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


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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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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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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The authors declare no conflict of interests.

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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).

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  • Litchi
  • Transcriptome
  • Seed size
  • Embryogenesis
  • Small seed