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Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking.

Klink VP, Hosseini P, MacDonald MH, Alkharouf NW, Matthews BF - BMC Genomics (2009)

Bottom Line: However, 1668 genes were found to be suppressed in NL1-RHg.These genes included steroid alpha reductase, serine proteinase and a collagen protein.The identification of genes like steroid alpha reductase and serine proteinase that are involved in feeding and nutritional uptake as being highly suppressed during the R response at 8d may indicate genes that the plant is targeting.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS 39762, USA. vklink@biology.msstate.edu

ABSTRACT

Background: A single Glycine max (soybean) genotype (Peking) reacts differently to two different populations of Heterodera glycines (soybean cyst nematode) within the first twelve hours of infection during resistant (R) and susceptible (S) reactions. This suggested that H. glycines has population-specific gene expression signatures. A microarray analysis of 7539 probe sets representing 7431 transcripts on the Affymetrix soybean GeneChip were used to identify population-specific gene expression signatures in pre-infective second stage larva (pi-L2) prior to their infection of Peking. Other analyses focused on the infective L2 at 12 hours post infection (i-L2(12h)), and the infective sedentary stages at 3 days post infection (i-L2(3d)) and 8 days post infection (i-L2/L3(8d)).

Results: Differential expression and false discovery rate (FDR) analyses comparing populations of pi-L2 (i.e., incompatible population, NL1-RHg to compatible population, TN8) identified 71 genes that were induced in NL1-RHg as compared to TN8. These genes included putative gland protein G23G12, putative esophageal gland protein Hgg-20 and arginine kinase. The comparative analysis of pi-L2 identified 44 genes that were suppressed in NL1-RHg as compared to TN8. These genes included a different Hgg-20 gene, an EXPB1 protein and a cuticular collagen. By 12 h, there were 7 induced genes and 0 suppressed genes in NL1-RHg. By 3d, there were 9 induced and 10 suppressed genes in NL1-RHg. Substantial changes in gene expression became evident subsequently. At 8d there were 13 induced genes in NL1-RHg. This included putative gland protein G20E03, ubiquitin extension protein, putative gland protein G30C02 and beta-1,4 endoglucanase. However, 1668 genes were found to be suppressed in NL1-RHg. These genes included steroid alpha reductase, serine proteinase and a collagen protein.

Conclusion: These analyses identify a genetic expression signature for these two populations both prior to and subsequently as they undergo an R or S reaction. The identification of genes like steroid alpha reductase and serine proteinase that are involved in feeding and nutritional uptake as being highly suppressed during the R response at 8d may indicate genes that the plant is targeting. The analyses also identified numerous putative parasitism genes that are differentially expressed. The 1668 genes that are suppressed in NL1-RHg, and hence induced in TN8 may represent genes that are important during the parasitic stages of H. glycines development. The potential for different arrays of putative parasitism genes to be expressed in different nematode populations may indicate how H. glycines evolve mechanisms to overcome resistance.

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Volcano plots comparing differential gene expression between NH1-RHg (R) and TN8 (S) sample types. A cutoff of ≥ /1.5/ fold cutoff and P ≤ 0.05 was used for the analyses. Induced genes (dark blue, upper right quadrant) are genes induced during the resistant reaction. Suppressed genes (dark blue, upper left quadrant) are genes suppressed during the resistant reaction. The differentially expressed genes are presented in context for NH1-RHg. A, L2 (pi-L2); B, 12 h (i-L212h); C, 3d (i-L23d); D, 8d (i-L2/L38d).
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Figure 2: Volcano plots comparing differential gene expression between NH1-RHg (R) and TN8 (S) sample types. A cutoff of ≥ /1.5/ fold cutoff and P ≤ 0.05 was used for the analyses. Induced genes (dark blue, upper right quadrant) are genes induced during the resistant reaction. Suppressed genes (dark blue, upper left quadrant) are genes suppressed during the resistant reaction. The differentially expressed genes are presented in context for NH1-RHg. A, L2 (pi-L2); B, 12 h (i-L212h); C, 3d (i-L23d); D, 8d (i-L2/L38d).

Mentions: In the first set of experiments, H. glycines gene expression was examined in the R reaction. This was done by directly comparing R expression to S expression. The analysis directly compared R to S at T1, T2, T3 and T4 (Fig. 2). The S reaction was used as the baseline at each time point by which gene expression in the R reaction was determined. In all analyses, a ≥ /1.5/ fold expression limit with a p-value of ≤ 0.05 was used. Volcano plots (Fig. 2) depict differential gene expression of all probe sets on the Affymetrix® soybean GeneChip® at T1 (Fig. 2A), T2 (Fig. 2B), T3 (Fig. 2C) and T4 (Fig 2D). The analysis presented here measures genes induced in the R reaction. Conversely, due to the nature of the volcano plot analysis, those same induced genes in R would be suppressed by the same measure in the S reaction.


Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking.

