect of the 3 amino acid replacements present among RLK allotypes, A87V, Q115K and H274N were predicted to alter domain stability and function. Therefore, the LRR domain of GmRLK18-1 might underlie both root development and disease resistance in soybean and provide an avenue to develop new variants and ligands that might promote reduced losses to SCN.
PMCID: PMC3626623  PMID: 23497186
Receptor; Leucine-rich repeat; Ligand; Peptide; Cross-link; Predicted
5.  Predicting In Silico Which Mixtures of the Natural Products of Plants Might Most Effectively Kill Human Leukemia Cells? 
The aim of the analysis of just 13 natural products of plants was to predict the most likely effective artificial mixtures of 2-3 most effective natural products on leukemia cells from over 364 possible mixtures. The natural product selected included resveratrol, honokiol, chrysin, limonene, cholecalciferol, cerulenin, aloe emodin, and salicin and had over 600 potential protein targets. Target profiling used the Ontomine set of tools for literature searches of potential binding proteins, binding constant predictions, binding site predictions, and pathway network pattern analysis. The analyses indicated that 6 of the 13 natural products predicted binding proteins which were important targets for established cancer treatments. Improvements in effectiveness were predicted for artificial combinations of 2 or 3 natural products. That effect might be attributed to drug synergism rather than increased numbers of binding proteins bound (dose effects). Among natural products, the combinations of aloe emodin with mevinolin and honokiol were predicted to be the most effective combination for AML-related predicted binding proteins. Therefore, plant extracts may in future provide more effective medicines than the single purified natural products of modern medicine, in some cases.
PMCID: PMC3569894  PMID: 23431350
6.  The receptor like kinase at Rhg1-a/Rfs2 caused pleiotropic resistance to sudden death syndrome and soybean cyst nematode as a transgene by altering signaling responses 
BMC Genomics  2012;13:368.
Soybean (Glycine max (L. Merr.)) resistance to any population of Heterodera glycines (I.), or Fusarium virguliforme (Akoi, O’Donnell, Homma & Lattanzi) required a functional allele at Rhg1/Rfs2. H. glycines, the soybean cyst nematode (SCN) was an ancient, endemic, pest of soybean whereas F. virguliforme causal agent of sudden death syndrome (SDS), was a recent, regional, pest. This study examined the role of a receptor like kinase (RLK) GmRLK18-1 (gene model Glyma_18_02680 at 1,071 kbp on chromosome 18 of the genome sequence) within the Rhg1/Rfs2 locus in causing resistance to SCN and SDS.
A BAC (B73p06) encompassing the Rhg1/Rfs2 locus was sequenced from a resistant cultivar and compared to the sequences of two susceptible cultivars from which 800 SNPs were found. Sequence alignments inferred that the resistance allele was an introgressed region of about 59 kbp at the center of which the GmRLK18-1 was the most polymorphic gene and encoded protein. Analyses were made of plants that were either heterozygous at, or transgenic (and so hemizygous at a new location) with, the resistance allele of GmRLK18-1. Those plants infested with either H. glycines or F. virguliforme showed that the allele for resistance was dominant. In the absence of Rhg4 the GmRLK18-1 was sufficient to confer nearly complete resistance to both root and leaf symptoms of SDS caused by F. virguliforme and provided partial resistance to three different populations of nematodes (mature female cysts were reduced by 30–50%). In the presence of Rhg4 the plants with the transgene were nearly classed as fully resistant to SCN (females reduced to 11% of the susceptible control) as well as SDS. A reduction in the rate of early seedling root development was also shown to be caused by the resistance allele of the GmRLK18-1. Field trials of transgenic plants showed an increase in foliar susceptibility to insect herbivory.
The inference that soybean has adapted part of an existing pathogen recognition and defense cascade (H.glycines; SCN and insect herbivory) to a new pathogen (F. virguliforme; SDS) has broad implications for crop improvement. Stable resistance to many pathogens might be achieved by manipulation the genes encoding a small number of pathogen recognition proteins.
