Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers.

In angiosperms cytoplasmic DNA is typically passed on maternally through ovules. Genes in the mtDNA may cause male sterility. When male-sterile (female) cytotypes produce more seeds than cosexuals, they pass on more copies of their mtDNA and will co-occur with cosexuals with a neutral cytotype. Cytoplasmic gynodioecy is a well-known phenomenon in angiosperms, both in wild and crop plants. In some conifer families (e.g. Pinaceae) mitochondria are also maternally inherited. However in some other families (e.g. Taxaceae and Cupressaceae) mtDNA is paternally inherited through the pollen. With paternal mtDNA inheritance, male cytotypes that produce more pollen than cosexuals are expected to co-occur with cosexuals. This is uncharted territory. An ESS model shows that the presence of male cytotypes selects for more female allocation in the cosexual, i.e. for sexual specialisation. An allele that switches sex from male to female can then invade. This leads to rapid loss of the neutral cytotype of the cosexual, fixation of the male cytotype and dioecy with 50% males and 50% females. The models suggest that paternal inheritance of mtDNA facilitates the evolution dioecy. Consistent with this hypothesis the Pinaceae are 100% monoecious, while dioecy is common in the Taxaceae family and in the genus Juniperus (Cupressaceae). However, no reliable data are yet available on both mode of inheritance of mtDNA and gender variation of the same species. When cosexuals benefit from reproductive assurance (high selfing rate, low inbreeding depression, low fertilisation) they maintain themselves next to males and females. This predicted pattern with three sex types present in the same population is observed in conifers in nature.

How to quantify plant tolerance to loss of biomass?

In some plant species the whole shoot is occasionally removed, as a result of specialist herbivory, grazing, mowing, or other causes. The plant can adapt to defoliation by allocating more to tolerance and less to growth and defense. Plant tolerance to defoliation (TOL1) is typically measured as the ratio between the average dry weight of a group of damaged plants and a control group of undamaged plants, both measured some time after recovery. We develop a model to clarify what TOL1 actually measures. We advocate keeping regrowth (REG2) and shoot-root ratio, both elements of TOL1, separate in the analysis. Based on a resource trade-off, exotic Jacobaea vulgaris plants from populations in the USA (no specialist herbivory) are expected to grow faster and be less tolerant than native Dutch populations (with specialist herbivory). Indeed Dutch plants had both a significantly larger fraction biomass in roots and faster regrowth (REG2), while US plants attained the highest weight in the control without defoliation. Using key-factor analysis, we illustrate how growth rates, regrowth, and shoot-root ratio each contribute to final biomass (plant fitness). Our proposed method gives more insight in the mechanisms that underly plant tolerance against defoliation and how tolerance contributes to fitness.

Assessing Teratogenicity from the Clustering of Abnormal Phenotypes in Individual Zebrafish Larvae.

In previous publications, we described the population incidence of abnormalities in zebrafish larvae exposed to toxicants. Here, we examine the phenomenon of clustering or co-occurrence of abnormalities in individual larva. Our aim is to see how this clustering can be used to assess the specificity and severity of teratogenic effect. A total of 11,214 surviving larvae, exposed continuously from 1 day postfertilization (dpf) to one of 60 toxicants, were scored at 5 dpf for the presence of eight different abnormal phenotypes. These were as follows: pericardial edema, yolk sac edema, dispersed melanocytes, bent tail, bent trunk, hypoplasia of Meckel's cartilage, hypoplasia of branchial arches, and uninflated swim bladder. For 43/60 compounds tested, there was a concentration-dependent increase in the severity score (number of different abnormalities per larva). Statistical analysis showed that abnormalities tended to cluster (i.e., to occur in the same larva) more often than expected by chance alone. Yolk sac edema and dispersed melanocytes show a relatively strong association with one another and were typically the first abnormalities to appear in single larvae as the concentration of compound was increased. By contrast, hypoplastic branchial arches and hypoplastic Meckel's cartilage were only frequently observed in the most severely affected larvae. We developed a metric of teratogenicity (TC3/8), which represents the concentration of a compound that produces, on average, 3/8 abnormalities per larva. On this basis, the most teratogenic compounds tested here are amitriptyline, chlorpromazine hydrochloride, and sodium dodecyl sulfate; the least teratogenic is ethanol. We find a strong correlation between TC3/8 and LC50 of the 43 compounds that showed teratogenic effects. When we examined the ratio of TC3/8 to LC50, benserazide hydrochloride, copper (II) nitrate trihydrate, and nicotine had the highest specific teratogenicity, while aconitine, hesperidin, and ouabain octahydrate had the lowest. We conclude that analyzing the clustering of abnormalities per larva can provide an enriched teratogenic dataset compared with simple measurement of the population frequency of abnormalities.

New insights into domestication of carrot from root transcriptome analyses.

BACKGROUND: Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. RESULTS: The root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst = 0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication. CONCLUSIONS: Western carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.

Selection against hybrids in mixed populations of Brassica rapa and Brassica napus: model and synthesis.

Pollen of the crop oilseed rape (Brassica napus, AACC) can cross-fertilize ovules of Brassica rapa (AA), which leads to an influx of unpaired C-chromosomes into wild B. rapa populations. The presence of such extra chromosomes is thought to be an indicator of introgression. Backcrosses and F(1) hybrids were found in Danish populations but, surprisingly, only F(1) hybrids were found in the UK and the Netherlands. Here, a model tests how the level of selection and biased vs unbiased transmission affect the population frequency of C-chromosomes. In the biased-transmission scenario the experimental results of the first backcross are extrapolated to estimate survival of gametes with different numbers of C-chromosomes from all crosses in the population. With biased transmission, the frequency of C-chromosomes always rapidly declines to zero. With unbiased transmission, the continued presence of plants with extra C-chromosomes depends on selection in the adult stage and we argue that this is the most realistic option for modeling populations. We suggest that selection in the field against plants with unpaired C-chromosomes is strong in Dutch and UK populations. The model highlights what we do not know and makes suggestions for further research on introgression.

