Mitotypes Based on Structural Variation of Mitochondrial Genomes Imply Relationships With Morphological Phenotypes and Cytoplasmic Male Sterility in Peppers.

Yeong Deuk Jo,Si-Yong Kang,Byoung-Cheorl Kang,Hea-Young Lee,Sang Hoon Kim,Na-Young Ro,Jin-Baek Kim

doi:10.3389/fpls.2019.01343

Abstract

Plant mitochondrial genomes characteristically contain extensive structural variation that can be used to define and classify cytoplasm types. We developed markers based on structural variation in the mitochondrial genomes of fertile and cytoplasmic male sterility (CMS) pepper lines and applied them to a panel of Capsicum accessions. We designed a total of 20 sequence characterized amplified region (SCAR) markers based on DNA rearrangement junctions or cytoplasm-specific segments that did not show high similarity to any nuclear mitochondrial DNA segments. We used those markers to classify the mitotypes of 96 C. annuum accessions into 15 groups. Precise genotyping of other Capsicum species (C. frutescens, C. chinense, and C. baccatum) was hampered because of various stoichiometric levels of marker amplicons. We developed a multiplex PCR system based on four of the markers that efficiently classified the C. annuum accessions into five mitotype groups. Close relationships between specific mitotypes and morphological phenotypes implied that diversification or domestication of C. annuum germplasm might have been accompanied by structural rearrangements of mitochondrial DNA or the selection of germplasms with specific mitotypes. Meanwhile, CMS lines shared the same amplification profile of markers with another mitotype. Further analysis using mitochondrial DNA (mtDNA) markers based on single-nucleotide polymorphisms (SNPs) or insertions and deletions (InDels) and CMS-specific open reading frames (orfs) provided new information about the origin of the CMS-specific mitotype and evaluation of candidates for CMS-associated genes, respectively.

Highlights

In comparison to animals, the rate of nucleotide substitution in mitochondrial genome is much slower in most plant species except for several independent lineages that show highly accelerated rate, whereas evolution of genome structure is much faster and on a large scale (Kress et al, 2005; Sloan et al, 2012; Wolfe et al, 1987)
We collected sequences that surround DNA rearrangement junctions or are unique to one of the two cytoplasms and used BLAST to compare them against the CM334 nuclear genome to select sequences that have no homologous nuclear mitochondrial sequences (Numts)
Characteristics of Markers Based on Structural Variation in mitochondrial DNA (mtDNA) in Pepper

Summary

Introduction

The rate of nucleotide substitution in mitochondrial genome is much slower in most plant species except for several independent lineages that show highly accelerated rate, whereas evolution of genome structure is much faster and on a large scale (Kress et al, 2005; Sloan et al, 2012; Wolfe et al, 1987). Diverse parental and recombinant molecules coexist in mitochondria, maintaining a certain relative ratio between them, but SSS can cause rapid amplification or loss of specific molecules (Janska et al, 1998; Arrieta-Montiel et al, 2001; Feng et al, 2009; Chen et al, 2011) Those extensive changes can be caused by wide crosses, in vitro culture, or the suppression or mutation of genes involved in the surveillance of mitochondrial DNA (mtDNA) recombination (Hanson and Bentolila, 2004; Sandhu et al, 2007; Shedge et al, 2007)

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