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Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

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

Ashish K Pathak^1,2, Sudhir P Singh^1,3, Ritika Sharma⁴

¹National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India.

|February 7, 2022

Summary

Small litchi seeds are preferred by consumers. Researchers identified key gene pathways, including those for salicylic acid and brassinosteroid, that are down-regulated in small-seeded litchi, offering insights into fruit development.

Keywords:

Embryogenesis Litchi Seed size Small seed Transcriptome

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Area of Science:

Plant Genetics and Genomics
Fruit Crop Improvement
Molecular Biology

Background:

Litchi (Litchi chinensis) is a sub-tropical fruit crop known for variable seed sizes among genotypes.
Small seed size is a commercially desirable trait, enhancing consumer appeal and processing efficiency.

Purpose of the Study:

To identify genes and molecular pathways regulating seed development and size in litchi.
To compare gene expression profiles between litchi genotypes with contrasting seed sizes.

Main Methods:

Performed seed-specific transcriptome analysis on two litchi genotypes with contrasting seed sizes.
Collected seed samples at mid-development stages (16-28 days after anthesis).
Utilized de novo assembly of transcriptomic sequence data and differential expression analysis.

Main Results:

Assembled 1,39,608 Trinity transcripts; identified 6,325 differentially expressed transcripts between genotypes.
Observed down-regulation of genes in salicylic acid, jasmonic acid, and brassinosteroid pathways in small-seeded litchi.
Found differential expression in transcripts related to embryogenesis, cell expansion, seed size, and stress responses.

Conclusions:

Specific molecular pathways and regulators are associated with litchi seed size determination.
Down-regulation of hormone signaling and seed maturation pathways may contribute to smaller seed size.
Further gene characterization is needed to elucidate early regulators of seed size in litchi.