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Transcriptome analysis reveals metabolic alteration due to consecutive monoculture and abiotic stress stimuli in Rehamannia glutinosa Libosch

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Abstract

Key message

We deeply investigated the mechanism underlying metabolic regulation in response to consecutive monoculture (replanting disease) and different abiotic stresses that unfolded the response mechanism to consecutive monoculture problem through RNA-seq analysis.

Abstract

The consecutive monoculture problem (CMP) resulted of complex environmental stresses mediated by multiple factors. Previous studies have noted that multiple stress factors in consecutive monoculture soils or plants severely limited the interpretation of the critical molecular mechanism, and made a predict that the specifically responding factor was autotoxic allelochemicals. To identify the specifically responding genes, we compared transcriptome changes in roots of Rehamannia glutinosa Libosch using consecutive monoculture, salt, drought, and ferulic acid as stress factors. Comparing with normal growth, 2502, 2672, 2485, and 1956 genes were differentially expressed in R. glutinosa under consecutive monoculture practice, salt, drought, and ferulic acid stress, respectively. In addition, 510 genes were specifically expressed under consecutive monoculture, which were not present under the other stress conditions. Integrating the biological and enrichment analyses of the differentially expressed genes, the result demonstrated that the plants could alter enzyme genes expression to reconstruct the complicated metabolic pathways, which used to tolerate the CMP and abiotic stresses. Furthermore, most of the affected pathway genes were closely related to secondary metabolic processes, and the influence of consecutive monoculture practice on the transcriptome genes expression profile was very similar to the profile under salt stress and then to the profile under drought stress. The outlined schematic diagram unfolded the putative signal regulation mechanism in response to the CMP. Genes that differentially up- or down-regulated under consecutive monoculture practice may play important roles in the CMP or replanting disease in R. glutinosa.

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Abbreviations

DEG:

Differentially expressed gene

CMP:

Consecutive monoculture problem

FP:

First year planting

SP:

Second year planting

SAP:

NaCl stress-treated plants

DP:

Drought stress-treated plants

FAP:

Ferulic acid treated plants

vs:

Versus

GO:

Gene ontology

CYP:

Cytochrome P450

UGT:

Uridine diphosphate glycosyl transferases

RPKM:

Per million mapped sequence reads

FDR:

False discovery rate

QCl:

Quality control

KEGG:

Kyoto encyclopedia of genes and genomes

SEA:

Singular enrichment analysis

EC:

Enzyme Commission

MVA:

Mevalonate

MEP:

Methylerythritol phosphate

HMGR:

Hydroxymethylglutaryl-CoA reductase

GPPS:

Geranyldiphosphate synthase

FPPS:

Farnesyldiphosphate synthase

GGPPS:

Geranylgeranyldiphosphate synthase

SQS:

Squalene synthase

SE:

Squalene monooxygenase

CAS:

Cycloartenol synthase

SMT2:

24-Methylene sterol C-methyl transferase

DWF5:

7-Dehydrocholesterol reductase

DWF1:

Delta24-sterol reductase

AACT:

Acetyl-CoA C-acetyl transferase

FK:

Delta 14-sterol reductase

BRs:

Sitosteroland brassinosteroids

CYP716A52V2:

B-Amyrin 28-oxidase

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (Nos. 81274022, 81573538, 81503193, 81403042, and 31271674), the Key Scientific Research Project of the higher Education Institutions of Fujian Province of China (No. JK2015013), and Fujian-Taiwan Joint Innovative Center for Germplasm Resources and cultivation of crop (FJ 2011 Program, No. 2015-75, China).

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Authors and Affiliations

  1. College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Yunhe Tian, Fajie Feng, Bao Zhang, Mingjie Li, Li Gu, Aiguo Chen, Zhanjie Li, Wenbo Shan & Zhongyi Zhang

  2. Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China

    Zhongyi Zhang

  3. Henan Agricultural University, Zhengzhou, 450002, China

    Fengqing Wang, Xiaoran Wang & Xinjian Chen

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  1. Yunhe Tian
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  2. Fajie Feng
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Communicated by Chun-Hai Dong.

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Tian, Y., Feng, F., Zhang, B. et al. Transcriptome analysis reveals metabolic alteration due to consecutive monoculture and abiotic stress stimuli in Rehamannia glutinosa Libosch. Plant Cell Rep 36, 859–875 (2017). https://doi.org/10.1007/s00299-017-2115-2

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