Genome-wide Identification of Chile Pepper Pentatricopeptide Repeat Domains Provides Insight into Fertility Restoration

Abstract

Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in plants. They are typically targeted to the mitochondria or chloroplast and bind to one or more organellar transcripts, influencing expression. Genes responsible for inhibiting the mitochondrial genes that cause cytoplasmic male sterility (CMS), restorer-of-fertility (Rf) genes, often encode PPRs. Using in silico techniques, 552 PPR domains were identified throughout the chile pepper (Capsicum annuum) genome. The domains were mapped across 12 chromosomes and were found to be largely distally or proximally located. About 28% of the chile pepper PPR domains identified in this study have high structural similarity to previously reported PPRs in arabidopsis (Arabidopsis thaliana). In addition, 11 candidate Rf genes clustered on chromosome 6, and 1 on chromosome 1 were identified that were characterized in 16 A- (S rfrf), B- (N rfrf), and C-line (N RfRf) backgrounds. These findings support a multigene model for fertility restoration and broaden our understanding of the restoration of fertility. This may be an explanation for the lack of widely applicable molecular markers for this important trait. With this new information, specific Rf markers may be developed and will facilitate the implementation of hybrid breeding programs in chile pepper. In addition, this work provides a basis for future research in PPRs, an increasingly important gene family.