Whole-genome gene expression profiling revealed genes and pathways potentially involved in regulating interactions of soybean with cyst nematode (Heterodera glycines Ichinohe)

Abstract

Background: Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most devastating pathogen of soybean. Many gene expression profiling studies have been conducted to investigate the responses of soybean to the infection by this pathogen using primarily the first-generation soybean genome array that covered approximately 37,500 soybean transcripts. However, no study has been reported yet using the second-generation Affymetrix soybean whole-genome transcript array (Soybean WT array) that represents approximately 66,000 predicted soybean transcripts.

Results: In the present work, the gene expression profiles of two soybean plant introductions (PIs) PI 437654 and PI 567516C (both resistant to multiple SCN HG Types) and cultivar Magellan (susceptible to SCN) were compared in the presence or absence of the SCN inoculum at 3 and 8 days post-inoculation using the Soybean WT array. Data analysis revealed that the two resistant soybean lines showed distinctive gene expression profiles from each other and from Magellan not only in response to the SCN inoculation, but also in the absence of SCN. Overall, 1,413 genes and many pathways were revealed to be differentially regulated. Among them, 297 genes were constitutively regulated in the two resistant lines (compared with Magellan) and 1,146 genes were responsive to the SCN inoculation in the three lines, with 30 genes regulated both constitutively and by SCN. In addition to the findings similar to those in the published work, many genes involved in ethylene, protein degradation, and phenylpropanoid pathways were also revealed differentially regulated in the present study. GC-rich elements (e.g., GCATGC) were found over-represented in the promoter regions of certain groups of genes. These have not been observed before, and could be new defense-responsive regulatory elements.

Conclusions: Different soybean lines showed different gene expression profiles in the presence and absence of the SCN inoculum. Both inducible and constitutive gene expression may contribute to resistance to multiple SCN HG Types in the resistant soybean PI lines. Ethylene, protein degradation, and phenylpropanoid pathways, as well as many other pathways reported previously, may play important roles in mediating the soybean-SCN interactions. The revealed genes, pathways, and promoter elements can be further explored to regulate or engineer soybean for resistance to SCN.

Figure 1

Hierarchical clustering of the constitutively-regulated genes. Each column represents a treatment and each row represents a gene. In total, 297 genes were constitutively regulated for at least 2 fold with a p value < 0.05. 654: PI 437654; 516C: PI 567516C; Mag: Magellan; con: control (mock) treatment; D0: 0 day post-inoculation; D3: 3 days post-inoculation; D8: 8 days post-inoculation. Red color: up-regulation; green color: down-regulation. The numbers on the left highlight the major clades.

Figure 2

Hierarchical clustering of the SCN-regulated genes. Each column represents a treatment and each row represents a gene. In total, 1,146 genes were regulated by SCN for at least 2 fold with a p value < 0.05. 654: PI 437654; 516C: PI 567516C; Mag: Magellan; D0: 0 day post-inoculation; D3: 3 days post-inoculation; D8: 8 days post-inoculation. Red color: up-regulation; green color: down-regulation. The numbers on the left highlight the major clades.

Figure 3

Functional categories of the constitutively-regulated genes. The 297 genes constitutively regulated (at least 2 fold, p < 0.05) in the two resistant lines were categorized using MapMan.

Figure 4

Venn diagrams to show commonality and uniqueness of the constitutively-regulated genes between the two resistant lines. In total, 297 genes were constitutively regulated in the two resistant soybean lines (at least 2 fold, p < 0.05).

Figure 5

Functional categories of the SCN-regulated genes. The 1,146 genes regulated by SCN (at least 2 fold, p < 0.05) in different soybean lines were categorized using MapMan.

Figure 6

Venn diagrams to show commonality and uniqueness of the SCN-regulated genes between different lines. In total, 1,146 genes were regulated by SCN in different soybean lines (at least 2 fold, p < 0.05). A at 3 dpi; B at 8 dpi. dpi: days post-inoculation.