Domestication rewired gene expression and nucleotide diversity patterns in tomato

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Plant domestication significantly modifies phenotypes from wild ancestors to modern crops.
• While key trait changes are documented, molecular mechanisms like reduced diversity and altered gene co-expression remain less understood.

Purpose of the Study:

• To investigate the molecular footprints of domestication in tomato using gene expression and population genetics.
• To identify changes in gene co-expression patterns and nucleotide diversity during tomato domestication.

Main Methods:

• Comparative analysis of gene expression profiles between wild and crop tomato.
• Population genetics approaches to assess nucleotide diversity.
• Identification and clustering of differentially expressed genes (DEGs).

Main Results:

• Identified 1729 differentially expressed genes (DEGs) between wild and crop tomato, organized into 17 co-expression clusters.
• Discovered that domestication impacts gene regulatory networks, not just individual genes.
• Found enrichment of functional terms related to carbohydrate metabolism and epigenetic regulation in five co-expression clusters.
• Observed specific differences in nucleotide diversity for DEGs between crop and wild tomato groups.

Conclusions:

• Domestication syndrome in tomato involves significant rewiring of gene co-expression networks.
• These changes affect molecular diversity and regulatory mechanisms, contributing to crop evolution.
• The study provides a comprehensive profile of domestication-induced gene expression alterations in tomato.