David A Lightfoot

Summary

Affiliation: Southern Illinois University
Country: USA

Publications

  1. pmc 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
    Jeffry L Shultz
    Genomics Core Facility, Southern Illinois University at Carbondale, Carbondale, IL 62901 4415, USA
    Nucleic Acids Res 34:D758-65. 2006
  2. pmc Soybean Genomics: Developments through the Use of Cultivar "Forrest"
    David A Lightfoot
    Department of Plant Soil and General Agriculture, Center for Excellence, The Illinois Soybean Center, Southern Illinois University at Carbondale, Carbondale, IL 62901 4415, USA
    Int J Plant Genomics 2008:793158. 2008
  3. pmc Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens
    Ahmed J Afzal
    Department of Molecular Biology, Microbiology and Biochemistry and Center for Excellence the Illinois Soybean Center, Southern Illinois University at Carbondale, IL 62901, USA
    BMC Plant Biol 13:43. 2013
  4. pmc A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population
    Sukhuman Whankaew
    Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
    BMC Genomics 12:266. 2011
  5. pmc A sequence based synteny map between soybean and Arabidopsis thaliana
    Jeffry L Shultz
    USDA ARS, Crop Genetics and Production Research Unit, Stoneville, MS 38776, USA
    BMC Genomics 8:8. 2007
  6. pmc Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA
    Jeffry L Shultz
    USDA ARS, Crop Genetics and Production Research Unit, PO Box 345, Stoneville, MS 38776, USA
    BMC Genomics 8:262. 2007
  7. doi request reprint Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode
    Ahmed J Afzal
    Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
    Theor Appl Genet 124:1027-39. 2012
  8. pmc 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
    Ali Srour
    Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
    BMC Genomics 13:368. 2012
  9. pmc The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots
    Ahmed J Afzal
    Department of Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
    Plant Physiol 151:1264-80. 2009
  10. pmc Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly
    Navinder Saini
    Dept of Plant, Soil and Agricultural Systems, Genomics and Biotechnology Core Facility, Center for Excellence, Southern Illinois University, Carbondale IL, 62901, USA
    BMC Genomics 9:323. 2008

