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Role of miRNAs in the regulation of proanthocyanidin biosynthesis in the legume Psophocarpus tetragonolobus (L.) DC.

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Abstract

Underutilised legume Psophocarpus tetragonolobus (L.) DC. accumulates various degrees of proanthocyanidin (PA) or condensed tannin (CT) on its seed coat. Screening for PA content among various lines of P. tetragonolobus through the vanillin-HCl assay identified two contrasting lines of P. tetragonolobus (HPW and LPW). HPW contained 59.23 mg/g of total PA, with catechin and epigallocatechin gallate monomer being found among the monomers identified in HPLC; the LPW line contained 8.68 mg/g of PA in its leaves. Comparative miRNA profiling of the leaf tissues of contrasting PA lines of P. tetragonolobus revealed a total of 139 mature miRNAs along with the identification of isoforms and novel miRNAs. Differentially expressed known miRNAs, e.g., miR156, miR396, miR4414b, miR4416c, miR894, miR2111, and miR5139, were validated through qRT-PCR. Target prediction of the identified miRNAs show possible involvement of certain miRNAs like miR396, miR4414b and miR862 in PA biosynthesis in P. tetragonolobus. Hence this study can provide a basis for understanding the role of miRNAs in regulation of PA biosynthesis.

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Data Availability

The generated data used in this study has been submitted in the public domain database of NCBI (SRA Accession No: SRR15115657 to SRR15115660) https://www.ncbi.nlm.nih.gov. The data will be made available publicly after publication of the manuscript.

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Acknowledgements

CSM and SPN acknowledge the Department of Biotechnology for the financial support to carry out this activity and Director, CSIR-National Botanical Research Institute for providing the infrastructure facility. We also acknowledge the National Bureau of Plant Genetic Resources for providing the required germplasm. PP and SPN acknowledge the University Grants Commission for a research fellowship grant. The authors also acknowledge Kirti Pandey and Arpit Chauhan for providing experimental support during the study.

Funding

The research was funded by the project “Bioresources and sustainable livelihoods of Northeast India”, Department of Biotechnology, Govt. of India; Pro.

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Author notes

  1. Sagar Prasad Nayak and Priti Prasad contributed equally to this work.

Authors and Affiliations

  1. CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India

    Sagar Prasad Nayak, Priti Prasad, Sumit Kumar Bag & Chandra Sekhar Mohanty

  2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Sagar Prasad Nayak, Priti Prasad, Sumit Kumar Bag & Chandra Sekhar Mohanty

  3. Department of Biology, Western University, London, ON, Canada

    Vinayak Singh

  4. Kuruom School of Advanced Sciences, Lucknow, 226302, India

    Abhinandan Mani Tripathi

  5. Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, 226 001, India

    Chandra Sekhar Mohanty

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Contributions

CSM, SPN, and VS designed the research work. SPN conducted most of the experiments and prepared samples for small RNA sequencing. PP performed all bioinformatics analyses. SPN and PP wrote the manuscript. VS and AMT provided the necessary suggestions for conducting experiments. CSM, VS, and SB helped in finalising the manuscript and critically assessing the report. All authors read and approved the manuscript.

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Correspondence to Chandra Sekhar Mohanty.

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10725_2023_971_MOESM1_ESM.tif

Supplementary material 1 (TIF 9236.5 kb)—Fig.S1 HPLC Chromatogram of standards (catechin, epicatechin and epigallocatechin)and methanolic (MeOH) extract of P. tetragonolobus leaves

10725_2023_971_MOESM2_ESM.tif

Supplementary material 2 (TIF 12163.6 kb)—Fig.S2 Nucleotide length variations of small RNAs in the sequenced library of HPW and LPW in P. tetragonolobus

10725_2023_971_MOESM3_ESM.tif

Supplementary material 3 (TIF 6538.9 kb)—Fig.S3 Correlation plot between the replicate 1 and replicate 2 of sequenced HPW and LPW library. R value represents correlation value of 0.93 and0.82 in HPW and LPW respectively with significant p-value < 2.2e-16

10725_2023_971_MOESM4_ESM.tif

Supplementary material 4 (TIF 7247.2 kb)—Fig.S4 Different number of identified conserved miRNAs in HPW and LPW library in 52 plant lineages. X-axis represented the different plant species while different numbers of miRNAs was scaled in Y-axis. Bold font scientific name was used for plant species that belongs to Poaceae family

10725_2023_971_MOESM5_ESM.tif

Supplementary material 5 (TIF 9050.7 kb)—Fig.S5 Volcano plot to represents the differentially expressed miRNAs between the HPW and LPW lines of P. tetragonolobus. X-axis was used for the log2 Fold change whereas Y-axis representing the –log2 (p-value). Each dot describes the expressed miRNAs; wherein red dots define the differentially expressed miRNAs

10725_2023_971_MOESM6_ESM.tif

Supplementary material 6 (TIF 10990.4 kb)—Fig.S6 Heat map visualizations of log2 fold change expression values of miRNAs fromthe HPW and LPW. Lower expression values are represented in the red color whilehigher expression values are illustrated in green color. The color scale isranged from 1 to 14

Supplementary material 7 (XLSX 322.7 kb)

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Nayak, S.P., Prasad, P., Singh, V. et al. Role of miRNAs in the regulation of proanthocyanidin biosynthesis in the legume Psophocarpus tetragonolobus (L.) DC.. Plant Growth Regul 102, 23–38 (2024). https://doi.org/10.1007/s10725-023-00971-9

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