Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Alternative splicing (AS) drives eukaryotic transcriptome diversity and is crucial for evolution and development.
• Investigating AS in maize and its ancestor, teosinte, offers insights into domestication and adaptation.
• Comparative transcriptomic analysis reveals AS roles in crop improvement.

Purpose of the Study:

• To analyze alternative splicing changes during maize domestication.
• To identify signatures of selection related to AS in maize improvement.
• To understand the role of transposable elements in AS variation.

Main Methods:

• Sequencing of six teosinte and ten maize transcriptomes.
• Identification and comparison of alternative splicing events between maize and teosinte.
• Analysis of gene selection signatures in alternatively spliced genes.

Main Results:

• Maize exhibits higher unique alternative splicing events per gene than teosinte.
• Transposable element insertion is linked to intron retention in maize.
• 151 alternatively spliced genes, involved in transcriptional regulation and stress response, show signatures of selection during maize improvement.

Conclusions:

• Maize and teosinte share similar AS mechanisms, but maize shows increased AS complexity post-domestication.
• Selected AS genes, particularly those related to stress response and transcription factors, likely contributed to maize improvement.