Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis.

Yuepeng Song,Yuanyuan Ren,Deqiang Zhang,Zeliang Wang,Zhiyi Zhang,Wenhao Bo

doi:10.1186/1471-2164-13-286

Abstract

BackgroundDrought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis.ResultsUsing the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique.ConclusionThe cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.

Highlights

Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide
Several techniques are available for such studies, including representational difference analysis (RDA), serial analysis of gene expression (SAGE), suppression subtractive hybridization (SSH), cDNA microarrays, oligo microarrays, and RNA-Seq to analyze the transcriptome and identify genes that are up- or downregulated during drought tolerance [9,10,11]
A total of 415 transcriptderived fragments (TDFs) was isolated from the silverstained cDNA-AFLP gels based on their presence/absence or difference in the levels of expression

Summary

Introduction

Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. We conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. The cDNA-AFLP method is an extremely efficient and sensitive mRNA fingerprinting technique to identify both common and rare transcripts [12,13]. This technique is a robust and high-throughput tool for analysis of genome-wide gene expression, and can be used for identifying genes that are differentially expressed under abiotic stress [14]

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