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Identification of transcripts associated with cell wall metabolism and development in the stem of sugarcane by Affymetrix GeneChip Sugarcane Genome Array expression profiling

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Abstract

Sugarcane is an important crop in tropical regions of the world, producing a very large biomass and accumulating large amounts of sucrose in the stem. In this study, we present the first report of transcript profiling using the GeneChip Sugarcane Genome Array. We have identified transcripts that are differentially expressed in the sugarcane stem during development by expression profiling using the array and total RNA derived from three disparate stem tissues (meristem, internodes 1–3, 8, and 20) from four replicates of the sugarcane variety Q117 grown in the field. We have identified 119 transcripts that were highly differentially expressed with development and have characterised members of the cellulose synthase (CesA) and cellulose synthase-like (Csl) gene families, which displayed coordinated expression during stem development. In addition, we determined that many other transcripts involved in cell wall metabolism and lignification were also co-expressed with members of the CesA and Csl gene families, offering additional insights into the dynamics of primary and secondary cell wall synthesis in the developing sugarcane stem.

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Acknowledgement

The authors would like to thank Michael Hewitt for assistance with tissue collection.

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Authors and Affiliations

  1. CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Queensland, 4067, Australia

    Rosanne E. Casu, Janine M. Jarmey, Graham D. Bonnett & John M. Manners

  2. Cooperative Research Centre for Sugar Industry Innovation through Biotechnology, University of Queensland, St. Lucia, Queensland, 4072, Australia

    Rosanne E. Casu, Janine M. Jarmey, Graham D. Bonnett & John M. Manners

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  1. Rosanne E. Casu
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  2. Janine M. Jarmey
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Corresponding author

Correspondence to Rosanne E. Casu.

Electronic supplementary materials

All supplementary data is available at http://www.csiro.au/mdata.

Supplementary Fig. 1

A Gene tree and Condition tree derived from the clustering of all probe sets based on their expression pattern and all biological replicates of each tissue type based on their overall similarity. M,I1–3: young stem; I8: maturing stem; I20: mature stem. Red: up-regulated; green: down-regulated; yellow: no change in expression; grey: not detected (DOC 354 kb)

Supplementary Fig. 2

Comparison of RFC in expression achieved using the Sugarcane Genome Array (GeneChip) and RT-qPCR. (i) StemV.01-StemV.04; (ii) StemV.05-StemV.08; (iii) StemV.09-StemV.12 (DOC 70 kb)

Supplementary Fig. 3

Comparison of RFC in expression achieved using the Sugarcane Genome Array (GeneChip) and RT-qPCR. (i) ShCesA2-ShCesA6; (ii) ShCesA7-ShCesA12; (iii) ShCslA9-ShCslF6 (DOC 65 kb)

Supplementary Table 1

Sequences of primers used for RT-qPCR analysis (DOC 57 kb)

Supplementary Table 2

Identity of the 774 probe sets were “absent”, i.e. did not register a signal on any GeneChip in this experiment (DOC 365 kb)

Supplementary Table 3

Library origin of sugarcane sequence-derived probe sets defined as “absent” for all GeneChips (DOC 28 kb)

Supplementary Table 4

List of probe sets present on the Affymetrix Sugar Cane Genome Array (XLS 3444 kb)

Supplementary Table 5

Expression ratios of 32 probe sets that are highly and robustly differentially up-regulated between young stem (M,I1–3) and more mature stem (I8 and I20). TC: The number of the Theoretical Contig as defined in the Sugarcane Gene Index hosted at TIGR (DOC 45 kb)

Supplementary Table 6

Expression ratios of 35 transcripts that are highly and robustly differentially down-regulated between young stem (M,I1–3) and more mature stem (I8 and I20). TC: The number of the Theoretical Contig as defined in the Sugarcane Gene Index hosted at TIGR (DOC 48 kb)

Supplementary Table 7

Expression ratios of transcripts that are differentially expressed in all three tissues sampled down the stem (DOC 31 kb)

Supplementary Table 8

Expression ratios of transcripts that were not detected in young stem but were differentially expressed in maturing and mature stem (DOC 33 kb)

Supplementary Table 9

Expression ratios of transcripts that were absent in young stem and expressed at similar levels in both maturing and mature stem (DOC 28 kb)

Supplementary Table 10

Expression ratios of transcripts that were expressed in young stem but absent in both maturing and mature stem. A: absent (DOC 44 kb)

Supplementary Table 11

Probe sets with similar expression patterns to each of the five cellulose synthase clusters sets. Data was required to be available for at least three of the four biological replicates for at least one tissue. Number pass: the number of GeneChips out of a possible 12 for which data was available. The probe sets used as a representative probe setto isolate all other members of each set are underlined (DOC 980 kb)

Supplementary Table 12

Examples of known proteins whose transcripts display similar regulation status in both microarray (Casu et al. 2003, 2004) and Affymetrix GeneChip expression profiles (DOC 30 kb)

Supplementary Methods

Analysis methods used to identify differentially expressed transcripts, irrespective of presumed functional identity (DOC 30 kb)

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Casu, R.E., Jarmey, J.M., Bonnett, G.D. et al. Identification of transcripts associated with cell wall metabolism and development in the stem of sugarcane by Affymetrix GeneChip Sugarcane Genome Array expression profiling. Funct Integr Genomics 7, 153–167 (2007). https://doi.org/10.1007/s10142-006-0038-z

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