Emergence of gynodioecy in wild beet (Beta vulgaris ssp. maritima L.): a genealogical approach using chloroplastic nucleotide sequences

Patterns of Genome-Wide Nucleotide Diversity in the Gynodioecious Plant Thymus vulgaris Are Compatible with Recent Sweeps of Cytoplasmic Genes

Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite individuals. In most cases, this dimorphism involves the interaction of cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Two scenarios can account for how these interactions maintain gynodioecy. Either CMS genes recurrently enter populations at low frequency via mutation or migration and go to fixation unimpeded (successive sweeps), or CMS genes maintain polymorphism over evolutionary time through interactions with a nuclear restorer allele (balanced polymorphism). To distinguish between these scenarios, we used transcriptome sequencing in gynodioecious Thymus vulgaris and surveyed genome-wide diversity in 18 naturally occurring individuals sampled from populations at a local geographic scale. We contrast the amount and patterns of nucleotide diversity in the nuclear and cytoplasmic genome, and find ample diversity at the nuclear level (π = 0.019 at synonymous sites) but reduced genetic diversity and an excess of rare polymorphisms in the cytoplasmic genome relative to the nuclear genome. Our finding is incompatible with the maintenance of gynodioecy via scenarios invoking long-term balancing selection, and instead suggests the recent fixation of CMS lineages in the populations studied.

Chloroplastic and nuclear diversity of wild beets at a large geographical scale: Insights into the evolutionary history of the Beta section

Historical demographic processes and mating systems are believed to be major factors in the shaping of the intraspecies genetic diversity of plants. Among Caryophyllales, the Beta section of the genus Beta, within the Amaranthaceae/Chenopodiaceae alliance, is an interesting study model with species and subspecies (Beta macrocarpa, Beta patula, Beta vulgaris maritima and B.v. adanensis) differing in geographical distribution and mating system. In addition, one of the species, B. macrocarpa, mainly diploid, varies in its level of ploidy with a tetraploid cytotype described in the Canary Islands and in Portugal. In this study, we analyzed the nucleotide diversity of chloroplastic and nuclear sequences on a representative sampling of species and subspecies of the Beta section (except B. patula). Our objectives were (1) to assess their genetic relationships through phylogenetic and multivariate analyses, (2) relate their genetic diversity to their mating system, and (3) reconsider the ploidy status and the origin of the Canarian Beta macrocarpa.

Gynodioecy in structured populations: understanding fine-scale sex ratio variation in Beta vulgaris ssp. maritima

Natural selection, random processes and gene flow are known to generate sex ratio variations among sexually polymorphic plant populations. In gynodioecious species, in which hermaphrodites and females coexist, the relative effect of these processes on the maintenance of sex polymorphism is still up for debate. The aim of this study was to document sex ratio and cytonuclear genetic variation at a very local scale in wind-pollinated gynodioecious Beta vulgaris ssp. maritima and attempt to elucidate which processes explained the observed variation. The study sites were characterized by geographically distinct patches of individuals and appeared to be dynamic entities, with recurrent establishment of distinct haplotypes through independent founder events. Along with substantial variation in sex ratio and unexpectedly low gene flow within study sites, our results showed a high genetic differentiation among a mosaic of genetically distinct demes, with isolation by distance or abrupt genetic discontinuities taking place within a few tens of metres. Overall, random founder events with restricted gene flow could be primary determinants of sex structure, by promoting the clumping of sex-determining genes. Such high levels of sex structure provide a landscape for differential selection acting on sex-determining genes, which could modify the conditions of maintenance of gynodioecy in structured populations.

Sex-specific fitness variation in gynodioecious Beta vulgaris ssp. maritima: do empirical observations fit theoretical predictions?

In gynodioecious species, in which hermaphroditic and female plants co-occur, the maintenance of sexual polymorphism relies on the genetic determination of sex and on the relative fitness of the different phenotypes. Flower production, components of male fitness (pollen quantity and pollen quality) and female fitness (fruit and seed set) were measured in gynodioecious Beta vulgaris spp. maritima, in which sex is determined by interactions between cytoplasmic male sterility (CMS) genes and nuclear restorers of male fertility. The results suggested that (i) female had a marginal advantage over hermaphrodites in terms of flower production only, (ii) restored CMS hermaphrodites (carrying both CMS genes and nuclear restorers) suffered a slight decrease in fruit production compared to non-CMS hermaphrodites and (iii) restored CMS hermaphrodites were poor pollen producers compared to non-CMS hermaphrodites, probably as a consequence of complex determination of restoration. These observations potentially have important consequences for the conditions of maintenance of sexual polymorphism in B. vulgaris and are discussed in the light of existing theory on evolutionary dynamics of gynodioecy.

