Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size

Pathak, Ashish K.; Singh, Sudhir P.; Sharma, Ritika; Nath, Vishal; Tuli, Rakesh

doi:10.1007/s13205-021-03098-8

Original Article
Published: 22 January 2022

Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size

Ashish K. Pathak ORCID: orcid.org/0000-0003-2114-396X^1,2,
Sudhir P. Singh^1,3,
Ritika Sharma⁴,
Vishal Nath⁵ &
Rakesh Tuli^1,2

3 Biotech volume 12, Article number: 47 (2022) Cite this article

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Abstract

Litchi is a sub-tropical fruit crop with genotypes that bear fruits with variable seed size. Small seed size is a desirable trait in litchi, as it improves consumers’ preference and facilitates fruit processing. Seed specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to identify the genes associated with seed development. The transcriptomic sequence data from seeds at mid-development stages (16–28 days after anthesis) were de-novo assembled into 1,39,608 Trinity transcripts. Out of these, 6325 transcripts expressed differentially between the two contrasting genotypes. Several putative genes for salicylic acid, jasmonic acid and brassinosteriod pathways were down-regulated in seeds of the small-seeded litchi. The putative regulators of seed maturation and seed storage were down-regulated in the small-seeded genotype. Embryogenesis, cell expansion, seed size and stress related Trinity transcripts exhibited differential expression. Further studies on gene characterization will reveal the early regulators of seed size in litchi.

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Acknowledgements

This work was supported by Department of Biotechnology (DBT), Govt. of India. AKP acknowledges DBT JRF-SRF fellowship. RT acknowledges JC Bose fellowship. Authors acknowledge Indian Council of Agriculture Research (ICAR), Govt. of India for creation and maintenance of litchi germplasm collection.

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Authors and Affiliations

National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India
Ashish K. Pathak, Sudhir P. Singh & Rakesh Tuli
Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
Ashish K. Pathak & Rakesh Tuli
Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
Sudhir P. Singh
Sardar Swaran Singh National Institute of Bioenergy, Jalandhar, India
Ritika Sharma
ICAR-National Research Centre of Litchi, Muzaffarpur, India
Vishal Nath

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Ashish K. Pathak
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Sudhir P. Singh
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Ritika Sharma
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Vishal Nath
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Rakesh Tuli
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Contributions

RT and SPS and proposed and designed the study. AKP performed the experiments, and analyzed data. RS performed qRT-PCR experimental analysis. SPS guided the experiments and participated in sample collection. VN guided and participated in plant sample collection. AKP wrote the manuscript, RT and SPS corrected and improved the manuscript. All authors read and approved the manuscript.

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Correspondence to Ashish K. Pathak or Sudhir P. Singh.

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Pathak, A.K., Singh, S.P., Sharma, R. et al. Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size. 3 Biotech 12, 47 (2022). https://doi.org/10.1007/s13205-021-03098-8

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Received: 16 October 2021
Accepted: 18 December 2021
Published: 22 January 2022
DOI: https://doi.org/10.1007/s13205-021-03098-8

Keywords

Litchi
Transcriptome
Seed size
Embryogenesis
Small seed