Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus...

Area of Science:

• Plant genomics
• Molecular biology
• Bioinformatics

Background:

• Alternative splicing (AS) is crucial for gene expression and proteome diversity in plants.
• Single nucleotide polymorphisms (SNPs) and insertion/deletions (InDels) are key genetic markers for plant germplasm identification and breeding.
• Limited information exists on AS events and SNP/InDel marker development from radish transcriptomes.

Purpose of the Study:

• To identify and characterize alternative splicing events in radish.
• To develop single nucleotide polymorphism (SNP) and insertion/deletion (InDel) markers from radish transcriptome data.
• To provide molecular resources for radish genetic improvement.

Main Methods:

• Collected and aligned three radish transcriptome datasets to the reference genome.
• Identified alternative splicing (AS) events, single nucleotide polymorphisms (SNPs), insertion/deletions (InDels), and simple sequence repeats (SSRs).
• Validated identified SNPs and InDels using Sanger sequencing and assessed their distribution on linkage groups.

Main Results:

• Identified 56,530 AS events, with intron retention being the most frequent type.
• Discovered 22,412 SNPs and 9,436 InDels, with validated polymorphism rates of 83.9% for SNPs and 70% for InDels.
• Developed 40 informative InDel markers used for genetic diversity analysis in 32 radish accessions.

Conclusions:

• The study provides insights into radish transcriptome complexity and AS regulation.
• Generated a substantial resource of molecular markers (SNPs, InDels, SSRs) for radish.
• These markers will aid in germplasm identification, genetic mapping, and breeding program advancements.