Associations between nuclear loci and chloroplast DNA genotypes in wild barley

Mating system and the critical migration rate for swamping selection

Crow et al. (1990) and Barton (1992) have examined the critical migration rate for swamping selection in the nuclear system. Here, I use the same methodology to examine the critical migration rate in the cytonuclear system for hermaphrodite plants with a mixed mating system. Two selection schemes for a nuclear gene (heterozygote disadvantage and directional selection) and the directional selection scheme for organelle genes are considered. Results show that under random mating, the previous results are applicable to plant species by appropriate re-parameterization of the migration rate for nuclear and paternal organelle genes. A simple complementary relationship exists between seed and pollen flow in contributing to the critical migration rate. Under the mixed mating system, the critical migration rate of seeds and pollen for nuclear and paternal organelle genes can be changed due to the effects of selection and the cytonuclear linkage disequilibrium generated by migration and inbreeding. A negative but not complementary relationship exists between seed and pollen flow in contributing to the critical migration rate, varying with the mating system. Partial selfing can also adjust the critical seed flow for the maternal organelle gene, with a small critical migration rate for species of a high selfing rate. Both concordance and discordance among cytonuclear genes can occur under certain conditions during the process of swamping selection. This theory predicts the presence of various contributions of seed versus pollen flow to genetic swamping for plants with diverse mating systems.

F(ST) in the cytonuclear system

Selection on nuclear (or organelle) sites inevitably affects the spatial distribution of a neutral organelle (or nuclear) allele via transient cytonuclear disequilibrium. Here I examine this effect in terms of F(st) for a neutral allele by bringing together cytonuclear genomes with contrasting modes of inheritance. The relationships between cytonuclear disequilibrium and increment in F(st) are explored and confirmed through Monte Carlo simulations. Results show that the transient increment in F(st) for a neutral allele is not only related to the vectors of seed and pollen dispersal but also to the mode of its inheritance. Such increments can be substantial under certain conditions. Seed dispersal is more effective than pollen dispersal in changing the transient increment. The cumulative effects from multiple selective nuclear sites can amplify the transient increment in F(st) for a neutral paternal or maternal organelle allele. Selection on selective organelle sites facilitates the transient increment in F(st) for a neutral nuclear allele. Partial selfing can significantly reinforce the transient increment in F(st). These theoretical insights highlight the roles of transient cytonuclear disequilibrium as a biological factor in evolving population differentiation and refine our practical interpretations of F(st) with cytonuclear markers.

The functional transfer of genes from the mitochondria to the nucleus: the effects of selection, mutation, population size and rate of self-fertilization

The transfer of mitochondrial genes to the nucleus is a recurrent and consistent feature of eukaryotic genome evolution. Although many theories have been proposed to explain such transfers, little relevant data exist. The observation that clonal and self-fertilizing plants transfer more mitochondrial genes to their nuclei than do outcrossing plants contradicts predictions of major theories based on nuclear recombination and leaves a gap in our conceptual understanding how the observed pattern of gene transfer could arise. Here, with a series of deterministic and stochastic simulations, we show how epistatic selection and relative mutation rates of mitochondrial and nuclear genes influence mitochondrial-to-nuclear gene transfer. Specifically, we show that when there is a benefit to having a mitochondrial gene present in the nucleus, but absent in the mitochondria, self-fertilization dramatically increases both the rate and the probability of gene transfer. However, absent such a benefit, when mitochondrial mutation rates exceed those of the nucleus, self-fertilization decreases the rate and probability of transfer. This latter effect, however, is much weaker than the former. Our results are relevant to understanding the probabilities of fixation when loci in different genomes interact.

Genetic analysis of nuclear-cytoplasmic incompatibility in pea associated with cytoplasm of an accession of wild subspecies Pisum sativum subsp. elatius (Bieb.) Schmahl

The genetic basis of nuclear-cytoplasmic incompatibility was examined using the wild pea (Pisum sativum subsp. elatius) accession VIR320. When this accession is used as the female parent in crosses with domesticated peas (Pisum sativum subsp. sativum) the F(1) is highly sterile and displays chlorophyll deficiency, chlorophyll variegation, reduction of leaflets and stipulae while the reciprocal cross produces hybrids that appear normal. A mapping recombinant inbred line (RIL) population was established based on a cross in a compatible direction of a tester line WL1238 with VIR320. The ability to cause nuclear-cytoplasmic conflict was analysed by crossing individual RIL plants as pollen parents with VIR320 as donor of cytoplasm and scoring each F(1) for major signs of the conflict. It is concluded that two unlinked nuclear genes are involved in the genetic control of the observed incompatibility. One of the genes, denoted as Scs1, is closely linked to the PhlC gene on linkage group III and the other, denoted as Scs2, is closely linked to the gp gene on linkage group V. Alleles of both genes in WL1238 are dominant and appear to be lethal in the homozygous condition in the VIR320 cytoplasm background.