PMCID: PMC3439264  PMID: 22857610
Segregation; Pleiotropy; Rhg1/Rfs2; Soybean; Resistance; Soybean cyst nematode (SCN); Sudden death syndrome (SDS); Insect herbivory
7.  A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population 
BMC Genomics  2011;12:266.
Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers.
The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1from 2008 at Rayong, CN09R1and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%.
Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait.
PMCID: PMC3123654  PMID: 21609492
8.  Allelopathic Effects of Water Hyacinth [Eichhornia crassipes] 
PLoS ONE  2010;5(10):e13200.
Eichhornia crassipes (Mart) Solms is an invasive weed known to out-compete native plants and negatively affect microbes including phytoplankton. The spread and population density of E. crassipes will be favored by global warming. The aim here was to identify compounds that underlie the effects on microbes. The entire plant of E. crassipes was collected from El Zomor canal, River Nile (Egypt), washed clean, then air dried. Plant tissue was extracted three times with methanol and fractionated by thin layer chromatography (TLC). The crude methanolic extract and five fractions from TLC (A–E) were tested for antimicrobial (bacteria and fungal) and anti-algal activities (green microalgae and cyanobacteria) using paper disc diffusion bioassay. The crude extract as well as all five TLC fractions exhibited antibacterial activities against both the Gram positive bacteria; Bacillus subtilis and Streptococcus faecalis; and the Gram negative bacteria; Escherichia coli and Staphylococcus aureus. Growth of Aspergillus flavus and Aspergillus niger were not inhibited by either E. crassipes crude extract nor its five fractions. In contrast, Candida albicans (yeast) was inhibited by all. Some antialgal activity of the crude extract and its fractions was manifest against the green microalgae; Chlorella vulgaris and Dictyochloropsis splendida as well as the cyanobacteria; Spirulina platensis and Nostoc piscinale. High antialgal activity was only recorded against Chlorella vulgaris. Identifications of the active antimicrobial and antialgal compounds of the crude extract as well as the five TLC fractions were carried out using gas chromatography combined with mass spectroscopy. The analyses showed the presence of an alkaloid (fraction A) and four phthalate derivatives (Fractions B–E) that exhibited the antimicrobial and antialgal activities.
PMCID: PMC2951916  PMID: 20949048
9.  In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme 
BMC Genomics  2008;9(Suppl 2):S6.
Sudden death syndrome (SDS) of soybean (Glycine max L. Merr.) is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines, recently renamed Fusarium virguliforme (Fv). Due to the complexity and length of the soybean-Fusarium interaction, the molecular mechanisms underlying plant resistance and susceptibility to the pathogen are not fully understood. F. virguliforme has a very wide host range for the ability to cause root rot and a very narrow host range for the ability to cause a leaf scorch. Arabidopsis thaliana is a host for many types of phytopathogens including bacteria, fungi, viruses and nematodes. Deciphering the variations among transcript abundances (TAs) of functional orthologous genes of soybean and A. thaliana involved in the interaction will provide insights into plant resistance to F. viguliforme.
In this study, we reported the analyses of microarrays measuring TA in whole plants after A. thaliana cv 'Columbia' was challenged with fungal pathogen F. virguliforme. Infection caused significant variations in TAs. The total number of increased transcripts was nearly four times more than that of decreased transcripts in abundance. A putative resistance pathway involved in responding to the pathogen infection in A. thaliana was identified and compared to that reported in soybean.
Microarray experiments allow the interrogation of tens of thousands of transcripts simultaneously and thus, the identification of plant pathways is likely to be involved in plant resistance to Fusarial pathogens. Dissection of the set functional orthologous genes between soybean and A. thaliana enabled a broad view of the functional relationships and molecular interactions among plant genes involved in F. virguliforme resistance.
PMCID: PMC2559896  PMID: 18831797
10.  Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly 
BMC Genomics  2008;9:323.
Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max) genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS). Here the aim was to use BAC end sequences (BES) derived from three minimum tile paths (MTP) to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches.
Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs) were single nucleotide polymorphisms (SNPs; 89%) and single nucleotide indels (SNIs 10%). Larger indels were rare but present (1%). Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed.
The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de-convolution and positioning of sequence scaffolds (see BES_scaffolds section of SoyGD). This approach will assist genome annotation for paleopolyploid and true polyploid genomes such as soybean and many important cereal and fruit crops.
PMCID: PMC2478686  PMID: 18606011
11.  Soybean Genomics: Developments through the Use of Cultivar “Forrest” 
Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar “Forrest” has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) ∼200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal at sprovides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses.
PMCID: PMC2376204  PMID: 18483614
12.  Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA 
BMC Genomics  2007;8:262.
Reference genome sequences within the major taxa can be used to assist the development of genomic tools for related organisms. A major constraint in the use of these sequenced and annotated genomes is divergent evolution. Divergence of organisms from a common ancestor may have occurred millions of years ago, leading to apparently un-related and un-syntenic genomes when sequence alignment is attempted.
A series of programs were written to prepare 36 Mbp of Fusarium graminearum sequence in 19 scaffolds as a reference genome. Exactly 4,152 Bacterial artificial chromosome (BAC) end sequences from 2,178 large-insert Fusarium virguliforme clones were tested against this sequence. A total of 94 maps of F. graminearum sequence scaffolds, annotated exonic fragments and associated F. virguliforme sequences resulted.
Developed here was a technique that allowed the comparison of genomes based on small, 15 bp regions of shared identity. The main power of this method lay in its ability to align diverged sequences. This work is unique in that discontinuous sequences were used for the analysis and information not readily apparent, such as match direction, are presented. The 94 maps and JAVA programs are freely available on the Web and by request.
PMCID: PMC1978504  PMID: 17683537
13.  A sequence based synteny map between soybean and Arabidopsis thaliana 
BMC Genomics  2007;8:8.
Soybean (Glycine max, L. Merr.) is one of the world's most important crops, however, its complete genomic sequence has yet to be determined. Nonetheless, a large body of sequence information exists, particularly in the form of expressed sequence tags (ESTs). Herein, we report the use of the model organism Arabidopsis thaliana (thale cress) for which the entire genomic sequence is available as a framework to align thousands of short soybean sequences.
A series of JAVA-based programs were created that processed and compared 341,619 soybean DNA sequences against A. thaliana chromosomal DNA. A. thaliana DNA was probed for short, exact matches (15 bp) to each soybean sequence, and then checked for the number of additional 7 bp matches in the adjacent 400 bp region. The position of these matches was used to order soybean sequences in relation to the A. thaliana genome.
Reported associations between soybean sequences and A. thaliana were within a 95% confidence interval of e-30 – e-100. In addition, the clustering of soybean expressed sequence tags (ESTs) based on A. thaliana sequence was accurate enough to identify potential single nucleotide polymorphisms (SNPs) within the soybean sequence clusters. An EST, bacterial artificial chromosome (BAC) end sequence and marker amplicon sequence synteny map of soybean and A. thaliana is presented. In addition, all JAVA programs used to create this map are available upon request and on the WEB.
PMCID: PMC1780048  PMID: 17210083
14.  Development of a pooled probe method for locating small gene families in a physical map of soybean using stress related paralogues and a BAC minimum tile path 
Plant Methods  2006;2:20.
Genome analysis of soybean (Glycine max L.) has been complicated by its paleo-autopolyploid nature and conserved homeologous regions. Landmarks of expressed sequence tags (ESTs) located within a minimum tile path (MTP) of contiguous (contig) bacterial artificial chromosome (BAC) clones or radiation hybrid set can identify stress and defense related gene rich regions in the genome. A physical map of about 2,800 contigs and MTPs of 8,064 BAC clones encompass the soybean genome. That genome is being sequenced by whole genome shotgun methods so that reliable estimates of gene family size and gene locations will provide a useful tool for finishing. The aims here were to develop methods to anchor plant defense- and stress-related gene paralogues on the MTP derived from the soybean physical map, to identify gene rich regions and to correlate those with QTL for disease resistance.
