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Methylome and transcriptome analysis reveals candidate genes for tuber shape variation in tissue culture-derived potato

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Abstract

We investigated genome-wide DNA methylation and transcriptome (RNA-seq) profiling for tuber shape variation in potato. Mother plant (M1, round) and tissue culture-derived clonal variant plant (M2, elongated) were used. Total number of DNA methylation sites at cytosine contexts (CpG, CHG and CHH) was higher in M2 than M1, where CHH was the highest followed by CHG and CpG. Differential methylation regions (DMRs) analysis in M1 (control) and M2 revealed maximum DMRs number on chromosome 5 in CHG context and hypo-methylation was higher than hyper-methylation. Further, transcriptome analysis revealed that a total of 20,747 genes were differentially expressed between M1 (control) and M2, of which 280 (over-expressed) and 612 (under-expressed) genes were statistically significant (p ≤ 0.05). The gene ontology (GO) annotation showed predominance of molecular function, whereas signal transduction and carbohydrate metabolism were major KEGG (Kyoto encyclopedia of genes and genomes) pathways. RNA-seq gene expression was validated for the ten selected genes by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Based on the comparative analysis, we observed a few candidate genes associated with tuber developmental processes such as phytohormones-related (e.g. SAUR family protein, abscisic acid environmental stress-inducible protein TAS14), sugar metabolism (e.g. UDP-glucosyltransferase, glycosyltransferase family GT8 protein), transcription factors (e.g. F-box family protein, MYB, WRKY, MADS-box), stress-responsive proteins (e.g. early-responsive to dehydration 3, cytochrome P450, proline-rich protein) and cell wall modifying genes (e.g. endo-1,4-beta-glucanase, glycine-rich cell wall structural protein 1.8, 3-ketoacyl-CoA synthase 10). Our study suggests that these candidate genes probably play key roles in tuber shape variation in potato.

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Availability of data and materials

The methylome and transcriptome (RNA-seq) sequences data has been deposited with the NCBI (i) Methylome sequences (BioProject: PRJNA476419, SRR7513135, BioSample: SAMN09433514), and (ii) Transcriptome sequences (BioProject: PRJNA494472, SRA: SRR8138708 and SRR8138709; BioSample: SAMN10345053 and SAMN10345054).

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Acknowledgements

The authors are grateful to the Competent Authority, ICAR-CPRI, Shimla for providing necessary facility and funds under the institute biotechnology programme, seed research and CABin scheme. We are thankful to M/s Eurofins Genomics India Pvt. Ltd., Bengaluru for bioinformatics support. We thank Dr. Amaresh Chandra for critical reading of the manuscript. We are highly thankful to the anonymous reviewers and editor for their comments to improve our article.

Funding

The funds were provided under the institute biotechnology programme and seed research of the Indian Council of Agricultural Research (ICAR)—Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, India.

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Authors and Affiliations

  1. Indian Council of Agricultural Research - Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India

    Jagesh Kumar Tiwari, Tanuja Buckseth, Rajesh Kumar Singh, Rasna Zinta, Aastha Saraswati, Manoj Kumar & Swarup Kumar Chakrabarti

  2. Indian Council of Agricultural Research - Central Potato Research Institute, Regional Station, Modipuram, Meerut, 250110, Uttar Pradesh, India

    Manoj Kumar

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  1. Jagesh Kumar Tiwari
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JKT planned the study. TB and RKS provided materials. JKT, TB, RZ and AS performed research work. JKT wrote the manuscript. MK and SKC edited the manuscript. All authors confirmed the manuscript.

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Correspondence to Jagesh Kumar Tiwari.

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Tiwari, J.K., Buckseth, T., Singh, R.K. et al. Methylome and transcriptome analysis reveals candidate genes for tuber shape variation in tissue culture-derived potato. Plant Growth Regul 93, 319–332 (2021). https://doi.org/10.1007/s10725-020-00690-5

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