Structural and content diversity of mitochondrial genome in beet: a comparative genomic analysis

Despite their monophyletic origin, mitochondrial (mt) genomes of plants and animals have developed contrasted evolutionary paths over time. Animal mt genomes are generally small, compact, and exhibit high mutation rates, whereas plant mt genomes exhibit low mutation rates, little compactness, larger sizes, and highly rearranged structures. We present the (nearly) whole sequences of five new mt genomes in the Beta genus: four from Beta vulgaris and one from B. macrocarpa, a sister species belonging to the same Beta section. We pooled our results with two previously sequenced genomes of B. vulgaris and studied genome diversity at the species level with an emphasis on cytoplasmic male-sterilizing (CMS) genomes. We showed that, contrary to what was previously assumed, all three CMS genomes belong to a single sterile lineage. In addition, the CMSs seem to have undergone an acceleration of the rates of substitution and rearrangement. This study suggests that male sterility emergence might have been favored by faster rates of evolution, unless CMS itself caused faster evolution.

Back-and-forth hermaphroditism: phylogenetic context of reproductive system evolution in subdioecious Daphne laureola

Recent phylogenetic analyses of sexual reproductive systems supported the evolutionary pathway from hermaphroditism to dioecy via gynodioecy in different groups of angiosperms. In this study, we explore the evolution of sexual reproductive systems in Daphne laureola L. (Thymelaeaceae), a species with variation in reproductive system among population. Sequences from the ITS region of the nuclear ribosomal cistron and two plastid markers (psbA-trnH and ndhF) were analyzed and used to map the population reproductive system along the molecular phylogeny. Our results support D. laureola as a monophyletic lineage with three different clades within the Iberian Peninsula. The hermaphroditic populations belong to two different clades, whereas gynodioecy is ubiquitous but characteristic of the third clade, which grouped together all the North-Western Iberian populations sampled, including the apparently oldest haplotype sampled. Gynodioecy appears as the most likely basal condition of the 13 analyzed populations, but different evolutionary transitions in reproductive sexual system were traced within each D. laureola clade. Both ecological conditions and (meta)population dynamics may help explain plant reproductive system evolution at the microevolutionary scale. Phylogenetic studies in which the historical relationships between populations differing in reproductive system can be ascertained will help to clarify the process.

A new source of cytoplasmic male sterility found in wild beet and its relationship to other CMS types

We found a number of male-sterile plants in a wild beet (Beta vulgaris L. subsp. maritima) accession line, FR4-31. The inheritance study of the male sterility indicated the trait to be of the cytoplasmic type. The mitochondrial genome of FR4-31 proved to lack the male-sterility-associated genes preSatp6 and orf129, which are characteristic of the Owen CMS and I-12CMS(3) cytoplasms of beets, respectively. Instead, the truncated cox2 gene involved in G CMS originating from wild beets was present in the FR4-31 mitochondrial genome. In Southern hybridization using four mitochondrial gene probes, the FR4-31 cytoplasm showed patterns similar to those typical of the G cytoplasm. It is thus likely that the FR4-31 cytoplasm has a different CMS mechanism from both Owen CMS and I-12CMS(3), and that the FR4-31 and G cytoplasms resemble each other closely. A restriction map of the FR4-31 mitochondrial DNA was generated and aligned with those published for the Owen and normal fertile cytoplasms. The FR4-31 mitochondrial genome was revealed to differ extensively in arrangement from the Owen and normal genomes, and the male-sterile Owen and FR4-31 genomes seem to be derived independently from an ancestral genome.

Pollen limitation of female reproductive success at fine spatial scale in a gynodioecious and wind-pollinated species, Beta vulgaris ssp. maritima

In sexually polymorphic plants, the spatial distribution of sexes is usually not random. Local variation in phenotype frequencies is expected to affect individual fitness of the different phenotypes. For gynodioecious species, with co-occurrence of hermaphrodites and females, if sexual phenotypes are structured in space and pollen flow is spatially restricted, local pollen availability should vary among patches. Female fitness may thus be low when hermaphrodites are locally rare. To test this hypothesis, we analysed how the reproductive output of females varied among patches within two natural study sites of the gynodioecious wind-pollinated Beta vulgaris ssp. maritima. Plants growing in female-biased areas and experiencing pollen limitation were found to have low fruit and seed sets but did not reallocate resources towards better offspring. Our results show that fine-scale processes influence individual fitness and the evolution of sex ratio in sexually polymorphic plants.

