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Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines).

Klink VP, Overall CC, Alkharouf NW, Macdonald MH, Matthews BF - J. Biomed. Biotechnol. (2010)

Bottom Line: The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods.Conclusion.DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS 39762, USA.

ABSTRACT
Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

No MeSH data available.


G.  					m					a					x					[PI  548402/Peking] seedlings were inoculated with incompatible or compatible H. glycines J2 nematodes. Roots were harvested and prepared for histological observation to confirm the establishment of feeding sites at three and 8 dpi.  (a)  3 dpi G.  max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell.  (b)  8 dpi G.  max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell.  (c)  3 dpi G.  max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell.  (d)  8 dpi G.  max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell. Bar = 50 μm.
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fig2: G. m a x [PI  548402/Peking] seedlings were inoculated with incompatible or compatible H. glycines J2 nematodes. Roots were harvested and prepared for histological observation to confirm the establishment of feeding sites at three and 8 dpi. (a) 3 dpi G. max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell. (b) 8 dpi G. max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell. (c) 3 dpi G. max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell. (d) 8 dpi G. max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell. Bar = 50 μm.

Mentions: Morphological and anatomical details of compatible and incompatible disease responses by G. max to H. glycines infection have been published previously [27–29, 36, 57–61]. Infection during the first 8 dpi (Figure 2) was focused on for this analysis because syncytial cells complete the incompatible reaction by 8 dpi under the experimental conditions in G. max[PI  548402/Peking]. During a compatible reaction, nematodes have selected and are establishing feeding sites by 3 dpi (Figure 2(a)) that are continuing to develop by 8 dpi (Figure 2(b)). During an incompatible reaction, nematodes have also selected and are establishing feeding sites at 3 dpi (Figure 2(c)). However, during an incompatible reaction, syncytial cells collapse by 8 dpi (Figure 2(d)). Syncytial cells (Figure 3(a)) for the various analyses were collected by LCM (Figure 3(b)).


Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines).

Klink VP, Overall CC, Alkharouf NW, Macdonald MH, Matthews BF - J. Biomed. Biotechnol. (2010)

G.  					m					a					x					[PI  548402/Peking] seedlings were inoculated with incompatible or compatible H. glycines J2 nematodes. Roots were harvested and prepared for histological observation to confirm the establishment of feeding sites at three and 8 dpi.  (a)  3 dpi G.  max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell.  (b)  8 dpi G.  max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell.  (c)  3 dpi G.  max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell.  (d)  8 dpi G.  max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell. Bar = 50 μm.
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig2: G. m a x [PI  548402/Peking] seedlings were inoculated with incompatible or compatible H. glycines J2 nematodes. Roots were harvested and prepared for histological observation to confirm the establishment of feeding sites at three and 8 dpi. (a) 3 dpi G. max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell. (b) 8 dpi G. max[PI  548402/Peking] infected with a compatible nematode, black arrowhead; area encircled in red, syncytial cell. (c) 3 dpi G. max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell. (d) 8 dpi G. max[PI  548402/Peking] infected with an incompatible nematode, black arrowhead; area encircled in red, syncytial cell. Bar = 50 μm.
Mentions: Morphological and anatomical details of compatible and incompatible disease responses by G. max to H. glycines infection have been published previously [27–29, 36, 57–61]. Infection during the first 8 dpi (Figure 2) was focused on for this analysis because syncytial cells complete the incompatible reaction by 8 dpi under the experimental conditions in G. max[PI  548402/Peking]. During a compatible reaction, nematodes have selected and are establishing feeding sites by 3 dpi (Figure 2(a)) that are continuing to develop by 8 dpi (Figure 2(b)). During an incompatible reaction, nematodes have also selected and are establishing feeding sites at 3 dpi (Figure 2(c)). However, during an incompatible reaction, syncytial cells collapse by 8 dpi (Figure 2(d)). Syncytial cells (Figure 3(a)) for the various analyses were collected by LCM (Figure 3(b)).

Bottom Line: The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods.Conclusion.DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS 39762, USA.

ABSTRACT
Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.

No MeSH data available.