Connecting the sun to flowering in sunflower adaptation

Species living in seasonal environments often adaptively time their reproduction in response to photoperiod cues. We characterized the expression of genes in the flowering-time regulatory network across wild populations of the common sunflower, Helianthus annuus, that we found to be adaptively differentiated for photoperiod response. The observed clinal variation was associated with changes at multiple hierarchical levels in multiple pathways. Paralogue-specific changes in FT homologue expression and tissue-specific changes in SOC1 homologue expression were associated with loss and reversal of plasticity, respectively, suggesting that redundancy and modularity are gene network characteristics easily exploited by natural selection to produce evolutionary innovation. Distinct genetic mechanisms contribute to convergent evolution of photoperiod responses within sunflower, suggesting regulatory network architecture does not impose strong constraints on the evolution of phenotypic plasticity.     

拟南芥开花时间调控的分子基础

在合适的时间开花对大多数植物的生存和成功繁衍极为重要。开花时间受错综复杂的环境因素和植物自身的遗传因子影响,由开花调控因子所构成的光周期、春化、温度、赤霉素、自主以及年龄等至少6条既相互独立又相互联系的遗传途径调控。该文综述了有关拟南芥(Arabidopsis thaliana)开花时间调控的分子机制的最新研究进展,并对今后的研究进行了展望。     

高等植物开花时程的调控与光受体Ⅰ.开花时程的基因与光受体调控

系统评述了高等植物开花时程的调控与植物光受体的联系.重点说明了控制开花时程的遗传途径以及光周期途径的有关基因的研究进展.影响高等植物开花的最重要的因子之一便是光周期,光周期对高等植物开花的调控是通过相关基因间的相互作用来实现的,这些基因包括参与花启动发育控制基因,昼夜节律时间钟调控基因及光受体信号转导基因.近5年左右的时间通过对拟南芥及其一系列突变体的研究为我们展示了这一热门领域的广阔的前景.     

Fitting models predicting dates of flowering of temperate-zone trees using simulated annealing

The aim of the present study was to test the four commonly used models to predict the dates of flowering of temperate-zone trees, the spring warming, sequential, parallel and alternating models. Previous studies concerning the performance of these models have shown that they were unable to make accurate predictions based on external data. One of the reasons for such inaccuracy may be wrong estimations of the parameters of each model due to the non-convergence of the optimization algorithm towards their maximum likelihood. We proposed to fit these four models using a simulated annealing method which is known to avoid local extrema of any kind of function, and thus is particularly well adapted to fit budburst models, as their likelihood function presents many local maxima. We tested this method using a phenological dataset deduced from aeropalynological data. Annual pollen spectra were used to estimate the dates of flowering of the populations around the sampling station. The results show that simulated annealing provides a better fit than traditional methods. Despite this improvement, classical models still failed to predict external data. We expect the simulated annealing method to allow reliable comparisons among models, leading to a selection of biologically relevant ones.     

光周期影响植物花时的分子机制

日长感知是植物所具有的重要的生物学功能,光周期是决定植物开花时间的关键环境因子之一。光周期的暗期长度是决定植物成花的决定因素。通过形态学和遗传学研究,揭示了光周期敏感的一些遗传特性,并确定了光敏感指数的标准。构建了光周期性状相关的分子标记连锁图谱,是进行基因定位、克隆和分子标记辅助选择的重要基础工作,也是进行光周期机理研究的有效途径。通过模式植物拟南芥的研究,建立了一个长日促进开花的遗传途径。它的机理可以综合为:光和感光信息体系结合产生信号并传导,CO表达被激活。在每日日长循环、光体系及遗传背景的变化基础上,如果CO的表达和日长状况协调,那么CO激活FT表达,随后开花。水稻、小麦、玉米等作物在光周期机理研究方面也取得了一些进展。     

Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa

Recent studies have demonstrated adaptive evolutionary responses to climate change, but little is known about how these responses may influence ecological interactions with other organisms, including natural enemies. We used a resurrection experiment in the greenhouse to examine the effect of evolutionary responses to drought on the susceptibility of Brassica rapa plants to a fungal pathogen, Alternaria brassicae. In agreement with previous studies in this population, we found an evolutionary shift to earlier flowering postdrought, which was previously shown to be adaptive. Here, we report the novel finding that postdrought descendant plants were also more susceptible to disease, indicating a rapid evolutionary shift to increased susceptibility. This was accompanied by an evolutionary shift to increased specific leaf area (thinner leaves) following drought. We found that flowering time and disease susceptibility displayed plastic responses to experimental drought treatments, but that this plasticity did not match the direction of evolution, indicating that plastic and evolutionary responses to changes in climate can be opposed. The observed evolutionary shift to increased disease susceptibility accompanying adaptation to drought provides evidence that even if populations can rapidly adapt in response to climate change, evolution in other traits may have ecological effects that could make species more vulnerable.     