A scenario of mitochondrial genome evolution in maize based on rearrangement events

BACKGROUND

Despite their monophyletic origin, animal and plant mitochondrial genomes have been described as exhibiting different modes of evolution. Indeed, plant mitochondrial genomes feature a larger size, a lower mutation rate and more rearrangements than their animal counterparts. Gene order variation in animal mitochondrial genomes is often described as being due to translocation and inversion events, but tandem duplication followed by loss has also been proposed as an alternative process. In plant mitochondrial genomes, at the species level, gene shuffling and duplicate occurrence are such that no clear phylogeny has ever been identified, when considering genome structure variation.

RESULTS

In this study we analyzed the whole sequences of eight mitochondrial genomes from maize and teosintes in order to comprehend the events that led to their structural features, i.e. the order of genes, tRNAs, rRNAs, ORFs, pseudogenes and non-coding sequences shared by all mitogenomes and duplicate occurrences. We suggest a tandem duplication model similar to the one described in animals, except that some duplicates can remain. This model enabled us to develop a manual method to deal with duplicates, a recurrent problem in rearrangement analyses. The phylogenetic tree exclusively based on rearrangement and duplication events is congruent with the tree based on sequence polymorphism, validating our evolution model.

CONCLUSIONS

This study suggests more similarity than usually reported between plant and animal mitochondrial genomes in their mode of evolution. Further work will consist of developing new tools in order to automatically look for signatures of tandem duplication events in other plant mitogenomes and evaluate the occurrence of this process on a larger scale.

Effects of fine-scale genetic structure on male mating success in gynodioecious Beta vulgaris ssp. maritima

Plant mating systems are known to influence population genetic structure because pollen and seed dispersal are often spatially restricted. However, the reciprocal outcomes of population structure on the dynamics of polymorphic mating systems have received little attention. In gynodioecious sea beet (Beta vulgaris ssp. maritima), three sexual types co-occur: females carrying a cytoplasmic male sterility (CMS) gene, hermaphrodites carrying a non-CMS cytoplasm and restored hermaphrodites that carry CMS genes and nuclear restorer alleles. This study investigated the effects of fine-scale genetic structure on male reproductive success of the two hermaphroditic forms. Our study population was strongly structured and characterized by contrasting local sex-ratios. Pollen flow was constrained over short distances and depended on local plant density. Interestingly, restored hermaphrodites sired significantly more seedlings than non-CMS hermaphrodites, despite the previous observation that the former produce pollen of lower quality than the latter. This result was explained by the higher frequency of females in the local vicinity of restored (CMS) hermaphrodites as compared to non-CMS hermaphrodites. Population structure thus strongly influences individual fitness and may locally counteract the expected effects of selection, suggesting that understanding fine scale population processes is central to predicting the evolution of gender polymorphism in angiosperms.

Recent advances in the study of gynodioecy: the interface of theory and empiricism

BACKGROUND

In this review we report on recent literature concerned with studies of gynodioecy, or the co-occurrence of female and hermaphrodite individuals in natural plant populations. Rather than review this literature in its entirety, our focus is on the interplay between theoretical and empirical approaches to the study of gynodioecy.

SCOPE

Five areas of active inquiry are considered. These are the cost of restoration, the influence of population structure on spatial sex-ratio variation, the influence of inbreeding on sex expression, the signature of cyto-nuclear coevolution on the mitochondrial genome, and the consequences of mitochondrial paternal leakage.

CONCLUSIONS

Recent advances in the study of gynodioecy have been made by considering both the ecology of female:hermaphrodite fitness differences and the genetics of sex expression. Indeed theory has guided empiricism and empiricism has guided theory. Future advances will require that some of the methods currently available only for model organisms be applied to a wider range of species.

Nuclear and cytoplasmic genetic diversity in weed beet and sugar beet accessions compared to wild relatives: new insights into the genetic relationships within the Beta vulgaris complex species

Hybridization between cultivated species and their wild relatives is now widely considered to be common. In the Beta vulgaris complex, the sugar beet seed multiplication areas have been the scene of inadvertent pollination of sugar beet seed bearers by wild ruderal pollen donors, generating a weedy form of beet which infests sugar beet fields in European countries. Up to now, investigations of evolutionary dynamics of genetic diversity within the B. vulgaris complex were addressed using few genetical markers and few accessions. In this study, we tackled this issue using a panel of complementary markers: five nuclear microsatellite loci, four mitochondrial minisatellite loci and one chloroplastic PCR-RFLP marker. We sampled 1,640 individuals that illustrate the actual distribution of inland ruderal beets of South Western France, weed beets and wild sea beets of northern France as well as the diversity of 35 contemporary European diploid cultivars. Nuclear genetic diversity in weed beets appeared to be as high as those of ruderal beets and sea beets, whereas the narrowness of cultivar accessions was confirmed. This genetic bottleneck in cultivars is even more important in the cytoplasmic genome as only one haplotype was found among all sugar beet cultivars. The large majority of weed beet populations also presented this unique cytoplasmic haplotype, as expected owing to their maternal cultivated origin. Nonetheless, various cytoplasmic haplotypes were found within three populations of weed beets, implying wild-to-weed seed flows. Finally, our findings gave new insights into the genetical relationships between the components of the B. vulgaris complex: (1) we found a very strong genetic divergence between wild sea beet and other relatives, which was unexpected given the recent evolutionary history and the full cross-compatibility of all taxa and (2) we definitely confirmed that the classification into cultivated, wild, ruderal and weed forms according to their geographical location, phenotype or their domesticated status is clearly in accordance with genetic clustering despite the very recent domestication process of sugar beet.

