Effect of aperture number on pollen germination, survival and reproductive success in Arabidopsis thaliana.

Background and Aims: Pollen grains of flowering plants display a fascinating diversity of forms, including diverse patterns of apertures, the specialized areas on the pollen surface that commonly serve as the sites of pollen tube initiation and, therefore, might play a key role in reproduction. Although many aperture patterns exist in angiosperms, pollen with three apertures (triaperturate) constitutes the predominant pollen type found in eudicot species. The aim of this study was to explore whether having three apertures provides selective advantages over other aperture patterns in terms of pollen survival, germination and reproductive success, which could potentially explain the prevalence of triaperturate pollen among eudicots. Methods: The in vivo pollen germination, pollen tube growth, longevity and competitive ability to sire seeds were compared among pollen grains of Arabidopsis thaliana with different aperture numbers. For this, an arabidopsis pollen aperture series was used, which included the triaperturate wild type, as well as mutants without an aperture (inaperturate) and with more than three apertures. Key Results: Aperture number appears to influence pollen grain performance. In most germination and longevity experiments, the triaperturate and inaperturate pollen grains performed better than pollen with higher aperture numbers. In mixed pollinations, in which triaperturate and inaperturate pollen were forced to compete with each other, the triaperturate pollen outperformed the inaperturate pollen. Conclusions: Triaperturate pollen grains might provide the best trade-off among various pollen performance traits, thus explaining the prevalence of this morphological trait in the eudicot clade.

GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis.

In angiosperms (as in other species), GC content varies along and between genes, within a genome, and between genomes of different species, but the reason for this distribution is still an open question. Grass genomes are particularly intriguing because they exhibit a strong bimodal distribution of genic GC content and a sharp 5'-3' decreasing GC content gradient along most genes. Here, we propose a unifying model to explain the main patterns of GC content variation at the gene and genome scale. We argue that GC content patterns could be mainly determined by the interactions between gene structure, recombination patterns, and GC-biased gene conversion. Recent studies on fine-scale recombination maps in angiosperms support this hypothesis and previous results also fit this model. We propose that our model could be used as a null hypothesis to search for additional forces that affect GC content in angiosperms.

Dearth of polymorphism associated with a sustained response to selection for flowering time in maize.

BACKGROUND: Long term selection experiments bring unique insights on the genetic architecture of quantitative traits and their evolvability. Indeed, they are utilized to (i) monitor changes in allele frequencies and assess the effects of genomic regions involved traits determinism; (ii) evaluate the role of standing variation versus new mutations during adaptation; (iii) investigate the contribution of non allelic interactions. Here we describe genetic and phenotypic evolution of two independent Divergent Selection Experiments (DSEs) for flowering time conducted during 16 years from two early maize inbred lines. RESULTS: Our experimental design uses selfing as the mating system and small population sizes, so that two independent families evolved within each population, Late and Early. Observed patterns are strikingly similar between the two DSEs. We observed a significant response to selection in both directions during the first 7 generations of selection. Within Early families, the response is linear through 16 generations, consistent with the maintenance of genetic variance. Within Late families and despite maintenance of significant genetic variation across 17 generations, the response to selection reached a plateau after 7 generations. This plateau is likely caused by physiological limits. Residual heterozygosity in the initial inbreds can partly explain the observed responses as evidenced by 42 markers derived from both Methyl-Sensitive Amplification- and Amplified Fragment Length- Polymorphisms. Among the 42, a subset of 13 markers most of which are in high linkage disequilibrium, display a strong association with flowering time variation. Their fast fixation throughout DSEs' pedigrees results in strong genetic differentiation between populations and families. CONCLUSIONS: Our results reveal a paradox between the sustainability of the response to selection and the associated dearth of polymorphisms. Among other hypotheses, we discuss the maintenance of heritable variation by few mutations with strong epistatic interactions whose effects are modified by continuous changes of the genetic background through time.

A successive time-to-event model of phyllochron dynamics for hypothesis testing: application to the analysis of genetic and environmental effects in maize.

