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.

Figure 1

Soybean roots infected by M. incognita at different time points. (a) galls formed on soybean roots at 12 dai; red arrows point to the galls; (b) giant cells and M. incognita in soybean roots at 12 dai (taken by LCM; bar 500 μm); red arrows point to giant cells; white arrowheads points to the nematode; (c) galls formed on soybean roots at 10 wai; red arrows point to the galls; (d) giant cells and M. incognita in soybean roots at 10 wai (taken by LCM; bar 500 μm); red arrows point to giant cells; white arrowhead points to the nematode

Figure 2

Volcano blots show significant changes in gene expression for soybean roots after infection with M. incognita. (a) Changes in gene expression at 12 dai (b) Changes in gene expression at 10 wai. The fold change was >1.5 with p values < 0.05, determined individually for each gene. The vertical lines on each graph represent p = 0.05. The horizontal lines represent the log2 of gene expression.

Figure 3

Transcript abundance of genes encoding enzymes in the pathway of starch and sucrose metabolism as represented by KEGG. Relative transcript abundance of genes encoding enzymes in the pathway at 12 dai compared to uninfected control overlaid as colors in the boxes containing the enzyme commission (EC) number of the enzyme. Enzymes colored in green are encoded by up-regulated genes. Boxes colored in red represent down-regulated genes. Boxes colored in yellow represent a gene family and different gene members are up- and down-regulated, respectively. The blue arrows point to pectin esterase [EC: 3.1.1.11] and cellulose synthase [EC: 2.41.12]. The blue arrows point to pectin esterase [EC: 3.1.1.11] and cellulose synthase [EC: 2.41.12].

Figure 4

Expression profiles of the genes encoding enzymes in phenylpropanoid biosynthesis pathway at 12 dai. The blue arrows point to extensin peroxidases [EC: 1.11.1.7] that participate in lignin biosynthesis. Boxes colored in red represent down-regulated genes encoding that enzyme. Boxes colored in green represent up-regulated genes. Boxes colored in yellow represent multiple genes encode the enzyme and some of those different gene copies are up-regulated, while others are down-regulated.

Figure 5

Expression profiles of the RNAs encoding enzymes in glycolysis/gluconeogenesis pathway. The blue arrows point to glucose-6-phosphate isomerase [EC: 5.3.19]. Boxes colored in red represent down-regulated genes encoding that enzyme. Boxes colored in green represent up-regulated genes. Boxes colored in yellow represent multiple genes encode the enzyme and some of those different gene copies are up-regulated, while others are down-regulated.

Figure 6

Expression profiles of the RNAs encoding enzymes in the alpha-linolenic acid pathway. (a) 12 dai; (b) 10 wai. The blue arrows point to lipoxygenase [EC: 1.13.11.12] and allene oxide synthase [EC: 4.2.1.92]. Boxes colored in red represent down-regulated genes encoding that enzyme. Boxes colored in green represent up-regulated genes. Boxes colored in yellow represent multiple genes encode the enzyme and some of those different gene copies are up-regulated, while others are down-regulated.

Figure 7

Microarray results were validated by comparison of microarray fold-change with qRT-PCR for specific genes. (a) genes involved in cell cycle progression; (b) Genes involved in cell wall remolding and modification; (c) genes participating in jasmonic acid biosynthesis.