Sequence and Expression Divergence during the Domestication of Eggplant

Given the need to feed an increasing population, it is vital to identify the alleles, genes, cultivars and crops which confer yield and stress-tolerance characteristics. Discerning the location and timing of crop domestication allows wild progenitors to be located, and helps identify the genetic changes that confer the traits that humans selected for thousands of years ago. Further, the study of domestication arguably serves as a contemporary and tractable model for evolutionary processes including the effect of selection on the genome and whether the targets of selection are coding or regulatory.

Here we investigate the domestication of eggplant using RNAseq and Genotyping-by-Sequencing. Comparisons of geographically diverse samples of the progenitor species and eggplant reveals an Indian origin, and does not support the previous hypothesis of a second domestication in China. Instead, individuals of the 'progenitor' species in China appear to be feral escapes from domestication, with evidence for hybridisation. Nucleotide diversity in eggplant was about half of that in the progenitor, indicating a moderate genome-wide domestication bottleneck.

The RNAseq data were used to investigate the targets of selection during domestication, both at the gene expression level and the sequence level. Analysis reveals over 80% of the ca. 2,000 differentially expressed (DE) loci were expressed at a lower level in the domesticated species with many genes putatively silenced. GO terms related to metabolism, development and response to stress were over-represented in the DE loci. The sequence-based tests for selection revealed similar GO terms were over-represented. Selective sweep analyses are underway to confirm the targets of selection.