BACKGROUND: The time between the appearance of successive leaves, or phyllochron, characterizes the vegetative development of annual plants. Hypothesis testing models, which allow the comparison of phyllochrons between genetic groups and/or environmental conditions, are usually based on regression of thermal time on the number of leaves; most of the time a constant leaf appearance rate is assumed. However regression models ignore auto-correlation of the leaf number process and may lead to biased testing procedures. Moreover, the hypothesis of constant leaf appearance rate may be too restrictive. METHODS: We propose a stochastic process model in which emergence of new leaves is considered to result from successive time-to-events. This model provides a flexible and more accurate modeling as well as unbiased testing procedures. It was applied to an original maize dataset collected in the field over three years on plants originating from two divergent selection experiments for flowering time in two maize inbred lines. RESULTS AND CONCLUSION: We showed that the main differences in phyllochron were not observed between selection populations but rather between ancestral lines, years of experimentation and leaf ranks. Our results highlight a strong departure from the assumption of a constant leaf appearance rate over a season which could be related to climate variations, even if the impact of individual climate variables could not be clearly determined.

Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments.

Quantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on nonfocal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (G×E) interactions are ignored. The Saclay divergent selection experiments (DSEs) on maize flowering time were used to track the fate of individual mutations combining genotyping data and phenotyping data from yearly measurements (DSEYM) and common garden experiments (DSECG) with four objectives: (1) to quantify the relative contribution of standing and mutational variance to the selection response, (2) to estimate genotypic mutation effects, (3) to study the impact of G×E interactions in the selection response, and (4) to analyze how trait correlations modulate the exploration of the phenotypic space. We validated experimentally the expected enrichment of fixed beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background. Fixation of unfavorable mutations reached up to 25% of incoming mutations, a genetic load possibly due to antagonistic pleiotropy, whereby mutations fixed in the selection environment (DSEYM) turned to be unfavorable in the evaluation environment (DSECG). Global patterns of trait correlations were conserved across genetic backgrounds but exhibited temporal patterns. Traits weakly or uncorrelated with flowering time triggered stochastic exploration of the phenotypic space, owing to microenvironment-specific fixation of standing variants and pleiotropic mutational input.

GC-biased gene conversion and selection affect GC content in the Oryza genus (rice).

Base composition varies among and within eukaryote genomes. Although mutational bias and selection have initially been invoked, more recently GC-biased gene conversion (gBGC) has been proposed to play a central role in shaping nucleotide landscapes, especially in yeast, mammals, and birds. gBGC is a kind of meiotic drive in favor of G and C alleles, associated with recombination. Previous studies have also suggested that gBGC could be at work in grass genomes. However, these studies were carried on third codon positions that can undergo selection on codon usage. As most preferred codons end in G or C in grasses, gBGC and selection can be confounded. Here we investigated further the forces that might drive GC content evolution in the rice genus using both coding and noncoding sequences. We found that recombination rates correlate positively with equilibrium GC content and that selfing species (Oryza sativa and O. glaberrima) have significantly lower equilibrium GC content compared with more outcrossing species. As recombination is less efficient in selfing species, these results suggest that recombination drives GC content. We also detected a positive relationship between expression levels and GC content in third codon positions, suggesting that selection favors codons ending with G or C bases. However, the correlation between GC content and recombination cannot be explained by selection on codon usage alone as it was also observed in noncoding positions. Finally, analyses of polymorphism data ruled out the hypothesis that genomic variation in GC content is due to mutational processes. Our results suggest that both gBGC and selection on codon usage affect GC content in the Oryza genus and likely in other grass species.

Gametophytic vs. sporophytic control of pollen aperture number: a generational conflict.

In flowering plants, the haploid phase is reduced to the pollen grain and embryo sac. These reproductive tissues (gametophytes) are actually distinct individuals that have a different genome from the plant (sporophyte), and are more or less independent. The morphology of pollen grains, particularly the openings permitting pollen tube germination (apertures), is crucial for determining the outcome of pollen competition. Many species of flowering plants simultaneously produce pollen grains with different aperture numbers in a single individual (heteromorphism). In this paper, we show that the heteromorphic pollen aperture pattern depends on the genetic control of pollen morphogenesis. This points out a conflict of interest between genes expressed in the sporophyte and genes expressed in the gametophyte. More generally, such a conflict should exist whenever heteromorphism is an ESS resulting from a bet-hedging strategy. For pollen aperture, heteromorphism has been observed in about 40% of angiosperm species, suggesting that conflicting situations are the rule. In this context, the sporo-gametophytic conflict could be one of the factors that led to the reduction of the haploid phase in plants.

