De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa

A sudden shift in environment or cellular context necessitates rapid adaptation. A dramatic example is genome duplication, which leads to polyploidy. In such situations, the waiting time for new mutations might be prohibitive; theoretical and empirical studies suggest that rapid adaptation will largely rely on standing variation already present in source populations. Here, we investigate the evolution of meiosis proteins in Arabidopsis arenosa, some of which were previously implicated in adaptation to polyploidy, and in a diploid, habitat. A striking and unexplained feature of prior results was the large number of amino acid changes in multiple interacting proteins, especially in the relatively young tetraploid. Here, we investigate whether selection on meiosis genes is found in other lineages, how the polyploid may have accumulated so many differences, and whether derived variants were selected from standing variation. We use a range-wide sample of 145 resequenced genomes of diploid and tetraploid A. arenosa, with new genome assemblies. We confirmed signals of positive selection in the polyploid and diploid lineages they were previously reported in and find additional meiosis genes with evidence of selection. We show that the polyploid lineage stands out both qualitatively and quantitatively. Compared with diploids, meiosis proteins in the polyploid have more amino acid changes and a higher proportion affecting more strongly conserved sites. We find evidence that in tetraploids, positive selection may have commonly acted on de novo mutations. Several tests provide hints that coevolution, and in some cases, multinucleotide mutations, might contribute to rapid accumulation of changes in meiotic proteins.     

Fitness of hybrids between rapeseed (Brassica napus) and wild Brassica rapa in natural habitats

Fitness of hybrids between genetically modified (GM) crops and wild relatives influences the likelihood of ecological harm. We measured fitness components in spontaneous (non-GM) rapeseed x Brassica rapa hybrids in natural populations. The F1 hybrids yielded 46.9% seed output of B. rapa, were 16.9% as effective as males on B. rapa and exhibited increased self-pollination. Assuming 100% GM rapeseed cultivation, we conservatively predict < 7000 second-generation transgenic hybrids annually in the United Kingdom (i.e. approximately 20% of F1 hybrids). Conversely, whilst reduced hybrid fitness improves feasibility of bio-containment, stage projection matrices suggests broad scope for some transgenes to offset this effect by enhancing fitness.     

Preferential exclusion of hybrids in mixed pollinations between oilseed rape (Brassica napus) and weedy B. campestris (Brassicaceae)

In most experimental hybridizations between oilseed rape (Brassica napus) and weedy B. campestris, either intra- or interspecific pollen has been applied to individual flowers. Under field conditions, however, stigmas will often receive a mixture of the two types of pollen, thereby allowing for competition between male gametophytes and/or seeds within pods. To test whether competition influences the success of hybridization, pollen from the two species was mixed in different proportions and applied to stigmas of both species. The resulting seeds were scored for paternity by isozyme and randomly amplified polymorphic DNA analysis. Using data on the proportion of fully developed seeds and the proportion of these seeds that were hybrids, a statistical model was constructed to estimate the fitness of conspecific and heterospecific pollen and the survival of conspecific and heterospecific zygotes to seeds. B. campestris pollen in B. napus styles had a significantly lower fitness than the conspecific pollen, whereas no difference between pollen types was found in B. campestris styles. Hybrid zygotes survived to significantly lower proportions than conspecific zygotes in both species, with the lowest survival of hybrid zygotes in B. napus pods. This is in contrast to the higher survival of hybrid seeds in B. napus than in B. campestris pods when pollinations are made with pure pollen. Altogether, the likelihood of a foreign pollen grain producing a seed was much lower on B. napus than on B. campestris. In addition, pods on B. napus developed to a lower extent the more heterospecific pollen was in the mix, whereas this had no effect on B. campestris.     

Expression profiles and genomic organisation of group A protein phosphatase 2C genes in Brassica oleracea

We investigated the expression profiles and genomic organisation of the ABA‐responsive genes encoding protein phosphatases 2C (PP2C, group A members) in Brassica oleracea to better understand their functional and genetic relations. Gene expression profiling of drought responsive genes in B. oleracea and Arabidopsis thaliana revealed significant differences in the gene expression pattern of a key regulator of ABA signalling—ABI1 PP2C. This finding prompted us to study genetic relations within the PP2Cs group A in the Brassica species. Twenty homologous B. oleracea sequences were identified and characterised as putative PP2C group A members. Phylogenetic analysis revealed that the B. oleracea homologues were closely related to the particular members of the A. thaliana PP2C. The genetic analysis corroborated the presence of two to three gene copies in B. oleracea in comparison to the nine unique PP2C genes in the A. thaliana genome. Gene expression analyses showed significant differences in PP2C gene expression pattern in B. oleracea. Our results indicate that PP2C‐based drought stress signalling in B. oleracea has evolved distinctly. Different reactions of particular B. oleracea PP2C genes to drought stress and ABA treatment indicate low conservation of gene expression patterns and functional divergence between B. oleracea and A. thaliana homologous genes.     

