Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication

Area of Science:

• Plant genomics
• Crop science
• Evolutionary biology

Background:

• Annual teosinte is the wild ancestor of cultivated maize (Zea mays ssp. mays).
• It represents a crucial source of genetic diversity for improving maize adaptability.
• Limited transcriptomic and genomic data hinder the use of teosinte's favorable genes.

Purpose of the Study:

• To generate a comprehensive transcriptomic resource for annual teosinte.
• To identify genes conserved or diverged during maize domestication.
• To develop molecular tools for teosinte germplasm utilization.

Main Methods:

• Illumina paired-end sequencing of six teosinte accessions.
• De novo assembly of the teosinte transcriptome.
• Comparative analysis with maize and other plant genomes.

Main Results:

• A high-quality teosinte transcriptome was assembled, with 63.99% annotated unigenes.
• Approximately 75% of genes are conserved between teosinte and maize.
• 1516 teosinte-specific unigenes were identified, including evidence-based expressed presence/absence variations (ePAVs).
• 99 unigenes showed strong selection signals, and 57 had Ka/Ks ratios >1, indicating selection during domestication.
• 11,286 teosinte unigene-derived simple sequence repeat (SSR) primer pairs were developed.

Conclusions:

• This study provides a valuable teosinte transcriptome dataset.
• Identified genes offer insights into maize domestication and evolution.
• Developed SSR markers facilitate teosinte germplasm utilization for maize improvement.