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Exploring Flowering Genes in Isabgol (Plantago ovata Forsk.) Through Transcriptome Analysis

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Abstract

Background

Flowering is one of the major developmental processes that govern the economic yield of crop plants. However, little is known about the molecular mechanisms underlying flowering in Isabgol, an important high-value medicinal crop. Here, we analyzed the leaf transcriptome of early and late flowering genotypes by high throughput next-generation sequencing to uncover the genes and pathways involved in flowering time and flower development.

Results

Illumina paired-end sequencing of Isabgol leaves at the stem elongation stage, generated 8,976,119 and 4,282,684 reads respectively in DPO-14 (early flowering) and DPO-185 (late flowering) genotypes. The sequence assembly resulted in 40,175 and 39,533 transcripts respectively in early and late genotypes. A total of 17,768 (95.50) in DPO-14 and 21,255 (94.10) in DPO-185 CDS were annotated. There were 8981CDS were differentially expressed of which 1220 (13.58%) were significantly upregulated while 1485 (16.53%) CDS were significantly downregulated in DPO-185 compared with DPO-14. In total, 229 genes were identified belongs to distinct flowering pathways in Isabgol. A putative schematic network of flowering pathway regulation in Isabgol was proposed. Significant DEGs (60 genes) related to flowering time and flower development were detected between the early and late flowering genotypes. Significant differences in fold change expression of 17 genes were observed in early and late flowering genotypes.

Conclusion

Many differentially expressed genes (DEGs) involved in flowering time and flower development were identified. The expression data will serve as a resource for unraveling the functions of specific genes involved in flower development in Isabgol and other plants. These findings are significant for further understanding of the molecular basis for flowering time regulation, breeding, and molecular biology in Isabgol as well as other crop plants.

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Data Availability

The datasets supporting the results of this article are available at the National Center for Biotechnology Information (NCBI) BioProject database (Short Read Archive) under accession number PRJNA382334 and the Transcriptome Shotgun Assembly (TSA) at DDBJ/EMBL/GenBank under the accession GFNS00000000. The version described in this paper is the first version, GFNS00000000.

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Acknowledgments

The authors gratefully acknowledge the Director, ICAR-Directorate of Medicinal and Aromatic Plants Research, Boriavi, Anand, Gujarat, India, and Indian Council of Agricultural research (ICAR), New Delhi, for the facilities to undertake the study.

Funding

The authors gratefully acknowledge the Department of Science and Technology (DST), Government of India (GOI) for financially supporting this work under SERB/EMR/2014/000317 and SERB/EEQ/2016/000693.

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Authors and Affiliations

  1. ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Boriavi, Anand, Gujarat, 387310, India

    Sandip Patel, Khushboo Pachhigar, Rakesh Ganvit, Manivel Ponnuchamy, Jitendra Kumar & Nagaraja Reddy Rama Reddy

  2. Department of Microbiology and Biotechnology, Gujarat University (GU), Navrangpura, Ahmedabad, Gujarat, 380009, India

    Rakeshkumar Ramanlal Panchal

Authors
  1. Sandip Patel
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  2. Khushboo Pachhigar
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  3. Rakesh Ganvit
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  4. Rakeshkumar Ramanlal Panchal
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  5. Manivel Ponnuchamy
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  6. Jitendra Kumar
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  7. Nagaraja Reddy Rama Reddy
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Contributions

Conceived and designed the experiments: NRRR, MP. Performed the experiments: AP, KP, RG, NRRR MP. Analyzed the data: SP, NRRR MP JK, RRP. Contributed reagents/materials/analysis tools: NRRR MP JK. Wrote the paper: NRRR MP RRP.

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Correspondence to Nagaraja Reddy Rama Reddy.

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Key Message

Flowering affects the yield and quality of crop plants. In this study, leaf transcriptome sequencing of early and late flowering genotypes has led to identification of 229 genes that belong to flowering time and flower developmental pathways in Isabgol. A schematic network of flowering pathway regulation in Isabgol was proposed.

Electronic Supplementary Materials

Supplementary Figure 1

Flowering pathways in Isabgol (Plantago ovata Forsk.). Adopted from https://www.wikipathways.org/index.php/Pathway:WP2312 (PDF 836 kb)

Additional file S1

Functional annotation of coding DNA sequences predicted in the leaf transcriptome of Isabgol (Plantago ovata Forsk.) (XLS 6115 kb)

Additional file S2

Differentially expressed genes (DEGs) identified in the leaf transcriptome of DPO-185 and DPO-14 genotypes of Isabgol (Plantago ovata Forsk.) (XLS 5624 kb)

Additional file S3

Flowering genes in the leaf transcriptome of Isabgol (Plantago ovata Forsk.) (XLSX 94 kb)

Additional file S4

ANOVA for the gene expression in fold change in early and late genotypes of Isabgol (Plantago ovata Forsk.) (DOCX 17 kb)

Additional file S5

GO ontology of significantly deferentially expressed genes in the leaf transcriptome of Isabgol (Plantago ovata Forsk.). Molecular function (MF), Biological processes (BP) and Cellular component (CC) (DOCX 39 kb)

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Patel, S., Pachhigar, K., Ganvit, R. et al. Exploring Flowering Genes in Isabgol (Plantago ovata Forsk.) Through Transcriptome Analysis. Plant Mol Biol Rep 39, 192–211 (2021). https://doi.org/10.1007/s11105-020-01237-8

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