Seed traits are pleiotropically regulated by the flowering time gene PERPETUAL FLOWERING 1 (PEP1) in the perennial Arabis alpina

The life cycles of plants are characterized by two major life history transitions—germination and the initiation of flowering—the timing of which are important determinants of fitness. Unlike annuals, which make the transition from the vegetative to reproductive phase only once, perennials iterate reproduction in successive years. The floral repressor PERPETUAL FLOWERING 1 (PEP1), an ortholog of FLOWERING LOCUS C, in the alpine perennial Arabis alpina ensures the continuation of vegetative growth after flowering and thereby restricts the duration of the flowering episode. We performed greenhouse and garden experiments to compare flowering phenology, fecundity and seed traits between A. alpina accessions that have a functional PEP1 allele and flower seasonally and pep1 mutants and accessions that carry lesions in PEP1 and flower perpetually. In the garden, perpetual genotypes flower asynchronously and show higher winter mortality than seasonal ones. PEP1 also pleiotropically regulates seed dormancy and longevity in a way that is functionally divergent from FLC. Seeds from perpetual genotypes have shallow dormancy and reduced longevity regardless of whether they after‐ripened in plants grown in the greenhouse or in the experimental garden. These results suggest that perpetual genotypes have higher mortality during winter but compensate by showing higher seedling establishment. Differences in seed traits between seasonal and perpetual genotypes are also coupled with differences in hormone sensitivity and expression of genes involved in hormonal pathways. Our study highlights the existence of pleiotropic regulation of seed traits by hub developmental regulators such as PEP1, suggesting that seed and flowering traits in perennial plants might be optimized in a coordinated fashion.     

Evaluation of Genetic and Epigenetic Modification in Rapeseed （Brassica napus） Induced by Salt Stress

Salinity is an important limiting environmental factor for rapeseed production worldwide. In this study, we assessed the extent and pattern of DNA damages caused by salt stress in rapeseed plants. Amplified fragment length polymorphism （AFLP） analysis revealed dose-related increases in sequence alterations in plantlets exposed to 10-1000 mmol/L sodium chloride. In addition, individual plantlets exposed to the same salt concentration showed different AFLP and selected region amplified polymorphism banding patterns. These observations suggested that DNA mutation in response to salt stress was random in the genome and the effect was dose-dependant. DNA methylation changes in response to salt stress were also evaluated by methylation sensitive amplified polymorphism （MSAP）. Three types of MSAP bands were recovered. Type Ⅰ bands were observed with both isoschizomers Hpa Ⅱ and Msp Ⅰ, while type Ⅱ and type Ⅲ bands were observed only with Hpa Ⅱ and Msp Ⅰ, respectively. Extensive changes in types of MSAP bands after NaCI treatments were observed, including appearance and disappearance of type Ⅰ, Ⅱ and Ⅲ bands, as well as exchanges between either type Ⅰand type Ⅱ or type Ⅰ and type Ⅲ bands. An increase of 0.2-17.6% cytosine methylated CCGG sites were detected in plantlets exposed to 10- 200 mmol/L salt compared to the control, and these changes included both de novo methylation and demethylation events. Nine methylation related fragments were also recovered and sequenced, and one sharing a high sequence homology with the ethylene responsive element binding factor was identified. These results demonstrated clear DNA genetic and epigenetic alterations in planUets as a response to salt stress, and these changes may suggest a mechanism for plants adaptation under salt stress.     

