The nuclear component of a cytonuclear hybrid incompatibility in Mimulus maps to a cluster of pentatricopeptide repeat genes

Abstract

Characterizing the genetic and molecular basis of hybrid incompatibilities is a first step toward understanding their evolutionary origins. We fine mapped the nuclear restorer (Rf) of cytoplasm-dependent anther sterility in Mimulus hybrids by identifying and targeting regions of the Mimulus guttatus genome containing large numbers of candidate pentatricopeptide repeat genes (PPRs). The single Mendelian locus Rf was first isolated to a 1.3-cM region on linkage group 7 that spans the genome's largest cluster of PPRs, then split into two tightly linked loci (Rf1 and Rf2) by <10 recombination events in a large (N = 6153) fine-mapping population. Progeny testing of fertile recombinants demonstrated that a dominant M. guttatus allele at each Rf locus was sufficient to restore fertility. Each Rf locus spans a physical region containing numerous PPRs with high homology to each other, suggesting recent tandem duplication or transposition. Furthermore, these PPRs have higher homology to restorers in distantly related taxa (petunia and rice) than to PPRs elsewhere in the Mimulus genome. These results suggest that the cytoplasmic male sterility (CMS)-PPR interaction is highly conserved across flowering plants. In addition, given our theoretical understanding of cytonuclear coevolution, the finding that hybrid CMS results from interactions between a chimeric mitochondrial transcript that is modified by Rf loci identified as PPRs is consistent with a history of selfish mitochondrial evolution and compensatory nuclear coevolution within M. guttatus.

Figure 1.—

Distribution of PPR genes on scaffolds of the Mimulus guttatus genome, with a very large majority of scaffolds containing no PPRs and a small number containing many. The actual number of PPR-coding genes in the M. guttatus genome is likely smaller than reported here due to spurious motif identification by HMMER and artificial splitting of single genes; however, we closely examined most of the PPRs on scaffold 14 (the rightmost bar) and it is clear that this scaffold is extremely PPR rich. While variation in number of PPRs among scaffolds is partially explained by scaffold size (r² = 0.42, P < 0.000), the majority of the variation observed in PPR number is not explained by scaffold size, and scaffold 14 falls as a clear outlier.

Figure 2.—

Genetic and physical maps of the Rf loci and candidate PPR genes in Mimulus. (A) Genetic map showing informative recombinants. Horizontal bars represent regions of heterozygosity for CSBG individuals. Shaded bars indicate male-fertile plants and solid bars indicate male-sterile plants. Restoration of fertility maps to a region of ∼1.3 cM. We refer to these loci as Rf1 and Rf2. (B) Physical map of the region containing Rf1 and Rf2 showing the location of markers (triangles) and PPR genes (bars). Solid bars indicate those PPRs that are mitochondrially targeted as identified in the program PREDOTAR (Small et al. 2004), and open bars indicate those that are not mitochondrially targeted.

Figure 3.—

Bayesian unrooted tree showing the relationships between M. guttatus Rf-linked PPRs, known Rf from crop taxa, Arabidopsis Rf homologs, and non-Rf PPRs from M. guttatus and other taxa. At, Arabidopsis thaliana. Numbers following M. guttatus PPRs refer to the scaffold followed by a PPR-specific number. Parentheses for M. guttatus PPRs indicate that the PPR has 13–16 motifs, and the number refers to the number of motifs. The inset expands the M. guttatus clade that contains all 16 (of the 17 total) PPRs used in this analysis within the region containing Rf1/Rf2.