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Towards identifying the full set of genes expressed during cassava post-harvest physiological deterioration

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Abstract

Storage roots of cassava (Manihot esculenta Crantz) exhibit a rapid post-harvest physiological deterioration (PPD) response that can occur within 24–72 h of harvest. PPD is an enzymatically mediated oxidative process with parallels to plant wound, senescence and defence responses. To characterise those genes that show significant change in expression during the PPD response we have used cDNA microarray technology to carry out a large-scale analysis of the cassava root transcriptome during the post-harvest period. We identified 72 non-redundant expressed sequence tags which showed altered regulation during the post-harvest period. Of these 63 were induced, whilst 9 were down-regulated. RNA blot analysis of selected genes was used to verify and extend the microarray data. Additional microarray hybridisation experiments allowed the identification of 21 root-specific and 24 root-wounding-specific sequences. Many of the up-regulated and PPD-specific expressed sequence tags were predicted to play a role in cellular processes including reactive oxygen species turnover, cell wall repair, programmed cell death, ion, water or metabolite transport, signal transduction or perception, stress response, metabolism and biosynthesis, and activation of protein synthesis.

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Abbreviations

ABA:

Abscisic acid

ACC:

1-aminocyclopropane-1-carboxylate

ADC:

Arginine decarboxylase

ADP:

Adenosine triphosphate

AKR:

Aldo/keto reductase

AP:

Adaptor protein

ATP:

Adenosine triphosphate

ARP:

Auxin repressed protein

cDNA:

Complementary deoxyribonucleic acid

CIAT:

International Centre for Tropical Agriculture

DNA:

Deoxyribonucleic acid

ELIP:

Early light inducible protein

EST:

Expressed sequence tag

FKBP:

FK binding protein

GLP:

Germin-like protein

GRP:

Glycine-rich protein

GST:

Glutathione-S-transferase

H+-PPase:

Proton translocating inorganic pyrophosphatase

H2O2 :

Hydrogen peroxide

HRGP:

Hydroxyproline-rich glycoprotein

LEA:

Late embryogenesis abundant

MIP:

Major intrinsic protein

OxO:

Oxalate oxidase

PCD:

Programmed cell death

PCR:

Polymerase chain reaction

PIP:

Plasma membrane intrinsic protein

PPD:

Post-harvest physiological deterioration

PPIase:

Peptidyl-prolyl cis/trans isomerase

PPR:

Pentatricopeptide repeat

PRP:

Proline-rich protein

RNA:

Ribonucleic acid

ROS:

Reactive oxygen species

SAM:

Significance Analysis of Microarrays

SIR:

Sulphite reductase

SOD:

Superoxide dismutase

TCTP:

Translationally controlled tumour protein

TDF:

Transcript-derived fragment

UBP:

Oligouridylate binding protein

UDP:

Uridine diphosphate

UTR:

Untranslated region

XET:

Xyloglucan endotransglcosylase

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Acknowledgements

RGV would like to acknowledge the support of CIF and Colciencias, Colombia. This publication is an output from a research project funded by the UK Department for International Development (DFID) for the benefit of developing countries. The views expressed are not necessarily those of DFID. R8156 Crop Post-Harvest Programme.

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Authors and Affiliations

  1. Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK

    Kim Reilly, Rocío Gómez-Vásquez & John R. Beeching

  2. International Centre for Tropical Agriculture (CIAT), AA 6713 , Cali, Colombia

    Diana Bernal, Diego F. Cortés & Joe Tohme

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  1. Kim Reilly
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  2. Diana Bernal
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  3. Diego F. Cortés
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  4. Rocío Gómez-Vásquez
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  5. Joe Tohme
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  6. John R. Beeching
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Correspondence to John R. Beeching.

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Reilly, K., Bernal, D., Cortés, D.F. et al. Towards identifying the full set of genes expressed during cassava post-harvest physiological deterioration. Plant Mol Biol 64, 187–203 (2007). https://doi.org/10.1007/s11103-007-9144-0

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