Tomato Domestication, From a Wild Ancestor to Crop Varieties : A Transcriptional Landscape Overview

Over the last 10,000 years, plant domestication has led to considerable phenotypic modifications. Though changes in key traits such as fruit morphology have been well documented, little is known about the underlying molecular consequences. Thus, we conducted a comparative study of cultivated and wild type accessions of tomato to measure the effects of domestication on the genome-wide patterns of nucleotide diversity and the levels of transcription.

The sequencing of 10 wild (Solanum pimpinellifolium) and 10 crop (S. lycopersicum) transcriptomes revealed that 35% of the genes experienced a 33% average loss of nucleotide diversity following domestication. Average π_N/π_S ratios were estimated to be 0.252 (crop) and 0.291 (wild types). At the transcriptional level, domestication significantly affected 6.39% of the genes, with 1433 genes differentially expressed between crop and wild, involved in metabolism and stress response. Moreover, a relaxation of the gene expression coefficient of variation was identified in crop when compared to wild types. Finally, a correlation between recombination and genes expression and diversity has been identified suggesting Hill-Robertson interference. Thus, these leads unravel the phenotypic divergence between wild and crop tomatoes.