A Review of the Developmental Processes and Selective Pressures Shaping Aperture Pattern in Angiosperms.

Pollen grains of flowering plants display a fascinating diversity of forms. The observed diversity is determined by the developmental mechanisms involved in the establishment of pollen morphological features. Pollen grains are generally surrounded by an extremely resistant wall displaying apertures that play a key role in reproduction, being the places at which pollen tube growth is initiated. Aperture number, structure, and position (collectively termed 'aperture pattern') are determined during microsporogenesis, which is the earliest step of pollen ontogeny. Here, we review current knowledge about aperture pattern developmental mechanisms and adaptive significance with respect to plant reproduction and how advances in these fields shed light on our understanding of aperture pattern evolution in angiosperms.

Correlation between pollen aperture pattern and callose deposition in late tetrad stage in three species producing atypical pollen grains.

PREMISE OF THE STUDY: Pollen grains of flowering plants display a fascinating diversity of forms, in spite of their minute size. The observed diversity is determined by the developmental mechanisms implicated in the establishment of pollen morphological features. Pollen grains are generally surrounded by an extremely resistant wall interrupted in places by apertures that play a key role in reproduction, being the places at which pollen tube growth is initiated. Aperture shape, number, and position are determined during microsporogenesis (male meiosis), the earliest step in pollen ontogeny. We investigate in detail the unfolding of microsporogenesis in three species that present uncommon aperture pattern (i.e., disulculate in Calycanthus floridus [Calycanthaceae, magnoliids], tetraporate in Hohenbergia stellata [Bromeliaceae, monocots], and monoporate in Typha latifolia [Typhaceae, monocots]). METHODS: We performed a comparative analysis of microsporogenesis and aperture distribution within tetrads in these species with contrasting aperture arrangements. This was done using aniline blue coloration and UV light microscope observations. KEYS RESULTS: We show that aperture localization and features of callose deposition on intersporal walls produced during cytokinesis coincide in all three species examined. Such a correlation suggests that patterns of callose deposition are strongly involved in determining aperture localization. CONCLUSION: In flowering plants, patterns of male meiosis and especially callose deposition following meiosis may be implicated in the diversity of pollen aperture patterns.

Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds.

BACKGROUND: In order to investigate the rate and limits of the response to selection from highly inbred genetic material and evaluate the respective contribution of standing variation and new mutations, we conducted a divergent selection experiment from maize inbred lines in open-field conditions during 7 years. Two maize commercial seed lots considered as inbred lines, F252 and MBS847, constituted two biological replicates of the experiment. In each replicate, we derived an Early and a Late population by selecting and selfing the earliest and the latest individuals, respectively, to produce the next generation. RESULTS: All populations, except the Early MBS847, responded to selection despite a short number of generations and a small effective population size. Part of the response can be attributed to standing genetic variation in the initial seed lot. Indeed, we identified one polymorphism initially segregating in the F252 seed lot at a candidate locus for flowering time, which explained 35% of the trait variation within the Late F252 population. However, the model that best explained our data takes into account both residual polymorphism in the initial seed lots and a constant input of heritable genetic variation by new (epi)mutations. Under this model, values of mutational heritability range from 0.013 to 0.025, and stand as an upper bound compare to what is reported in other species. CONCLUSIONS: Our study reports a long-term divergent selection experiment for a complex trait, flowering time, conducted on maize in open-field conditions. Starting from a highly inbred material, we created within a few generations populations that strikingly differ from the initial seed lot for flowering time while preserving most of the phenotypic characteristics of the initial inbred. Such material is unique for studying the dynamics of the response to selection and its determinants. In addition to the fixation of a standing beneficial mutation associated with a large phenotypic effect, a constant input of genetic variance by new mutations has likely contributed to the response. We discuss our results in the context of the evolution and mutational dynamics of populations characterized by a small effective population size.

The influence of tetrad shape and intersporal callose wall formation on pollen aperture pattern ontogeny in two eudicot species.

