Changes in Alternative Splicing in Response to Domestication and Polyploidization in Wheat

Area of Science:

• Plant genetics
• Molecular biology
• Evolutionary biology

Background:

• Alternative splicing (AS) is a key regulator of transcriptome and proteome diversity in eukaryotes.
• Understanding AS variation during crop domestication and polyploidization is crucial for crop improvement.
• Hexaploid wheat (Triticum aestivum) provides an excellent model due to its complex polyploid history.

Purpose of the Study:

• To investigate changes in the alternative splicing landscape of wheat during domestication and polyploidization.
• To analyze the impact of polyploidization events on AS frequency and patterns across different wheat ploidy levels.
• To explore subgenome-specific AS responses and inter-subgenome interactions in hexaploid wheat.

Main Methods:

• High-throughput transcriptome sequencing of roots and leaves from wheat species with varying ploidies.
• Comparative analysis of AS events in wild, domesticated, and synthetic wheat lines.
• Investigation of homeolog-specific AS and subgenome interactions in hexaploid wheat.

Main Results:

• Approximately 22.1% of wheat genes exhibit alternative splicing, with intron retention being the predominant type.
• Domestication led to a decrease in the number of AS events in both diploid and tetraploid wheat.
• Polyploidization generally reduced AS frequency, supporting a functional sharing model in polyploid crops.
• ~87.1% of homeologs displayed AS partitioning, and D-subgenome substitution altered AS patterns in A- and B-subgenomes.

Conclusions:

• Alternative splicing undergoes extensive variation in response to domestication and polyploidization in wheat.
• Subgenome interplay plays a significant role in reprogramming genome-wide AS profiles during polyploidization.
• These findings provide insights into the regulatory mechanisms underlying wheat evolution and adaptation.