Mitochondrial DNA phylogeny of cultivated and wild beets: relationships among cytoplasmic male-sterility-inducing and nonsterilizing cytoplasms

Cytoplasmic male sterility (CMS), the maternally inherited failure to produce functional pollen, has been used in the breeding of sugar beet (Beta vulgaris ssp. vulgaris). At least three different sources of CMS can be distinguished from one another as well as from normal fertile cytoplasm by polymorphisms in their mitochondrial genomes. Here we analyzed 50 accessions of cultivated and wild beets to investigate the phylogenetic relationships among male-sterility-inducing and normal cytoplasms. The haplotypes were characterized by the nucleotide sequence of the mitochondrial cox2-cox1 spacer region and mitochondrial minisatellite loci. The results indicated that (1) a normal cytoplasm line, cv. TK81-O, was situated at the major core node of the haplotype network, and (2) the three sterilizing cytoplasms in question derived independently from the core haplotype. The evolutionary pathway was investigated by physical mapping study of the mitochondrial genome of a wild beet (B. vulgaris ssp. orientalis) accession BGRC56777 which shared the same mitochondrial haplotype with TK81-O, but was not identical to TK81-O for the RFLP profiles of mitochondrial DNA. Interestingly, three sets of inverted repeated sequences appeared to have been involved in a series of recombination events during the course of evolution between the BGRC56777 and the TK81-O mitochondrial genomes.

Modelling the maintenance of male-fertile cytoplasm in a gynodioecious population

Gynodioecy is the co-occurrence of females and hermaphrodites in populations. It is usually due to the combined action of cytoplasmic male sterility (CMS) genes and nuclear genes that restore male fertility. According to previous theoretical studies, it is very difficult to explain the maintenance of gynodioecy with CMS and male-fertile cytotypes, although it has been observed in some species. However, only very specific situations have been investigated so far. We present a model to investigate the conditions that promote the maintenance of this breeding system in the case of an outcrossed species when CMS and male-fertile (non-CMS) cytotypes are present in an infinite panmictic population. We show that the type of cost of restoration strongly affects the conditions for stable maintenance of gynodioecy. Stable nuclear-cytoplasmic gynodioecy requires a female advantage, which is a classical condition for gynodioecy, but also a cost of CMS for female fitness, which had been rarely investigated. A cost of restoration is also needed, which could affect either pollen or seeds. Finally, we found that gynodioecy was attainable for a large set of parameter values, including low differences in fitness among genotypes and phenotypes. Our theoretical predictions are compared with previous theoretical work and with results of empirical studies on various gynodioecious species.

The Owen mitochondrial genome in sugar beet (Beta vulgaris L.): possible mechanisms of extensive rearrangements and the origin of the mitotype-unique regions

The mitochondrial genomes of normal fertile and male-sterile (Owen CMS) cytoplasms of sugar beet are highly rearranged relative to each other and dozens of inversional recombinations and other reshuffling events must be postulated to interconvert the two genomes. In this paper, a comparative analysis of the entire nucleotide sequences of the two genomes revealed that most of the inversional recombinations involved short repeats present at their endpoints. Attention was also focused on the origin of the Owen CMS-unique mtDNA regions, which occupy 13.6% of the Owen genome and are absent from the normal mtDNA. BLAST search was performed to assign the sequences, and as a result, 7.6% of the unique regions showed significant homology to previously determined mitochondrial sequences, 17.9% to nuclear DNA, 4.6% to mitochondrial episomes, and 0.1% to plastid DNA. Southern blot analysis revealed that additional sequences of nuclear origin may be included within the unique regions. We also found that the copies of many short repeat families are scattered throughout the unique regions. This suggests that, in addition to the incorporation of foreign DNAs, extensive duplication of short repetitive sequences and continued scrambling of mtDNA sequences may be implicated in the generation of the Owen CMS-unique regions.