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Comparative RNA-Seq profiling of a resistant and susceptible peanut (Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis

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Abstract

The goal of this study was to identify differentially expressed genes (DEGs) responsible for peanut plant (Arachis hypogaea) defence against Puccinia arachidis (causative agent of rust disease). Genes were identified using a high-throughput RNA-sequencing strategy. In total, 86,380,930 reads were generated from RNA-Seq data of two peanut genotypes, JL-24 (susceptible), and GPBD-4 (resistant). Gene Ontology (GO) and KEGG analysis of DEGs revealed essential genes and their pathways responsible for defence response to P. arachidis. DEGs uniquely upregulated in resistant genotype included pathogenesis-related (PR) proteins, MLO such as protein, ethylene-responsive factor, thaumatin, and F-box, whereas, other genes down-regulated in susceptible genotype were Caffeate O-methyltransferase, beta-glucosidase, and transcription factors (WRKY, bZIP, MYB). Moreover, various genes, such as Chitinase, Cytochrome P450, Glutathione S-transferase, and R genes such as NBS-LRR were highly up-regulated in the resistant genotype, indicating their involvement in the plant defence mechanism. RNA-Seq analysis data were validated by RT-qPCR using 15 primer sets derived from DEGs producing high correlation value (R2 = 0.82). A total of 4511 EST-SSRs were identified from the unigenes, which can be useful in evaluating genetic diversity among genotypes, QTL mapping, and plant variety improvement through marker-assisted breeding. These findings will help to understand the molecular defence mechanisms of the peanut plant in response to P. arachidis infection.

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Data availability

The datasets generated during and/or analyzed during the current study are available in the GenBank repository. For rust infected samples, resources are BioProject ID: PRJNA489546: Arachis hypogaea (Resistant GPBD-4 Infected) SRA ID SRX4779274 and Arachis hypogaea (susceptible JL-24 Infected) SRA ID SRX4779275 while for control samples, they are BioProject ID: PRJNA490412: Arachis hypogaea (Resistant GPBD-4 control) SRA ID SRX4782027 and Arachis hypogaea (susceptible JL-24 control) SRA ID SRX4782028. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA489546https://www.ncbi.nlm.nih.gov/bioproject/PRJNA490412.

Abbreviations

GO:

Gene Ontology

DEG:

Differentially Expressed Gene

NGS:

Next Generation Sequencing

PR:

Pathogenesis related

GST:

Glutathione S-Transferase

JA:

Jasmonic Acid

ERF:

Ethylene responsive factor

RT-qPCR:

Reverse Transcription quantitative PCR

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Acknowledgments

Authors are very thankful to Dr. B. A. Golakiya at the Department of Agricultural Biotechnology and Biochemistry, Junagadh for extending their support and guidance in the execution of the experiment. The authors would like to acknowledge the contribution of Mr. Manoj Parakhia for support to carry out research work and the generation of electron microscope images.

Funding

We are thankful to the Department of Agricultural Biotechnology and Biochemistry, Junagadh Agricultural University for providing peanut resistant and susceptible germplasm and laboratory facility during the experiment.

Author information

Authors and Affiliations

  1. Institute of Science, Nirma University, Ahmedabad, Gujarat, India

    Visha Rathod, Rushika Patel & Nasreen S. Munshi

  2. Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Mashhad, Iran

    Rasmieh Hamid

  3. Department of Biotechnology and Biochemistry, Junagadh Agricultural University, Junagadh, Gujarat, India

    Rukam S. Tomar, Shital Padhiyar & Jasminkumar Kheni

  4. ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India

    P. P. Thirumalaisamy

Authors
  1. Visha Rathod
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  2. Rasmieh Hamid
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  4. Rushika Patel
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  5. Shital Padhiyar
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  6. Jasminkumar Kheni
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  7. P. P. Thirumalaisamy
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  8. Nasreen S. Munshi
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Contributions

VR executed laboratory and fieldwork of the project, analysed data as well as drafted the manuscript, RH assisted in data analysis as well as improving the manuscript, RST guided throughout the experiment, provided germ-plasm and laboratory facility to generate NGS data and validation using RT-qPCR, RP assisted in the improving the manuscript. SP and JK assisted in the laboratory and fieldwork of the project. PT guided throughout the experiment and helped in pathogen confirmation, NM conceptualized the project, supervised overall experiment and finalised the manuscript.

Corresponding author

Correspondence to Nasreen S. Munshi.

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None of the authors have any financial or personal relationships that could inappropriately influence or bias the content of the research paper.

Electronic supplementary material

Below is the link to the electronic supplementary material.

13205_2020_2270_MOESM1_ESM.xlsx

Supplementary Table 1 A detailed information of expression profile of DEGs between GPBD-4_infected and GPBD-4_control (XLSX 53 kb)

13205_2020_2270_MOESM2_ESM.xlsx

Supplementary Table 2 A detailed information of expression profile of DEGs between JL-24_infected and JL-control (XLSX 48 kb)

13205_2020_2270_MOESM3_ESM.xlsx

Supplementary Table 3 A detailed information of expression profile of DEGs between GPBD-4_infected and JL-24_infected (XLSX 41 kb)

13205_2020_2270_MOESM4_ESM.xlsx

Supplementary Table 4 A detailed information of expression profile of DEGs between GPBD-4_control and JL-24_control (XLSX 15 kb)

Supplementary Table 5 GO classification of expressed genes in RI/RC and SI/SC by WEGO (XLS 25 kb)

Supplementary Table 6 GO classification of expressed genes by REVIGO tool. (XLSX 20 kb)

13205_2020_2270_MOESM7_ESM.xlsx

Supplementary Table7 KEGG enrichment analysis of DEGs between resistant and susceptible genotypes of Arachis hypogaea. (XLSX 11 kb)

13205_2020_2270_MOESM8_ESM.xlsx

Supplementary Table 8 List of primers with details of sequence and expression profile used for RT-qPCR validation (XLSX 11 kb)

Supplementary Table 9 SSR analysis and primers list (XLS 33 kb)

13205_2020_2270_MOESM10_ESM.pdf

Supplementary Fig. 1 GO classification of non-redundantly expressed genes among RI/RC and SI/SC. Bars show the percentages of genes matches to each GO term using a web-based tool, WEGO. Results are grouped by three main functional categories; biological process, cellular component, and molecular function (PDF 611 kb)

13205_2020_2270_MOESM11_ESM.pdf

Supplementary Fig. 2 A. category-wise distribution of genes. B. Enrichment GO analysis of DEGs performed by REVIGO to identify genes associated with defence mechanism processes. Each bubble in the scatter plot indicates a different GO term. (PDF 1391 kb)

Supplementary Fig. 3 RT-qPCR analysis of DEGs compared with the RNA-Seq data. (PDF 66 kb)

13205_2020_2270_MOESM13_ESM.pdf

Supplementary Fig. 4 SSR validation by using 15 SSR with both resistant and susceptible varieties of peanut through PCR Gel-Doc image. (PDF 141 kb)

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Rathod, V., Hamid, R., Tomar, R.S. et al. Comparative RNA-Seq profiling of a resistant and susceptible peanut (Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis. 3 Biotech 10, 284 (2020). https://doi.org/10.1007/s13205-020-02270-w

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