Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

Understanding genome to phenotype linkages has been greatly enabled by genomic sequencing. However, most genome analysis is typically confined to the nuclear genome. We conducted a metabolomic QTL analysis on a reciprocal RIL population structured to examine how variation in the organelle genomes affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation was a central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation in metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural variation.

Sexually Antagonistic Cytonuclear Fitness Interactions inDrosophila melanogaster

Theoretical and empirical studies have shown that selection cannot maintain a joint nuclear-cytoplasmic polymorphism within a population except under restrictive conditions of frequency-dependent or sex-specific selection. These conclusions are based on fitness interactions between a diploid autosomal locus and a haploid cytoplasmic locus. We develop a model of joint transmission of X chromosomes and cytoplasms and through simulation show that nuclear-cytoplasmic polymorphisms can be maintained by selection on X-cytoplasm interactions. We test aspects of the model with a “diallel” experiment analyzing fitness interactions between pairwise combinations of X chromosomes and cytoplasms from wild strains of Drosophila melanogaster. Contrary to earlier autosomal studies, significant fitness interactions between X chromosomes and cytoplasms are detected among strains from within populations. The experiment further demonstrates significant sex-by-genotype interactions for mtDNA haplotype, cytoplasms, and X chromosomes. These interactions are sexually antagonistic—i.e., the “good” cytoplasms in females are “bad” in males—analogous to crossing reaction norms. The presence or absence of Wolbachia did not alter the significance of the fitness effects involving X chromosomes and cytoplasms but tended to reduce the significance of mtDNA fitness effects. The negative fitness correlations between the sexes demonstrated in our empirical study are consistent with the conditions that maintain cytoplasmic polymorphism in simulations. Our results suggest that fitness interactions with the sex chromosomes may account for some proportion of cytoplasmic variation in natural populations. Sexually antagonistic selection or reciprocally matched fitness effects of nuclear-cytoplasmic genotypes may be important components of cytonuclear fitness variation and have implications for mitochondrial disease phenotypes that differ between the sexes.

Genetics of male sterility in gynodioecious Plantago coronopus. I. Cytoplasmic variation.

Inheritance of male sterility was studied in the gynodioecious species Plantago coronopus using five plants and their descendants from an area of approximately 50 m2 in each of six locations. The crosses were planned to test for cytoplasmic inheritance of male sterility. In four locations significant differences between reciprocal crosses were observed. The progenies of these reciprocal crosses were used in a crossing scheme designed to test whether these reciprocal differences were caused by different cytoplasmic types between the plants. In all four locations, the existence of at least two cytoplasmic types could be shown. Moreover, the results of the crosses between locations showed that the same two cytoplasmic types were present in all four locations. We therefore argue that there is only limited cytoplasmic variation in P. coronopus. In each cytoplasmic type a series of intermediate sex forms occurred. A marked difference in restoration level existed between the two cytoplasmic types. Plants with cytoplasmic type 2 hardly segregated male steriles, in contrast to plants with cytoplasmic type 1.