Flowering and morphogenic responses of new Aster hybrids to photoperiod

Photoperiod treatments of 13, 14.5, 16 and 17.5 h were used to determine the photoperiodic response of the interspecific Aster hybrids 'Painted Lady', 'Snowflake' and 'Blue Butterfly' belonging to 'Butterfly' series, under glasshouse conditions. Rate of flowering was higher under 13-h photoperiods decreasing up to 16-h photoperiods. The rate of flowering for 13- and 17.5-h photoperiods was nearly similar but under the longest photoperiod flowering was erratic and sometimes abortion of the apical bud was observed. Pholoperiod affected the morphology of the plant. Increasing photo-periods up to 16 h induced an increase of internode length of the main axis, of total length of lateral shoots, the number of ray florets. In a 13-h photoperiod the plants produced a paniculate-racemose shaped inflorescence while in longer photoperiods the inflorescence was paniculate-corymbose shaped.     

Selection for population‐specific adaptation shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post‐glacial colonization

Spatially varying selection can lead to population‐specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location‐specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine populations of the perennial herb Arabidopsis lyrata, which has a wide but patchy distribution in temperate and boreal regions of the northern hemisphere. The populations differ in their recent population demographic and colonization histories and current environmental conditions, especially in the growing season length. We searched for population‐specific molecular signatures of directional selection by comparing a set of candidate flowering time loci with a genomic reference set within each population using multiple approaches and contrasted the patterns of different populations. The candidate loci possessed approximately 20% of the diversity of the reference loci. On average the flowering time loci had more rare alleles (a smaller Tajima's D) and an excess of highly differentiated sites relative to the reference, suggesting positive selection. The strongest signal of selection was detected in photoperiodic pathway loci in the colonizing populations of Northwestern Europe, whereas no evidence of positive selection was detected in the Central European populations. These findings emphasized the population‐specific nature of selection and suggested that photoperiodic adaptation was important during postglacial colonization of the species.     

Response of grain sorghum to enhanced-ammonium supply

Two greenhouse experiments were conducted to examine the effects of increased levels of soil NH ₄ ⁺ on the growth and yield of grain sorghum (Sorghum bicolor (L.) Moench). Nitrogen was supplied as urea plus the nitrification inhibitor nitrapyrin (enhanced-NH ₄ ⁺ supply) or as a 41 molar ratio of CA(NO₃)₂ and Mg(NO₃)₂ at rates of 0 to 450 mg N kg^–1 soil in 37.5 mg N increments. Enhanced-NH ₄ ⁺ supply, in comparison to the NO₃ treatment, increased grain yield 15 and 18% in the two experiments. In one experiment this yield increase occurred through increased number of kernels and in a second experiment, through increased weight of kernels. During the first 28 days after plant emergence, the number of leaves, stalk width, plant weight, and plant N content were greater with enhanced-NH ₄ ⁺ supply than with NO ₃ ^– . However, at harvest total plant weight and plant N content were minimally affected by enhanced-NH ₄ ⁺ supply.     

Genetics of drought adaptation in Arabidopsis thaliana: I. Pleiotropy contributes to genetic correlations among ecological traits

We examined patterns of genetic variance and covariance in two traits (i) carbon stable isotope ratio delta13C (dehydration avoidance) and (ii) time to flowering (drought escape), both of which are putative adaptations to local water availability. Greenhouse screening of 39 genotypes of Arabidopsis thaliana native to habitats spanning a wide range of climatic conditions, revealed a highly significant positive genetic correlation between delta13C and flowering time. Studies in a range of C3 annuals have also reported large positive correlations, suggesting the presence of a genetically based trade-off between mechanisms of dehydration avoidance (delta13C) and drought escape (early flowering). We examined the contribution of pleiotropy by using a combination of mutant and near-isogenic lines to test for positive mutational covariance between delta13C and flowering time. Ecophysiological mutants generally showed variation in delta13C but not flowering time. However, flowering time mutants generally demonstrated pleiotropic effects consistent with natural variation. Mutations that caused later flowering also typically resulted in less negative delta13C and thus probably higher water use efficiency. We found strong evidence for pleiotropy using near-isogenic lines of Frigida and Flowering locus C, cloned loci known to be responsible for natural variation in flowering time. These data suggest the correlated evolution of delta13C and flowering time is explained in part by the fixation of pleiotropic alleles that alter both delta13C and time to flowering.     