Dynamic expression of green fluorescent protein and Bacillus thuringiensis Cry1Ac endotaxin in interspecific hybrids and successive backcross generations (BC1 and BC2) between transgenic Brassica napus crop and wild Brassica juncea

The persistence and stability of a transgene encoding a Bacillus thuringiensis (Bt) Cry1Ac insecticidal protein was investigated in hybrids between crop Brassica napus and a recurrent wild Brassica juncea population. Interspecific hybrids (F₁) and backcross progenies (BC₁, BC₂) containing green fluorescent protein (GFP) and Bt genes were successfully produced in the greenhouse. Stable Bt toxin levels were found in hybrid and advanced backcross progenies formed in wild B. juncea. Bt Cry1Ac concentration was significantly lower in BC₂ plants than in transgenic B. napus, F₁, BC₁, while no significant differences were detected among the latter three plant genotypes. A GFP marker gene was used as a scorable marker and indicator of Bt transgene expression. GFP fluorescence intensity was significantly correlated with Bt Cry1Ac concentration at the flowering stage and the pod formation stage in both transgenic oilseed rape hybrids and backcrossed progenies (BC₁, BC₂). It was demonstrated that GFP was a suitable marker for Bt protein in the backcross of B. juncea, which could facilitate the detection of gene flow and is useful in biosafety management.     

Nuclear and chloroplast microsatellites reveal extreme population differentiation and limited gene flow in the Aegean endemic Brassica cretica (Brassicaceae)

Nuclear and chloroplast microsatellite markers were used to study population structure and gene flow among seven Cretan populations of the Aegean endemic plant species Brassica cretica (Brassicaceae). Both nuclear and chloroplast markers revealed exceptionally high levels of population differentiation (overall F(ST)=0.628 and 1.000, respectively) and relatively little within-population diversity (overall H(S)=0.211 and 0.000, respectively). Maximum-likelihood estimates of directional migration rates were low among all pairs of populations (average Nm=0.286). There was no evidence that differences in flower colour between populations had any influence on historical levels of gene flow. In addition, a haplotype network showed that all five chloroplast haplotypes found in the sample were closely related. Together, these results suggest that current patterns of diversification in B. cretica are mainly a result of genetic drift during the last half million years. The main conclusions from the present study are consistent with the prevailing hypothesis that plant diversification in the Aegean region is driven by random rather than adaptive differentiation among isolated populations.     

Histone modification and signalling cascade of the dormancy‐associated MADS‐box gene,PpMADS13‐1, in Japanese pear (Pyrus pyrifolia) during endodormancy

Dormancy‐associated MADS‐box (DAM) genes play an important role in endodormancy phase transition. We investigated histone modification in the DAM homolog (PpMADS13‐1) from Japanese pear, via chromatin immunoprecipitation–quantitative PCR, to understand the mechanism behind the reduced expression of the PpMADS13‐1 gene towards endodormancy release. Our results indicated that the reduction in the active histone mark by trimethylation of the histone H3 tail at lysine 4 contributed to the reduction of PpMADS13‐1 expression towards endodormancy release. In contrast, the inactive histone mark by trimethylation of the histone H3 tail at lysine 27 in PpMADS13‐1 locus was quite low, and these levels were more similar to a negative control [normal mouse immunoglobulin G (IgG)] than to a positive control (AGAMOUS) in endodormancy phase transition. The loss of histone variant H2A.Z also coincided with the down‐regulation of PpMADS13‐1. Subsequently, we investigated the PpMADS13‐1 signalling cascade and found that PpCBF2, a pear C‐repeated binding factor, regulated PpMADS13‐1 expression via interaction of PpCBF2 with the 5′‐upstream region of PpMADS13‐1 by transient reporter assay. Furthermore, transient reporter assay confirmed no interaction between the PpMADS13‐1 protein and the pear FLOWERING LOCUS T genes. Taken together, our results enhance understanding of the molecular mechanisms underlying endodormancy phase transition in Japanese pear.     

Quantitative trait and allozyme divergence in the Greenfinch (Carduelis chloris, Aves: Fringillidae)

Quantitative trait divergence and variability among 12 greenfinch populations across continental Europe was examined and compared to divergence in neutral genetic markers (allozymes). The added among locality variance component for 16 skeletal traits was large (mean 28%, range 4–48%) equalling a divergence of up to three SD units. The divergence in quantitative traits (Qst = 0.04-0.48) greatly exceeded that in alloymes (F_ST= 0.01-0.07), indicating the differentiation in quantitative traits to be larger than expected by mutation and drift alone. This conclusion was consistent also with results from the multivariate approach of Rogers & Harpending. However, genetic and morphometric distances between populations were positively correlated, even when controlling for the geographic distance separating pairs of populations. In concordance with Bergmann's rule, most traits were strongly and positively correlated with latitude, indicating latitudinally ordered genetic or/and environmental effects. However, the correlation between lower mandible width and latitude was strongly negative, demonstrating an inverse relationship between beak size and body size across the populations. These results are interpreted to reflect the re-colonization of history of northern Europe (genetic and geographic distances correlated) which has been paralleled by selection acting on quantitative traits (Q_ST>F_ST)- In particular, the counter-gradient variation in beak width, a functionally important trait, is suggestive of an adaptive basis for quantitative trait divergence.     

