Analysis of Gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways

Abstract

BackgroundRoot-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.ResultsWe 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.ConclusionsA 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.

A survey of genes involved in Arachis stenosperma resistance to Meloidogyne arenaria race 1

“…Likewise, altered expression of numerous genes during the interaction with Meloidogyne spp. in soybean roots has also been demonstrated (Ibrahim et al 2011;de Sá et al 2012).…”

“…Nematode infection triggers pathways related to defence response, including HR genes, as well as those involved in the redesign of root morphology to form galls and giant cells for feeding (Ibrahim et al 2011). As a vast suite of genes are induced in defence response against root-knot nematodes and other pests, a specific recognition of the pathogen by the plant may lead to resistance through HR, accompanied by rapid cell death in and around the infection site, thus, effectively containing pathogens at their site of entry (Lam 2004).…”

Not to be suppressed? Rethinking the host response at a root-parasite interface

“…Conversely, conflicting changes in the expression of genes involved in the biosynthesis of defense compounds or encoding pathogenesis-related proteins were observed in a microarray analysis of infested soybean roots at 12 days that were compared to control non-infested roots [28]. Increased transcript accumulation for several defense-related genes was observed in a mRNA-Seq analysis of galls on rice roots at 7 days post inoculation compared to non-infested root tips that included the root meristem, although a different putative defense-related gene was suppressed in the same samples [26].…”

Changes in the Expression of Genes in Soybean Roots Infected by Nematodes

“…The expansion of the syncytium and the giant cell are accompanied by extensive cell wall modification. Microarray data indicate that the expression of many genes involved in cell wall extension and remodeling is altered (Klink et al 2007b(Klink et al , 2009aIthal et al 2007;Ibrahim et al 2011). For example more pectinases are expressed in the syncytium during a compatible interaction at 10 dai than in an incompatible reaction at 9 dai (Fig 3).…”

“…The experiments provided a means for examining expression at the genomic scale. Also, changes in gene expression in the cells at the feeding site of the nematode have been examined using microarrays (Klink et al 2007b(Klink et al , 2009a(Klink et al , 2010a(Klink et al , 2011bIbrahim et al 2011). In all of these studies approximately two to ten per cent of the genes represented on the microarray changed in expression by over 1.5-fold.…”