Differential adaptation to a harsh granite outcrop habitat between sympatric Mimulus species

Understanding which environmental variables and traits underlie adaptation to harsh environments is difficult because many traits evolve simultaneously as populations or species diverge. Here, we investigate the ecological variables and traits that underlie Mimulus laciniatus’ adaptation to granite outcrops compared to its sympatric, mesic‐adapted progenitor, Mimulus guttatus. We use fine‐scale measurements of soil moisture and herbivory to examine differences in selective forces between the species’ habitats, and measure selection on flowering time, flower size, plant height, and leaf shape in a reciprocal transplant using M. laciniatus × M. guttatus F₄ hybrids. We find that differences in drought and herbivory drive survival differences between habitats, that M. laciniatus and M. guttatus are each better adapted to their native habitat, and differential habitat selection on flowering time, plant stature, and leaf shape. Although early flowering time, small stature, and lobed leaf shape underlie plant fitness in M. laciniatus’ seasonally dry environment, increased plant size is advantageous in a competitive mesic environment replete with herbivores like M. guttatus’. Given that we observed divergent selection between habitats in the direction of species differences, we conclude that adaptation to different microhabitats is an important component of reproductive isolation in this sympatric species pair.     

Pattern analysis of international sorghum multi-environment trials for grain-yield adaptation

 Pattern analysis, which consists of joint and complementary use of classification and ordination techniques, was applied to grain-yield data of 12 sorghum genotypes in 25 environments to identify the grouping of genotypes and environments. The 12 genotypes represented a wide geographical origin, different genetic diversity, and three photoperiod-sensitive classes. The 25 environments represented a super population of widely different environments covering latitudes from 20°S to 45°N. The knowledge of environmental and genotype grouping helped reveal several patterns of genotype×environment (GE) interaction. The existence of two mega-environments – African and Asian – was indicated. Within these mega-environments, several subgroups were further discernible. The Asian-type subgroups of environments tended to be closer to one another, suggesting that they discriminated genotypes similarly. By contrast, the African-type sub-groups of environments were more divergent. Differential genotype adaptation patterns existed in the two mega-environments. The repeatability of the GE patterns seen in this multi-environmental trial, however, needs to be established over time. Received: 4 April 1997 / Accepted: 6 October 1997     

In the presence of population structure: From genomics to candidate genes underlying local adaptation

Understanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. To identify loci underlying local adaptation, models that combine allelic and environmental variation while controlling for the effects of population structure have emerged as the method of choice. Despite being evaluated in simulation studies, there has not been a thorough investigation of empirical evidence supporting local adaptation across these alleles. To evaluate these methods, we use 875 Arabidopsis thaliana Eurasian accessions and two mixed models (GEMMA and LFMM) to identify candidate SNPs underlying local adaptation to climate. Subsequently, to assess evidence of local adaptation and function among significant SNPs, we examine allele frequency differentiation and recent selection across Eurasian populations, in addition to their distribution along quantitative trait loci (QTL) explaining fitness variation between Italy and Sweden populations and cis‐regulatory/nonsynonymous sites showing significant selective constraint. Our results indicate that significant LFMM/GEMMA SNPs show low allele frequency differentiation and linkage disequilibrium across locally adapted Italy and Sweden populations, in addition to a poor association with fitness QTL peaks (highest logarithm of odds score). Furthermore, when examining derived allele frequencies across the Eurasian range, we find that these SNPs are enriched in low‐frequency variants that show very large climatic differentiation but low levels of linkage disequilibrium. These results suggest that their enrichment along putative functional sites most likely represents deleterious variation that is independent of local adaptation. Among all the genomic signatures examined, only SNPs showing high absolute allele frequency differentiation (AFD) and linkage disequilibrium (LD) between Italy and Sweden populations showed a strong association with fitness QTL peaks and were enriched along selectively constrained cis‐regulatory/nonsynonymous sites. Using these SNPs, we find strong evidence linking flowering time, freezing tolerance, and the abscisic‐acid pathway to local adaptation.     

Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections

Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively.     

Divergent selection on flowering time contributes to local adaptation in Mimulus guttatus populations

The timing of when to initiate reproduction is an important transition in any organism's life cycle. There is much variation in flowering time among populations, but we do not know to what degree this variation contributes to local adaptation. Here we use a reciprocal transplant experiment to examine the presence of divergent natural selection for flowering time and local adaptation between two distinct populations of Mimulus guttatus. We plant both parents and hybrids (to tease apart differences in suites of associated parental traits) between these two populations into each of the two native environments and measure floral, vegetative, life-history, and fitness characters to assess which traits are under selection at each site. Analysis of fitness components indicates that each of these plant populations is locally adapted. We obtain striking evidence for divergent natural selection on date of first flower production at these two sites. Early flowering is favored at the montane site, which is inhabited by annual plants and characterized by dry soils in midsummer, whereas intermediate (though later) flowering dates are selectively favored at the temperate coastal site, which is inhabited by perennial plants and is almost continually moist. Divergent selection on flowering time contributes to local adaptation between these two populations of M. guttatus, suggesting that genetic differentiation in the timing of reproduction may also serve as a partial reproductive isolating barrier to gene flow among populations.