Klink VP, Hosseini P, MacDonald MH, Alkharouf NW, Matthews BF - BMC Genomics (2009)

Volcano plots comparing differential gene expression between NH1-RHg (R) and TN8 (S) sample types. A cutoff of ≥ /1.5/ fold cutoff and P ≤ 0.05 was used for the analyses. Induced genes (dark blue, upper right quadrant) are genes induced during the resistant reaction. Suppressed genes (dark blue, upper left quadrant) are genes suppressed during the resistant reaction. The differentially expressed genes are presented in context for NH1-RHg. A, L2 (pi-L2); B, 12 h (i-L212h); C, 3d (i-L23d); D, 8d (i-L2/L38d).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2662880&req=5

Figure 2: Volcano plots comparing differential gene expression between NH1-RHg (R) and TN8 (S) sample types. A cutoff of ≥ /1.5/ fold cutoff and P ≤ 0.05 was used for the analyses. Induced genes (dark blue, upper right quadrant) are genes induced during the resistant reaction. Suppressed genes (dark blue, upper left quadrant) are genes suppressed during the resistant reaction. The differentially expressed genes are presented in context for NH1-RHg. A, L2 (pi-L2); B, 12 h (i-L212h); C, 3d (i-L23d); D, 8d (i-L2/L38d).
Mentions: In the first set of experiments, H. glycines gene expression was examined in the R reaction. This was done by directly comparing R expression to S expression. The analysis directly compared R to S at T1, T2, T3 and T4 (Fig. 2). The S reaction was used as the baseline at each time point by which gene expression in the R reaction was determined. In all analyses, a ≥ /1.5/ fold expression limit with a p-value of ≤ 0.05 was used. Volcano plots (Fig. 2) depict differential gene expression of all probe sets on the Affymetrix® soybean GeneChip® at T1 (Fig. 2A), T2 (Fig. 2B), T3 (Fig. 2C) and T4 (Fig 2D). The analysis presented here measures genes induced in the R reaction. Conversely, due to the nature of the volcano plot analysis, those same induced genes in R would be suppressed by the same measure in the S reaction.

Bottom Line: However, 1668 genes were found to be suppressed in NL1-RHg.These genes included steroid alpha reductase, serine proteinase and a collagen protein.The identification of genes like steroid alpha reductase and serine proteinase that are involved in feeding and nutritional uptake as being highly suppressed during the R response at 8d may indicate genes that the plant is targeting.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS 39762, USA. vklink@biology.msstate.edu

ABSTRACT

Background: A single Glycine max (soybean) genotype (Peking) reacts differently to two different populations of Heterodera glycines (soybean cyst nematode) within the first twelve hours of infection during resistant (R) and susceptible (S) reactions. This suggested that H. glycines has population-specific gene expression signatures. A microarray analysis of 7539 probe sets representing 7431 transcripts on the Affymetrix soybean GeneChip were used to identify population-specific gene expression signatures in pre-infective second stage larva (pi-L2) prior to their infection of Peking. Other analyses focused on the infective L2 at 12 hours post infection (i-L2(12h)), and the infective sedentary stages at 3 days post infection (i-L2(3d)) and 8 days post infection (i-L2/L3(8d)).

Results: Differential expression and false discovery rate (FDR) analyses comparing populations of pi-L2 (i.e., incompatible population, NL1-RHg to compatible population, TN8) identified 71 genes that were induced in NL1-RHg as compared to TN8. These genes included putative gland protein G23G12, putative esophageal gland protein Hgg-20 and arginine kinase. The comparative analysis of pi-L2 identified 44 genes that were suppressed in NL1-RHg as compared to TN8. These genes included a different Hgg-20 gene, an EXPB1 protein and a cuticular collagen. By 12 h, there were 7 induced genes and 0 suppressed genes in NL1-RHg. By 3d, there were 9 induced and 10 suppressed genes in NL1-RHg. Substantial changes in gene expression became evident subsequently. At 8d there were 13 induced genes in NL1-RHg. This included putative gland protein G20E03, ubiquitin extension protein, putative gland protein G30C02 and beta-1,4 endoglucanase. However, 1668 genes were found to be suppressed in NL1-RHg. These genes included steroid alpha reductase, serine proteinase and a collagen protein.

Conclusion: These analyses identify a genetic expression signature for these two populations both prior to and subsequently as they undergo an R or S reaction. The identification of genes like steroid alpha reductase and serine proteinase that are involved in feeding and nutritional uptake as being highly suppressed during the R response at 8d may indicate genes that the plant is targeting. The analyses also identified numerous putative parasitism genes that are differentially expressed. The 1668 genes that are suppressed in NL1-RHg, and hence induced in TN8 may represent genes that are important during the parasitic stages of H. glycines development. The potential for different arrays of putative parasitism genes to be expressed in different nematode populations may indicate how H. glycines evolve mechanisms to overcome resistance.

Show MeSH
Related in: MedlinePlus