Patterns of polymorphism detected in the chloroplast and nuclear genomes of barley landraces sampled from Syria and Jordan

In order to examine how molecular polymorphism in barley landraces, sampled from five different ecogeographical regions of Syria and Jordan, is organised and partitioned, genetic variability at 21 nuclear and 10 chloroplast microsatellite loci were examined. Chloroplast polymorphism was detected, with most variation being ascribed to differences between the five regions (Fst 0.45) and to within sites within each region (Fst 0.44). Moreover, the distribution of chloroplast polymorphism is structured and not distributed randomly across the barley landraces sampled. From a total of 125 landrace accessions (five lines from each of five sites from each of five regions) genotyped with 21 SSRs a total of 244 alleles were detected, of which 38 were common to the five regions sampled. Most nuclear variation was detected within sites. Significant differentiation between sites (Fst 0.29) was detected with nuclear SSRs and this partially mirrored polymorphism in the chloroplast genome. Strong statistical associations/interaction was also detected between the chloroplast and nuclear SSRs, together with non-random association (linkage disequilibrium) of alleles at both linked and unlinked SSR loci. These results are discussed in the context of adaptation of landraces to the extreme environment, the concept of 'adapted gene complexes' and the exploitation of landraces in breeding programmes.

Sexually antagonistic cytonuclear fitness interactions in Drosophila 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.

Sampling theory for cytonuclear disequilibria

We examine the statistical properties of cytonuclear disequilibria within a system including one diploid nuclear locus and one haploid cytoplasmic locus, each with two alleles. The results provide practical guidelines for the design and interpretation of cytonuclear surveys seeking to utilize the novel evolutionary information recorded in the observed pattern of cytonuclear associations. Important applications include population studies of nuclear allozymes in conjunction with genes from mitochondria, chloroplasts, or cytoplasmically inherited microorganisms. Our attention focuses on the allelic and genotypic disequilibria, which respectively measure the nonrandom associations between the cytotypes and the nuclear alleles and genotypes. We first derive the maximum likelihood estimators and their approximate large sample variances for each disequilibrium measure. These are each in turn used to set up an asymptotic test of the null hypothesis of no disequilibrium. We then calculate the minimum sample sizes required to detect the disequilibria under specified alternate hypotheses. The work also incorporates the deviation from Hardy-Weinberg equilibrium at the nuclear locus, which can significantly affect the results. The practical utility of this new sampling theory is illustrated through applications to two nuclear-mitochondrial data sets.

Paternally inherited chloroplast polymorphism in Pinus: estimation of diversity and population subdivision, and tests of disequilibrium with a maternally inherited mitochondrial polymorphism

We have surveyed a chloroplast DNA restriction fragment length polymorphism in 745 individuals, distributed rangewide in eight allopatric natural populations of jack pine (Pinus banksiana Lamb.) and eight allopatric natural populations of lodgepole pine (Pinus contorta Dougl.). The polymorphic region of the chloroplast genome is located near duplicated psbA genes. Fourteen length variants were found in the survey, and these variants distinguished the two species qualitatively. Variant diversities were high in both species (hes = 0.43 in jack pine; hes = 0.44 in lodgepole pine). Population subdivision was weak within and among lodgepole pine subspecies and in jack pine (i.e., theta values were less than 0.05). This weak subdivision is compatible with theoretical predictions for paternally inherited markers in wind-pollinated outcrossers, as well as for polymorphisms with high length mutation rates. If these populations are at a drift-migration equilibrium, the chloroplast DNA restriction fragment data and previous mitochondrial frequency data from the same individuals are consistent with gene flow that is differential through seeds and pollen. The new data have permitted the first empirical tests of disequilibrium between maternally and paternally inherited factors. As expected, these tests failed to detect convincing evidence of nonrandom association between chloroplast and mitochondrial variants.

Comparative diversity analysis of RFLPs and isozymes within and among populations of Hordeum vulgare ssp. spontaneum

DNA restriction fragment length polymorphisms (RFLPs) and isozyme variation were surveyed in 268 accessions of a wild barley (Hordeum vulgare ssp. spontaneum) sampled from diverse ecogeographical areas in Israel and Iran. A total of 24 markers was used: 7 well characterized isozyme loci and 15 DNA probes which detected 17 putative loci and included three classes of DNA sequences (single copy, low copy and repetitive) representing all 7 barley chromosomes. Survey results indicated that both RFLPs and isozymes are highly polymorphic both within and among populations of this wild barley. The number of alleles per locus and average level of diversity do not differ between isozymes and RFLPs. However, the relative amounts of within vs. between population components vary greatly between these two sets of molecular markers. Isozymes demonstrated a larger amount of within population diversity, whereas RFLPs resolved a higher proportion of between population differentiation. Furthermore, RFLPs detected more heterozygosity than did isozymes. Both classes of markers resolved large numbers of multilocus combinations, the majority of which were represented by only one individual in the total sample. Up to 30% of the loci differ among individuals within populations, and about 50% of the loci differ among plants in different populations. While many important aspects of population diversity as determined by RFLPs are significantly correlated with those of isozymes, such correlation values are generally low, indicating that only a small proportion of the genetic variation detected by one class of markers can be predicted by the other.

Evolution of multilocus genetic structure in an experimental barley population

Data from 311 selfed families isolated from four generations (F8, F13, F23, F45) of an experimental barley population were analyzed to determine patterns of change in character expression for seven quantitative traits, and in single-locus allelic frequencies, and multilocus genetic structure, for 16 Mendelian loci that code for discretely recognizable variants. The analyses showed that large changes in single-locus allelic frequencies and major reorganizations in multilocus genetic structure occurred in each of the generation-to-generation transitions examined. Although associations among a few traits persisted over generations, dynamic dissociations and reassociations occurred among several traits in each generation-transition period. Overall, the restructuring that occurred was characterized by gradual decreases in the number of clusters of associated traits and increases in the number of traits within each cluster. The observed changes in single-locus frequencies and in multilocus genetic structure were attributed to interplay among various evolutionary factors among which natural selection acting in a temporally heterogeneous environment was the guiding force.