Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process.

Ana Garcés-Claver,Corina Hayano-Kanashiro,Octavio Martínez,Neftalí Ochoa-Alejo,José J Ordaz-Ortiz,M Humberto Reyes-Valdés,Felipe Cervantes-Hernández,Fernando Hernández-Godínez,Fernando G Razo-Mendivil,Christian Escoto-Sandoval,Magda L Arce-Rodríguez

doi:10.3390/plants10030585

Abstract

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles 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.

Highlights

Chili peppers of the genus Capsicum and the Solanaceae family are native to the American continent
To study the divergence caused by domestication in gene expression profiles during chili pepper fruit development, we examined fruit transcriptomes of six domesticated and four wild accessions using RNA sequencing (RNA-Seq) every 10 days from anthesis until fruiting at 60 days after anthesis (DAA)
A total of 22,427 genes, representing approximately 64% of the genes annotated in the Capsicum genome, were consistently expressed during fruit development in all of the accessions analyzed

Summary

Introduction

Chili peppers of the genus Capsicum and the Solanaceae family are native to the American continent. Among these species, C. annuum is the most important worldwide as a vegetable and spice crop, and production of this type of chili pepper has been steadily increasing in terms of both area harvested and yield [2]. C. annuum is the most important worldwide as a vegetable and spice crop, and production of this type of chili pepper has been steadily increasing in terms of both area harvested and yield [2] In addition to their economic importance, chili peppers are a source of antioxidants, such as flavonoids, phenolic acids, carotenoids, and vitamins [3,4], as well as a plant model for studying the genetic and biochemical basis for the synthesis of these compounds [5,6,7]. Differential expression analysis during chili pepper fruit development allowed the identification of regulatory and biosynthetic genes related to different metabolic processes during fruit development and ripening, including fruit softening, pigmentation, ripening time, and metabolite accumulation [11,12,13]

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