甘蓝型油菜分子标记连锁图谱的构建及显性细胞核雄性不育基因的图谱定位

在显性细胞核雄性不育系Rs1046A和双低油菜品种Samourai构建的回交分离群体中,运用AFLP和SSR两种标记技术构建了一个甘蓝型油菜(Brassica napus L.)的分子标记遗传连锁图谱。该图谱共包含138个AFL．P标记、83个SSR标记和1个形态标记,分布于18个主要连锁群、2个三联体和1个连锁对上,图谱总长度为2646cM,偏分离标记的比例为11．7％。显性细胞核雄性不育基因Ms被定位到第10连锁群(LG10)上。同时,偏分离标记聚集于第8连锁群(LG8)和第16连锁群(LGl6)的末端,形成了十分明显的偏分离标记密集区域。研究结果对于油菜核不育两型系的分子标记辅助选择育种具有重要意义,同时也为克隆和分离核不育基因以及研究核不育的分子机理打下了良好的基础。     

Variations in life history traits and flight capacity among populations of the light brown apple moth Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae)

Abstract The empirical study of interpopulation variation in life history and other fitness traits has been an important approach to understanding the ecology and evolution of organisms and gaining insight into possible sources of variation. We report a quantitative analysis for variations of five life history traits (larval developmental time, adult body weight, adult lifespan, age at first reproduction, total fecundity) and flight capacity among populations of Epiphyas postvittana originating from four localities in Australia and one in New Zealand. These populations were compared at two temperatures (15° and 25°C) after being maintained under uniform laboratory conditions for 1.5 generations, so that the relative role of genetic divergence and phenotypic plasticity in determining interpopulation variation could be disentangled. Genetic differentiation between populations was shown in all measured traits, with the greatest divergence occurring in developmental time, fecundity and adult body size. However, these traits were highly sensitive to changes in environmental temperatures; and furthermore, significant interactions between population and temperature occurred in all traits except for flight capacity of female moths. Thus, phenotypic plasticity may be another cause of interpopulation variation. The interpopulation variation for some measured traits was apparently related to climatic differences found where the populations originated. Individuals of the populations from the warmer climates tended to develop more slowly at immature stages, producing smaller and less fecund moths but with stronger flight capacity, in comparison to those from the cooler regions. It seems, therefore, that natural populations of E. postvittana have evolved different strategies to cope with local environmental conditions.     

Integration of Random Forest with population‐based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

Anadromous Chinook salmon populations vary in the period of river entry at the initiation of adult freshwater migration, facilitating optimal arrival at natal spawning. Run timing is a polygenic trait that shows evidence of rapid parallel evolution in some lineages, signifying a key role for this phenotype in the ecological divergence between populations. Studying the genetic basis of local adaptation in quantitative traits is often impractical in wild populations. Therefore, we used a novel approach, Random Forest, to detect markers linked to run timing across 14 populations from contrasting environments in the Columbia River and Puget Sound, USA. The approach permits detection of loci of small effect on the phenotype. Divergence between populations at these loci was then examined using both principle component analysis and F_ST outlier analyses, to determine whether shared genetic changes resulted in similar phenotypes across different lineages. Sequencing of 9107 RAD markers in 414 individuals identified 33 predictor loci explaining 79.2% of trait variance. Discriminant analysis of principal components of the predictors revealed both shared and unique evolutionary pathways in the trait across different lineages, characterized by minor allele frequency changes. However, genome mapping of predictor loci also identified positional overlap with two genomic outlier regions, consistent with selection on loci of large effect. Therefore, the results suggest selective sweeps on few loci and minor changes in loci that were detected by this study. Use of a polygenic framework has provided initial insight into how divergence in a trait has occurred in the wild.     

