Differential gene expression and alternative splicing between diploid and tetraploid watermelon

Area of Science:

• Plant genetics and genomics
• Molecular biology
• Agricultural science

Background:

• Seedless watermelon production relies on synthetic polyploids, with tetraploid progenitors showing distinct phenotypes from diploids.
• The impact of autopolyploidization on alternative splicing (AS) in plants remains largely unexplored.

Purpose of the Study:

• To investigate the effects of autopolyploidization on gene expression and alternative splicing (AS) in diploid and tetraploid sweet watermelon.
• To identify genes and pathways affected by ploidy changes in various watermelon tissues.

Main Methods:

• Comparative transcriptomic analysis using RNA-sequencing on leaf, stem, and fruit tissues from diploid and tetraploid watermelon.
• Validation of gene expression and AS events using reverse transcription quantitative PCR (RT-qPCR) and rapid amplification of cDNA ends (RACE)-PCR.
• Ploidy level confirmation using a ploidy analyzer.

Main Results:

• Tetraploid watermelon exhibited increased AS levels in vegetative tissues (leaf, stem) compared to diploids.
• 5362 genes were upregulated and 1288 downregulated in tetraploids versus diploids; 22 genes showed AS events across tissues.
• Key metabolic pathways (arginine, chlorophyllide, GDP mannose biosynthesis, trehalose biosynthesis, starch/sucrose degradation) were upregulated in autotetraploids.

Conclusions:

• Autopolyploidization significantly reshapes the transcriptome and splicing patterns in watermelon, particularly in vegetative tissues.
• Identified AS events in genes like MYB transcription factor and transporters suggest potential for altered protein functions and improved seedless watermelon traits.
• Findings contribute valuable transcriptomic data for enhancing seedless watermelon quality and understanding polyploidization effects in cucurbits.