Identifying Genomic Regions Targeted During Eggplant Domestication Using Transcriptome Data

Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A bottom-up population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solarium insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high F-ST, between the 2 populations (evidence of significant divergence) and low pi for the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.

Automated summary

This study utilized a bottom-up population genetics approach to investigate genomic changes involved in eggplant domestication. It identified SNPs and genes associated with domestication traits, with a focus on genes related to photosynthesis and environmental response. The research revealed shared chromosomal regions involved in the domestication of eggplant and tomato, highlighting the importance of understanding genetic changes for crop improvement.