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

Abstract

ADDITIONAL INDEX WORDS. bioinformatics, chile pepper, cytoplasmic male sterility, hybrid breeding, PPR, restorer of fertility, single nucleotide polymorphism 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.

A predicted NEDD8 conjugating enzyme gene identified as a Capsicum candidate Rf gene using bulk segregant RNA sequencing

“…It is interesting that the candidate Rf genes in our study and the previous studies were all located on the terminus of chromosome 6, such as CaPPR_46 77 , 78 , CaRf032 79 , and Capa06g002866 80 (Fig. 7 ).…”

“…It is worth mentioning that the majority of Rf genes encode PPR proteins 8 , 20 , 21 . The PPR genes are members of a protein family that is exceptionally large in plants, and pepper is no exception, with more than 550 putative PPR genes identified 77 . Some attempts have been made to find pepper Rf genes with a PPR structure 77 , 78 .…”

“…The PPR genes are members of a protein family that is exceptionally large in plants, and pepper is no exception, with more than 550 putative PPR genes identified 77 . Some attempts have been made to find pepper Rf genes with a PPR structure 77 , 78 . In this study, it is interesting that a gene, Capana06g002814, is a predicted PPR protein that was mapped to the same region related to the restorer-of-fertility for CMS in pepper.…”

Molecular advancements in male sterility systems of Capsicum: A review

“…A molecular marker, Co1Mod1‐CAPS (on chromosome 6), which is closest to the CaPPR6 gene, was developed as co‐dominant marker and performs significantly better than any of the previously reported markers in terms of their applicability to a wide range of breeding lines. Using in silico techniques, 552 PPR domains were identified throughout the Capsicum genome by Barchenger et al (). The domains were mapped across 12 chromosomes.…”

Comparative transcriptional analysis of Capsicum flower buds between a sterile flower pool and a restorer flower pool provides insight into the regulation of fertility restoration

“…A PPR gene, CaPPR6 , was identified as a strong Rf candidate based on expression pattern and characteristics of coding sequence [37]. Recently, 12 candidate PPR genes with similarity to previously reported Rf genes were also identified in pepper [38]. These candidate Rf genes provide a basis for further study of fertility restoration in pepper.…”