Collaborators

Detail Information

Publications22

  1. pmc 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
    Jeffry L Shultz
    Genomics Core Facility, Southern Illinois University at Carbondale, Carbondale, IL 62901 4415, USA
    Nucleic Acids Res 34:D758-65. 2006
    ..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...
  2. pmc Soybean Genomics: Developments through the Use of Cultivar "Forrest"
    David A Lightfoot
    Department of Plant Soil and General Agriculture, Center for Excellence, The Illinois Soybean Center, Southern Illinois University at Carbondale, Carbondale, IL 62901 4415, USA
    Int J Plant Genomics 2008:793158. 2008
    ..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...
  3. pmc Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens
    Ahmed J Afzal
    Department of Molecular Biology, Microbiology and Biochemistry and Center for Excellence the Illinois Soybean Center, Southern Illinois University at Carbondale, IL 62901, USA
    BMC Plant Biol 13:43. 2013
    ..and causal agent of sudden death syndrome (SDS) Fusarium virguliforme (Aoki). Previously the leucine rich repeat (LRR) domain was expressed in Escherichia coli...
  4. pmc A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population
    Sukhuman Whankaew
    Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
    BMC Genomics 12:266. 2011
    ..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...
  5. pmc A sequence based synteny map between soybean and Arabidopsis thaliana
    Jeffry L Shultz
    USDA ARS, Crop Genetics and Production Research Unit, Stoneville, MS 38776, USA
    BMC Genomics 8:8. 2007
    ..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...
  6. pmc Development of a physical map of the soybean pathogen Fusarium virguliforme based on synteny with Fusarium graminearum genomic DNA
    Jeffry L Shultz
    USDA ARS, Crop Genetics and Production Research Unit, PO Box 345, Stoneville, MS 38776, USA
    BMC Genomics 8:262. 2007
    ..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...
  7. doi request reprint Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode
    Ahmed J Afzal
    Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
    Theor Appl Genet 124:1027-39. 2012
    ..Finally, rhg1 was shown to reduce the plant root development. A model for rhg1 as a dominant multi-gene resistance locus based on the developmental control was inferred...
  8. pmc 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
    Ali Srour
    Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
    BMC Genomics 13:368. 2012
    ..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...
  9. pmc The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots
    Ahmed J Afzal
    Department of Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901, USA
    Plant Physiol 151:1264-80. 2009
    ..3.1.45]) and two metabolites (maltose and an unknown) differed in resistant and susceptible NILs without SCN infestation and may form the basis of a new assay for the selection of resistance to SCN in soybean...
  10. pmc Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly
    Navinder Saini
    Dept of Plant, Soil and Agricultural Systems, Genomics and Biotechnology Core Facility, Center for Excellence, Southern Illinois University, Carbondale IL, 62901, USA
    BMC Genomics 9:323. 2008
    ....
  11. pmc In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme
    Jiazheng Yuan
    Department of Plant, Soil Sciences and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
    BMC Genomics 9:S6. 2008
    ..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...
  12. doi request reprint Iso-lines and inbred-lines confirmed loci that underlie resistance from cultivar 'Hartwig' to three soybean cyst nematode populations
    Samreen Kazi
    Plant Biotechnology and Genomics Core Facility, Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
    Theor Appl Genet 120:633-44. 2010
    ..3- from Hartwig and Pyramid. The QTL detected will allow marker assisted selection for multigenic resistance to complex nematode populations in combination with sudden death syndrome resistance (SDS) and other agronomic traits...
  13. ncbi request reprint The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean
    Jeffry L Shultz
    Genomics Core Facility and Center of Excellence in Soybean Research, Teaching and Outreach, and Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
    Theor Appl Genet 114:1081-90. 2007
    ..Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited...
  14. doi request reprint Molecular mapping and breeding with microsatellite markers
    David A Lightfoot
    Department of Plant, Soil and General Agriculture, Center of Excellence in Soybean Research, Teaching and Outreach, Southern Illinois University at Carbondale, Carbondale, IL, USA
    Methods Mol Biol 1006:297-317. 2013
    ..When combined with high-throughput methods for genotyping and a genome sequence, the use of association mapping with microsatellite markers will provide critical advances in the analysis of crop traits...
  15. doi request reprint The genetic control of tolerance to aluminum toxicity in the 'Essex' by 'Forrest' recombinant inbred line population
    Aman D Sharma
    Plant Biotechnology and Genomics Core Facility, Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
    Theor Appl Genet 122:687-94. 2011
    ..Two major loci and at least nine minor loci were inferred to underlie tolerance to Al. RILs and markers may be used to select alleles that increase tolerance to soybean against Al stress...
  16. ncbi request reprint Root response to Fusarium solani f. sp . glycines: temporal accumulation of transcripts in partially resistant and susceptible soybean
    M J Iqbal
    Plant Biotechnology and Genome Center, Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 176 Agriculture Building, Carbondale, IL 62901, USA
    Theor Appl Genet 110:1429-38. 2005
    ..Pathways that responded included the protein phosphorylation cascade, the phospholipase cascade and the phenolic natural products pathways, including isoflavone and cell wall synthesis...
  17. doi request reprint Plant receptor-like serine threonine kinases: roles in signaling and plant defense
    Ahmed J Afzal
    Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA
    Mol Plant Microbe Interact 21:507-17. 2008
    ..Further elucidated were the genomic and structural organizations of RLK gene families, with special emphasis on RLK implicated in resistance to disease and development...
  18. doi request reprint Association between serotonin transporter polymorphisms and problem behavior in adult males with intellectual disabilities
    Michael E May
    Educational Psychology and Special Education, Southern Illinois University, Carbondale, IL 62901, USA
    Brain Res 1357:97-103. 2010
    ..The association with aggression appears to be genetically complex, suggesting there may be other genes, interactions between genes, and/or environmental relations occasioning aggression in people with intellectual disabilities...
  19. ncbi request reprint Soybean disease resistance protein RHG1-LRR domain expressed, purified and refolded from Escherichia coli inclusion bodies: preparation for a functional analysis
    Ahmed J Afzal
    Department of Molecular Biology, Microbiology and Biochemistry and Center for Excellence in Soybean Research, Teaching and Outreach, Southern Illinois University at Carbondale, IL 62901, USA
    Protein Expr Purif 53:346-55. 2007
    ....