Life‐history traits and geographical divergence in wild rice (Oryza rufipogon) gene pool in Indochina Peninsula region

Indochina Peninsula is the primary centre of diversity of rice and lies partly in the centre of origin of cultivated rice (Oryza sativa) where the wild ancestor (Oryza rufipogon) is still abundant. The wild gene pool is potentially endangered by urbanisation and the expansion of agriculture, and by introgression hybridisation with locally cultivated rice varieties. To determine genetic diversity and structure of the wild rice of the region we genotyped nearly 1000 individuals using 20 microsatellite loci. We found ecological differentiation in 48 populations, distinguishable by their life‐history traits and the country of origin. Geographical divergence was suggested by isolation of the perennial Myanmar populations from those of Cambodia, Laos and Thailand. The annual types would be most likely to have lost genetic variation because of genetic drift and inbreeding. The growing of cultivated and wild rice together, however, gives ample opportunities for hybridisation, which already shows signs of genetic mixing, and will ultimately lead to replacement of the original wild rice gene pool. For conservation we suggest that wild rice should be conserved ex situ in order to prevent introgression from cultivated rice, along with in situ conservation in individual countries for the recurrent evolutionary process through local adaptation, but with sufficient isolation from cultivated rice fields to preserve genetic integrity of the wild populations.     

Re-establishment of clinal variation in flowering time among introduced populations of purple loosestrife (Lythrum salicaria, Lythraceae)

Range expansion during biological invasion requires that invaders adapt to geographical variation in climate, which should yield latitudinal clines in reproductive phenology. We investigated geographic variation in life history among 25 introduced populations of Lythrum salicaria, a widespread European invader of North American wetlands. We detected a strong latitudinal cline in initiation of flowering and size at flowering, which paralleled that reported among native populations. Plants from higher latitudes flowered earlier and at a smaller size than those from lower latitudes, even when raised in a uniform glasshouse. Early flowering was associated with greatly reduced reproductive output, but this was not associated with latitudinal variation in abundance, and probably did not result from a genetic correlation between time to and size at flowering. As introduction to North America c. 200 years ago, L. salicaria has re-established latitudinal clines in life history, probably as an evolutionary response to climatic selection.     

Evidence for association of chromosomal form and development time from complex clines and geographic races in the grasshopper Caledia captiva (Orthoptera: Acridadae)

Evidence for an association between chromosomal form and development time in the grasshopper Caledia captiva (F.) was obtained through comparison of two geographic taxa and analysis of a complex latitudinal cline within one of the taxa. Northern populations of the Moreton taxon possess a metacentric genome and are slow-developing. In contrast, the Torresian taxon, distributed throughout northern, coastal Australia, a region of pronounced seasonality in rainfall, and southern populations of the Moreton taxon, which inhabit a region of pronounced seasonality in temperature, Soth have an acrocentric genome and are fast-developing. The convergence of chromosomal form and development time between Torresian and southern Moreton populations appears to be driven by convergence in life history. Seasonality limits grasshoppers to one generation per year and favours fast development. The transition between relatively acrocentric southern Moreton populations and relatively metacentric northern Moreton populations is gradual but not monotonic. Instead, a shift to a bivoltine life history in the middle of the transect occurs and is associated with shifts in both development time and chromosomal form. These results imply an adaptive role for chromosomal form, although the causative link between chromosomal variation and variation in development time remains to be established.     

Selection for developmental time in bean weevil (Acanthoscelides obtectus): correlated responses for other life history traits and genetic architecture of line differentiation

In this article we investigate the direct and correlated responses to selection for developmental time in order to discern differences between lines in several preadult and adult life history traits of Acanthoscelides obtectus (Coleoptera, Bruchidae). Selection for fast development was about five times as effective as selection for slow development, as judged by realized heritabilities. The correlated responses on the following life‐history traits were studied: egg size, hatching success, embryonic developmental time, egg‐to‐adult viability, body weight, first day of egg laying, total fecundity, and longevity. Analyses of the terminal generation of selection showed that all life history traits examined, except for hatching success, were affected by selection. The findings suggest that body weight, total fecundity, and longevity traded off to preadult developmental time. Unlike the adult traits, none of the preadult traits showed negative correlations with developmental time. We also present data concerning the underlying genetic basis that produces changes in preadult developmental time, body weight, and egg‐to‐adult viability in the lines selected for fast and slow preadult developmental time. Additive‐dominance genetic architecture for both preadult developmental time and body weight was found. In addition, it appears that the responses to selection for preadult developmental time involved between 10 and 28 loci, which were correlated with at least one to four genes for body weight. Epistasis makes a significant contribution to genetic divergence between fast and slow selected lines only with respect to preadult viability. The observed levels of dominance and epistasis underscore the important role of nonadditive genetic effects to the adaptive diversifications of bean weevil populations.