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Comparative transcriptome profiling of two sweetpotato cultivars with contrasting flooding stress tolerance levels

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Abstract

Sweetpotato (Ipomoea batatas [L.] Lam) is an important starch crop that ensures food and nutrition security in the era of climate change. Sweetpotato is tolerant to environmental stresses such as drought, high temperature, and high salt, and therefore, is well adapted to marginal lands; however, it is relatively vulnerable to flooding stress, which severely reduces its yield and commercial value. To understand the flooding stress response of sweetpotato, we performed comparative transcriptome analysis of the leaves of two sweetpotato cultivars with contrasting flooding stress tolerance levels: Yeonjami (YJM; flooding tolerant) and Jeonmi (JM; flooding sensitive). Both cultivars were partially submerged in water for 0, 0.5, and 3 days. RNA-seq data of both cultivars revealed 14,229 differentially expressed genes (DEGs), which were categorized into seven clusters and six groups, based on the expression pattern of co-expressed DEGs and expression duration of DEGs, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DEGs of distinguishing functions between the two cultivars were involved in plant hormone signaling, carbohydrate transport, and mitogen-activated protein kinase (MAPK) signaling. Based on these results, we predict that YJM promotes adventitious growth, whereas JM exhibits shoot elongation under flooding stress. The expression levels of several key candidate genes involved in flooding tolerance correlated well with the comparative transcriptomics data. Overall, this study provides further insights into the molecular mechanism of flooding stress response in sweetpotato, and reveals candidate genes that could be used for developing new flooding tolerant sweetpotato cultivars.

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Abbreviations

ABA:

Abscisic acid

ACC:

1-Aminocyclopropane-1-carboxylic acid

ADH:

Alcohol dehydrogenase

ARF:

ADP-ribosylation factor

CTR1:

CONSTITUTIVE TRIPLE RESPONSE 1

DEG:

Differentially expressed gene

EIN3:

Ethylene-insensitive protein 3

ERF:

Ethylene-responsive transcription factor

ETR:

Ethylene receptor

FDR:

False discovery rate

GA:

Gibberellic acid

GO:

Gene Ontology

JM:

Jeonmi

KO:

KEGG Orthology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

LDH:

Lactate dehydrogenase

MAPK:

Mitogen-activated protein kinase

nr:

Non-redundant

NumReads:

Number of reads per transcript

qRT-PCR:

Quantitative real-time PCR

RNA-seq:

RNA sequencing

TOM:

Topological overlap matrix

YJM:

Yeonjami

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Acknowledgements

This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry (IPET) through the Agri-Bio Industry Technology Development Program funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (118038-3) and the KRIBB initiative program.

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  1. Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, 34141, Korea

    Sul-U Park, Chan-Ju Lee, So-Eun Kim, Ye-Hoon Lim, Ung-Han Yoon, Ho Soo Kim & Sang-Soo Kwak

  2. Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Daejeon, 34113, Korea

    Sul-U Park, Chan-Ju Lee, So-Eun Kim, Ye-Hoon Lim & Sang-Soo Kwak

  3. Department of Biology Education, College of Education, and IALS, Gyeongsang National University, 501 Jinjudae-ro, Jinju, 52828, Korea

    Yun-Hee Kim

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Park, SU., Kim, YH., Lee, CJ. et al. Comparative transcriptome profiling of two sweetpotato cultivars with contrasting flooding stress tolerance levels. Plant Biotechnol Rep 14, 743–756 (2020). https://doi.org/10.1007/s11816-020-00650-5

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