Modelling pollen-mediated gene flow in rice: risk assessment and management of transgene escape.

Fast development and commercialization of genetically modified plants have aroused concerns of transgene escape and its environmental consequences. A model that can effectively predict pollen-mediated gene flow (PMGF) is essential for assessing and managing risks from transgene escape. A pollen-trap method was used to measure the wind-borne pollen dispersal in cultivated rice and common wild rice, and effects of relative humidity, temperature and wind speed on pollen dispersal were estimated. A PMGF model was constructed based on the pollen dispersal pattern in rice, taking outcrossing rates of recipients and cross-compatibility between rice and its wild relatives into consideration. Published rice gene flow data were used to validate the model. Pollen density decreased in a simple exponential pattern with distances to the rice field. High relative humidity reduced pollen dispersal distances. Model simulation showed an increased PMGF frequency with the increase of pollen source size (the area of a rice field), but this effect levelled off with a large pollen-source size. Cross-compatibility is essential when modelling PMGF from rice to its wild relatives. The model fits the data well, including PMGF from rice to its wild relatives. Therefore, it can be used to predict PMGF in rice under diverse conditions (e.g. different outcrossing rates and cross-compatibilities), facilitating the determination of isolation distances to minimize transgene escape. The PMGF model may be extended to other wind-pollinated plant species such as wheat and barley.

Parental conflict does not necessarily lead to the evolution of imprinting.

For some genes, the epigenetic state (whether they are expressed) depends on whether the gene is inherited through the mother or the father. Such imprinting, or parent-specific gene expression (PSGE), occurs in mammals, including humans, and higher plants. The theory that PSGE solves genetic conflict between mother and father is widely accepted. We argue, however, that the conditions for PSGE to evolve are restricted. With respect to seed size, PSGE can only evolve when the developing offspring has a strong effect on its own resource acquisition. When seed size is close to the optimum for the maternal parent, there is no internal conflict in the offspring because maternally and paternally derived genes both favour increased seed size. Although the literature generally suggests that the maternal parent controls seed size, a number of observations suggest an additional role for the paternal parent. Here, we critically evaluate these studies and suggest a rigorous methodology for establishing paternal effects on seed size, which can be applied to the model species Arabidopsis thaliana.

Plant size, geitonogamy and seed set in Ipomopsis aggregata.

We used powdered fluorescent dyes to estimate receipt of self vs. outcross pollen in the self-incompatible species Ipomopsis aggregata (Polemoniaceae). Flowers on small and large plants received equal amounts of outcross pollen, whereas flowers on large plants received more self pollen, so the proportion of self pollen delivered through geitonogamy increased with plant size. In natural populations emasculation of all flowers on a plant raised average seed set per flower from 5.19 to 6.99 and also raised fruit set, though not significantly. From these results one expects a negative correlation between plant size and seeds per flower. The opposite trend was observed in a sample of plants in the field, suggesting that deleterious effects of geitonogamy on female fecundity in large plants can be overruled by other factors such as size-related fruit or seed abortion. Results are discussed in relation to the evolution of gynodioecy.

Limiting factors for seed production in Cynoglossum officinale.

Over three years of study, small plants of Cynoglossum officinale consistently produced more flowers per unit of dry weight than large plants. In contrast to earlier results, weight of all seeds tended to increase more than proportional to size. As a result a positive correlation existed between seed set per flower and plant size. The correlation between the mean number of pollinator visits per flower and size was positive but not significant. In a field experiment we found that resources rather than pollen were limiting seed set. Thus, it is unlikely that enhanced pollination of the largest plants causes the size-dependency of seed set per flower. Alternative hypotheses are discussed briefly.

PLANT SIZE AND SEED PRODUCTION IN THE MONOCARPIC PERENNIAL CYNOGLOSSUM OFFICINALE L.

In a study of Cynoglossum officinale L. it was found that the number of seeds per flower increased with plant weight, and that flower production was inversely related to the number of seeds per flower. As a result, the number of seeds and total seed weight increased proportionally with plant weight. Seed size was not related to plant weight. Differences in seed size within the individual were, in part, related to the position of the seed on the cyme and not related to the number of seeds within a flower. The relationship, between plant size and female fitness found in this study is discussed in relation to life-history theory.

The negative effects of litter of parent plants of Cirsium vulgare on their offspring: autotoxicity or immobilization?

It is shown that litter of flowering plants of Cirsium vulgare inhibits the growth of seedlings of the same species at concentrations as low as 0.4% (g litter/g soil). The inhibition of growth cannot be fully compensated by adding nutrients, which indicates that autotoxicity may occur. It must be concluded, however, from an analysis of the results that immobilization of nutrients by microorganisms is the main cause of growth reduction if litter is added to the soil. In a field experiment under nutrient rich conditions plant litter did not affect germination, survival or growth of seedlings. The hypothesis is put forward that under conditions of nutrient deficiency and at high population densities, immobilization of nitrogen by Cirsium vulgare litter may influence plant growth. Results are discussed in relation to those of Stachon and Zimdahl (1980) and Wilson (1981) who claimed allelopathy for the related Cirsium arvense.