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Transcriptome analysis of apical meristem enriched bud samples for size dependent flowering commitment in Crocus sativus reveal role of sugar and auxin signalling

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Abstract

Background

Cultivation of Crocus sativus (saffron) faces challenges due to inconsistent flowering patterns and variations in yield. Flowering takes place in a graded way with smaller corms unable to produce flowers. Enhancing the productivity requires a comprehensive understanding of the underlying genetic mechanisms that govern this size-based flowering initiation and commitment. Therefore, samples enriched with non-flowering and flowering apical buds from small (< 6 g) and large (> 14 g) corms were sequenced.

Methods and results

Apical bud enriched samples from small and large corms were collected immediately after dormancy break in July. RNA sequencing was performed using Illumina Novaseq 6000 to access the gene expression profiles associated with size dependent flowering. De novo transcriptome assembly and analysis using flowering committed buds from large corms at post-dormancy and their comparison with vegetative shoot primordia from small corms pointed out the major role of starch and sucrose metabolism, Auxin and ABA hormonal regulation. Many genes with known dual responses in flowering development and circadian rhythm like Flowering locus T and Cryptochrome 1 along with a transcript showing homology with small auxin upregulated RNA (SAUR) exhibited induced expression in flowering buds. Thorough prediction of Crocus sativus non-coding RNA repertoire has been carried out for the first time. Enolase was found to be acting as a major hub with protein–protein interaction analysis using Arabidopsis counterparts.

Conclusion

Transcripts belong to key pathways including phenylpropanoid biosynthesis, hormone signaling and carbon metabolism were found significantly modulated. KEGG assessment and protein–protein interaction analysis confirm the expression data. Findings unravel the genetic determinants driving the size dependent flowering in Crocus sativus.

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Data availability

The Sequencing files were submitted to NCBI under Sequence Read Archive (SRA) with bioproject accession number PRJNA1021807. In addition, supporting datasets are available on public repository platform Zenodo under the DOI: https://doi.org/https://doi.org/10.5281/zenodo.10852852.

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Acknowledgements

AC is thankful to CSIR, India for fellowship.

Funding

Work was supported by CSIR project MLP0168 (MLP0049).

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Authors and Affiliations

  1. CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India

    Anjali Chaudhary & Kunal Singh

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

    Anjali Chaudhary & Kunal Singh

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  1. Anjali Chaudhary
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KS and AC designed and conceptualized the work. AC executed the experiments. AC and KS analyzed the data and wrote the manuscript. KS arranged funding.

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Correspondence to Kunal Singh.

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Chaudhary, A., Singh, K. Transcriptome analysis of apical meristem enriched bud samples for size dependent flowering commitment in Crocus sativus reveal role of sugar and auxin signalling. Mol Biol Rep 51, 605 (2024). https://doi.org/10.1007/s11033-024-09574-7

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