The probes included 143 ESTs from a root library selected by subtractive hybridization from a multiply disease resistant soybean cultivar 'Forrest' 14 days after inoculation with Fusarium solani f. sp. glycines (F. virguliforme). Another 166 probes were chosen from a root EST library (Gm-r1021) prepared from a non-inoculated soybean cultivar 'Williams 82' based on their homology to the known defense and stress related genes. Twelve and thirteen pooled EST probes were hybridized to high-density colony arrays of MTP BAC clones from the cv. 'Forrest' genome. The EST pools located 613 paralogues for 201 of the 309 probes used (range 1–13 per functional probe). One hundred BAC clones contained more than one kind of paralogue. Many more BACs (246) contained a single paralogue of one of the 201 probes detectable gene families. ESTs were anchored on soybean linkage groups A1, B1, C2, E, D1a+Q, G, I, M, H, and O.
Estimates of gene family sizes were more similar to those made by Southern hybridization than by bioinformatics inferences from EST collections. When compared to Arabidopsis thaliana there were more 2 and 4 member paralogue families reflecting the diploidized-tetraploid nature of the soybean genome. However there were fewer families with 5 or more genes and the same number of single genes. Therefore the method can identify evolutionary patterns such as massively extensive selective gene loss or rapid divergence to regenerate the unique genes in some families.
PMCID: PMC1716159  PMID: 17156445
15.  The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max 
Nucleic Acids Research  2005;34(Database issue):D758-D765.
Genomes that have been highly conserved following increases in ploidy (by duplication or hybridization) like Glycine max (soybean) present challenges during genome analysis. At the Soybean Genome Database (SoyGD) genome browser has, since 2002, integrated and served the publicly available soybean physical map, bacterial artificial chromosome (BAC) fingerprint database and genetic map associated genomic data. The browser shows both build 3 and build 4 contiguous sets of clones (contigs) of the soybean physical map. Build 4 consisted of 2854 contigs that encompassed 1.05 Gb and 404 high-quality DNA markers that anchored 742 contigs. Many DNA markers anchored sets of 2–8 different contigs. Each contig in the set represented a homologous region of related sequences. GBrowse was adapted to show sets of homologous contigs at all potential anchor points, spread laterally and prevented from overlapping. About 8064 minimum tiling path (MTP2) clones provided 13 473 BAC end sequences (BES) to decorate the physical map. Analyses of BES placed 2111 gene models, 40 marker anchors and 1053 new microsatellite markers on the map. Estimated sequence tag probes from 201 low-copy gene families located 613 paralogs. The genome browser portal showed each data type as a separate track. Tetraploid, octoploid, diploid and homologous regions are shown clearly in relation to an integrated genetic and physical map.
PMCID: PMC1347413  PMID: 16381975
16.  Quantitative Trait Loci Associated with Foliar Trigonelline Accumulation in Glycine Max L 
The objective of this study was to utilize a Glycine max RIL population to (1) evaluate foliar trigonelline (TRG) content in field-grown soybean, (2) determine the heritability of TRG accumulation, and (3) identify DNA markers linked to quantitative trait loci (QTLs) conditioning variation in TRG accumulation. Frequency distributions of 70 recombinant inbred lines showed statistically no significant departure from normality (P > .05) for TRG accumulation measured at pod development stage (R4). Six different molecular linkage groups (LGs) (B2, C2, D2, G, J, and K) were identified to be linked to QTLs for foliar TRG accumulation. Two unique microsatellite markers (SSR) on two different linkage groups identified QTL significantly associated with foliar TRG accumulation: a region on LG J (Satt285) (P = .0019, R2 = 15.9%) and a second region on LG C2 (Satt079) (P = .0029, R2 = 13.4%).
PMCID: PMC161363  PMID: 12488580

Results 1-16 (16)