Transcriptomic Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into Domestication Process

Abstract

Chili pepper (Capsicum spp.) is both an important crop and a model for domestication studies. Here we performed a time course experiment to estimate standardized gene expression profiles across fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptome every 10 days, from flower to fruit at 60 Days After Anthesis (DAA), and found that the mean standardized expression profile for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time-shift in expression which explains some of the differences between domesticated and wild phenotypes.