BACKGROUND AND AIMS: In flowering plants, microsporogenesis is accompanied by various types of cytoplasmic partitioning (cytokinesis). Patterns of male cytokinesis are suspected to play a role in the diversity of aperture patterns found in pollen grains of angiosperms. The relationships between intersporal wall formation, tetrad shape and pollen aperture pattern ontogeny are studied. METHODS: A comparative analysis of meiosis and aperture distribution was performed within tetrads in two triporate eudicot species with contrasting aperture arrangements within their tetrads [Epilobium roseum (Onagraceae) and Paranomus reflexus (Proteaceae)]. KEY RESULTS AND CONCLUSIONS: Intersporal wall formation is a two-step process in both species. Cytokinesis is first achieved by the formation of naked centripetal cell plates. These naked cell plates are then covered by additional thick, localized callose deposits that differ in location between the two species. Apertures are finally formed in areas in which additional callose is deposited on the cell plates. The recorded variation in tetrad shape is correlated with variations in aperture pattern, demonstrating the role of cell partitioning in aperture pattern ontogeny.

Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes.

Plant genomes present a continuous range of variation in nucleotide composition (G + C content). In coding regions, G + C-poor species tend to have unimodal distributions of G + C content among genes within genomes and slight 5'-3' gradients along genes. In contrast, G + C-rich species display bimodal distributions of G + C content among genes and steep 5'-3' decreasing gradients along genes. The causes of these peculiar patterns are still poorly understood. Within two species (Arabidopsis thaliana and rice), each representative of one side of the continuum, we studied the consequences of intron presence on coding region and intron G + C content at different scales. By properly taking intron structure into account, we showed that, in both species, intron presence is associated with step changes in nucleotide, codon, and amino acid composition. This suggests that introns have a barrier effect structuring G + C content along genes and that previous continuous characterizations of the 5'-3' gradients were artifactual. In external gene regions (located upstream first or downstream last introns), species-specific factors, such as GC-biased gene conversion, are shaping G + C content whereas in internal gene regions (surrounded by introns), G + C content is likely constrained to remain within a range common to both species.

Flowering time in maize: linkage and epistasis at a major effect locus.

In a previous study, we identified a candidate fragment length polymorphism associated with flowering time variation after seven generations of selection for flowering time, starting from the maize inbred line F252. Here, we characterized the candidate region and identified underlying polymorphisms. Then, we combined QTL mapping, association mapping, and developmental characterization to dissect the genetic mechanisms responsible for the phenotypic variation. The candidate region contained the Eukaryotic Initiation Factor (eIF-4A) and revealed a high level of sequence and structural variation beyond the 3'-UTR of eIF-4A, including several insertions of truncated transposable elements. Using a biallelic single-nucleotide polymorphism (SNP) (C/T) in the candidate region, we confirmed its association with flowering time variation in a panel of 317 maize inbred lines. However, while the T allele was correlated with late flowering time within the F252 genetic background, it was correlated with early flowering time in the association panel with pervasive interactions between allelic variation and the genetic background, pointing to underlying epistasis. We also detected pleiotropic effects of the candidate polymorphism on various traits including flowering time, plant height, and leaf number. Finally, we were able to break down the correlation between flowering time and leaf number in the progeny of a heterozygote (C/T) within the F252 background consistent with causal loci in linkage disequilibrium. We therefore propose that both a cluster of tightly linked genes and epistasis contribute to the phenotypic variation for flowering time.

Origin and diversification dynamics of self-incompatibility haplotypes.

Self-incompatibility (SI) is a genetic system found in some hermaphrodite plants. Recognition of pollen by pistils expressing cognate specificities at two linked genes leads to rejection of self pollen and pollen from close relatives, i.e., to avoidance of self-fertilization and inbred matings, and thus increased outcrossing. These genes generally have many alleles, yet the conditions allowing the evolution of new alleles remain mysterious. Evolutionary changes are clearly necessary in both genes, since any mutation affecting only one of them would result in a nonfunctional self-compatible haplotype. Here, we study diversification at the S-locus (i.e., a stable increase in the total number of SI haplotypes in the population, through the incorporation of new SI haplotypes), both deterministically (by investigating analytically the fate of mutations in an infinite population) and by simulations of finite populations. We show that the conditions allowing diversification are far less stringent in finite populations with recurrent mutations of the pollen and pistil genes, suggesting that diversification is possible in a panmictic population. We find that new SI haplotypes emerge fastest in populations with few SI haplotypes, and we discuss some implications for empirical data on S-alleles. However, allele numbers in our simulations never reach values as high as observed in plants whose SI systems have been studied, and we suggest extensions of our models that may reconcile the theory and data.

Microsporogenesis variation in Codiaeum producing inaperturate pollen grain.

