title: Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways.
abstract: BACKGROUND
  Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plant cells. The expression of some plant genes is altered by the nematode as it establishes its feeding site.
  
  
  RESULTS
  We examined the expression of soybean (Glycine max) genes in galls formed in roots by the root-knot nematode, Meloidogyne incognita, 12 days and 10 weeks after infection to understand the effects of infection of roots by M. incognita. Gene expression was monitored using the Affymetrix Soybean GeneChip containing 37,500 G. max probe sets. Gene expression patterns were integrated with biochemical pathways from the Kyoto Encyclopedia of Genes and Genomes using PAICE software. Genes encoding enzymes involved in carbohydrate and cell wall metabolism, cell cycle control and plant defense were altered.
  
  
  CONCLUSIONS
  A number of different soybean genes were identified that were differentially expressed which provided insights into the interaction between M. incognita and soybean and into the formation and maintenance of giant cells. Some of these genes may be candidates for broadening plants resistance to root-knot nematode through over-expression or silencing and require further examination.
authors.affiliation: United States Department of Agriculture, Plant Sciences Institute, Beltsville, MD 20705, USA.
authors.forename: Heba M M
authors.initials: HM
authors.lastname: Ibrahim
authors.forename: Parsa
authors.initials: P
authors.lastname: Hosseini
authors.forename: Nadim W
authors.initials: NW
authors.lastname: Alkharouf
authors.forename: Ebtissam H A
authors.initials: EH
authors.lastname: Hussein
authors.forename: Abd El Kader Y
authors.initials: Ael K
authors.lastname: Gamal El-Din
authors.forename: Mohammed A M
authors.initials: MA
authors.lastname: Aly
authors.forename: Benjamin F
authors.initials: BF
authors.lastname: Matthews
mesh_terms: D000818:Animals; D002244:Carbon / Q000378:metabolism; D002473:Cell Wall / Q000235:genetics; D030541:Databases, Genetic; D004734:Energy Metabolism / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D017343:Genes, Plant / Q000235:genetics; D008938:Mitosis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics; D018517:Plant Roots / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000469:parasitology; D010941:Plant Tumors / Q000235:genetics* / Q000469:parasitology; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D012984:Software; D013025:Glycine max / Q000166:cytology / Q000235:genetics* / Q000378:metabolism / Q000469:parasitology; D014431:Tylenchoidea / Q000502:physiology*
chemical_list: D010940:Plant Proteins; D002244:Carbon