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De novo assembly and comparative transcriptome analysis of contrasting pearl millet (Pennisetum glaucum L.) genotypes under terminal drought stress using illumina sequencing

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Abstract

Pearl millet (Pennisetum glaucum L.) is one of the most important small-grained annual cereal crops grown in the arid and semi-arid regions of India and Africa, where terminal drought is a major constraint for its productivity. Terminal drought stress is more damaging to pearl millet than drought at vegetative stage as 50% or more reduction in yield may incur. However, a pearl millet genotype, PRLT2/89-33, parent of a mapping population is tolerant to terminal drought stress. With the aim to understand the molecular mechanism underlying terminal drought tolerance in this naturally drought tolerant crop, we examined the leaf transcriptome of contrasting pearl millet genotypes namely, PRLT2/89-33 and H77/833-2 differing for terminal drought tolerance using illumina Miseq sequencing platform. In this study, 40,880 genes were found to be differentially expressed and 8273 unigenes showed significant similarities to known sequences in NCBI non-redundant (nr) database and were classified into 189 Gene Ontology and 24 Clusters of Orthologous Group terms for both the genotypes. Expression profiling of 13 randomly selected transcripts was done to validate the RNA-Seq data. The study revealed that the genes for phytohormones biosynthesis, secondary metabolites and abiotic stress related transcription factors were more expressed in PRLT2/89-33, throwing insights into the molecular basis of its terminal drought tolerance. The study also supported that Illumina Miseq Platform is a powerful tool for transcriptome analysis and molecular-marker development in economically important non-model crop species, particularly those with large and complex genomes.

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Data availabilty

Raw Illumina sequences were submitted to NCBI (BioProject ID: PRJNA607164). The raw reads can be accessed with accession number SAMN14122710 for PRLT2/89-33 samples and SAMN14122711 for H77/833-2 samples.

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Acknowledgements

CL acknowledges the INSPIRE Faculty Award [IFA-11LSPA-01] from Department of Science & Technology (DST), GoI, New Delhi. RS acknowledges Senior Research Fellowship (Fellow No. 31/08(348)/2018-EMR-I) from Council of Scientific and Industrial Research (CSIR), GoI, New Delhi. The authors are thankful to Dr. Rakesh Srivastava, International Crops Research Institute for the Semi- Arid Tropics, Patancheru, India for providing pearl millet seed materials.

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  1. Charu Lata

    Present address: CSIR-National Institute of Science Communication and Information Resources, 14 Satsang Vihar Marg, New Delhi, 110067, India

Authors and Affiliations

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

    Radha Shivhare, Deepika Lakhwani, Mehar H. Asif, Puneet S. Chauhan & Charu Lata

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

    Radha Shivhare, Mehar H. Asif, Puneet S. Chauhan & Charu Lata

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  1. Radha Shivhare
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  2. Deepika Lakhwani
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Contributions

CL conceived and designed the experiment and did the funding acquisition. RS and CL conducted the experiments. RS, DL, MHA, PSC and CL analyzed the data. RS and CL wrote the manuscript. All authors read and approved the manuscript.

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Correspondence to Charu Lata.

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13237_2020_324_MOESM1_ESM.xlsx

DEGs identified in PRLT2/89-33 and H77/833-2. All the genes were sorted with log2 fold change in the range ≥+2.0 and ≤-2.0 and corrected P-values <0.05 (XLSX 7830 kb)

13237_2020_324_MOESM2_ESM.xlsx

Functional annotation of DEGs identified in PRLT2/89-33 and H77/833-2. All the genes were sorted with log2 fold change in the range ≥+2.0 and ≤-2.0 and corrected P-values <0.05. (XLSX 2063 kb)

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Shivhare, R., Lakhwani, D., Asif, M.H. et al. De novo assembly and comparative transcriptome analysis of contrasting pearl millet (Pennisetum glaucum L.) genotypes under terminal drought stress using illumina sequencing. Nucleus 63, 341–352 (2020). https://doi.org/10.1007/s13237-020-00324-1

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