A study of microsporogenesis (the earliest stage of pollen ontogeny) was undertaken in seven cultivars of Codiaeum variegatum var. pictum, a eudicot species that produces inaperturate pollen grains. Microsporogenesis appears highly variable for the developmental events suspected to be implicated in the determination of aperture pattern. Most eudicots have tri-aperturate pollen grains and microsporogenesis is described as highly conserved in this clade. The observed burst of variation in C. variegatum therefore appears especially remarkable. A plausible hypothesis to explain the variation is that the pollen being inaperturate, the selective forces applying on the ontogeny of the aperture pattern are relaxed.

Phylogenetic comparative analysis of microsporogenesis in angiosperms with a focus on monocots.

This paper presents the first broad overview of three main features of microsporogenesis (male meiosis) in angiosperms: cytokinesis (cell division), intersporal wall formation, and tetrad form. A phylogenetic comparative approach was used to test for correlated evolution among these characters and to make hypotheses about evolutionary trends in microsporogenesis. The link between features of microsporogenesis and pollen aperture type was examined. We show that the pathway associated with successive cytokinesis (cytoplasm is partitioned after each meiotic division) is restricted to wall formation mediated by centrifugally developing cell plates, and tetragonal (or decussate, T-shaped, linear) tetrads. Conversely, much more flexibility is observed when cytokinesis is simultaneous (two meiotic divisions completed before cytoplasmic partitioning). We suggest that the ancestral type of microsporogenesis for angiosperms, and perhaps for all seed plants, associated simultaneous cytokinesis with centripetal wall formation, resulting in a large diversity in tetrad forms, ranging from regular tetrahedral to tetragonal tetrads, including rhomboidal tetrads. From this ancestral pathway, switches toward successive cytokinesis occurred among basal angiosperms and monocots, generally associated with a switch toward centrifugal intersporal wall formation, whereas eudicots evolved toward an almost exclusive production of regular tetrahedral tetrads. No straightforward link is found between the type of microsporogenesis and pollen aperture type.

Post-meiotic cytokinesis and pollen aperture pattern ontogeny: comparison of development in four species differing in aperture pattern.

Pollen aperture patterns vary widely in angiosperms. An increasing number of studies indicate that aperture pattern ontogeny is correlated with the way in which cytokinesis that follows male meiosis is completed. The formation of the intersporal callose walls that isolate the microspores after meiosis was studied in four species with different aperture patterns (two monocots, Phormium tenax and Asphodelus albus, and two eudicots, Helleborus foetidus and Protea lepidocarpodendron). The way in which post-meiotic cytokinesis is performed differs between all four species, and variation in callose deposition appears to be linked to aperture pattern definition.

Aperture pattern ontogeny in angiosperms.

Pollen grains display a wide range of variation in aperture number and arrangement (pattern) in angiosperms. Apertures are well-defined areas of the pollen wall surface that permit pollen tube germination. For low aperture numbers, aperture patterns are characteristic of the major taxonomic divisions of angiosperms. This paper presents a developmental model that explains most of the aperture patterns that are recorded in angiosperms. It is based on the analysis of the different events that occur during meiosis and lead to microspore differentiation. It demonstrates that variation occurring during meiosis in angiosperms is sufficient to produce the core morphological set of the most commonly observed pollen morphologies.

Correlated variation in microtubule distribution, callose deposition during male post-meiotic cytokinesis, and pollen aperture number across Nicotiana species (Solanaceae).

In most flowering plants, a single cytokinesis follows the two meiotic divisions during pollen-grain ontogeny. Aperture pattern (i.e., aperture number and distribution on pollen surface) ontogeny could be linked to the processes ensuring the apportionment of the cytoplasm to the four microspores.This apportionment is achieved by radial arrays of microtubules organized around the nuclei. The cleavage planes are defined in the overlapping regions of opposing arrays extending from different nuclei. We followed the establishment of these arrays in two different lines of plants belonging to the genus Nicotiana that produce pollen grains with different aperture numbers. Different distributions of the microtubules have been observed, which can be interpreted as resulting from variation in the interactions between nuclei; these distributions appear to be correlated with aperture number.As a consequence, we propose that simultaneous cytokinesis allows the formation of multiple pollen morphologies. This mechanism is consistent with aperture number distribution within angiosperms and provides clues to help our understanding of the evolution of aperture number.