植物干旱胁迫响应机制研究进展——从表型到分子

干旱胁迫是抑制植物生长发育的主要限制因子之一,植物为适应干旱的外界环境,会依据自身的习性启动响应机制。从植物外部形态、生理代谢、生化过程、细胞及分子水平的变化阐述了植物对干旱胁迫的响应机制,详细阐述了生理及分子水平的响应机制,并对分子和遗传水平的响应机制和植物抗旱性关系的未来研究方向提出了展望,以期为植物抗逆性及遗传育种研究提供参考。     

新疆野苹果GRAS转录因子家族全基因组鉴定与响应腐烂病菌侵染的表达分析

在植物中,GRAS转录因子通过参与光信号通路和赤霉素通路等多种信号传导途径来响应植物非生物胁迫过程已被广泛研究,但对其在生物胁迫中的响应机制研究较少。本研究基于新疆野苹果（Malus sieversii）基因组,通过TBtools、Pfam和NCBI-CDD分析软件,对新疆野苹果GRAS家族基因（MsGRAS）进行筛选与验证;随后利用Protein Paramter Calc分析MsGRAS家族成员蛋白的理化性质,用MEGA构建系统发育树;最后利用PlantCARE和Graphics软件分析MsGRAS的2 000 bp顺式作用元件。此外,分析MsGRAS基因与栽培苹果（Malus domesitica）MdGRAS基因的共线性关系。通过腐烂病菌（Valsa mali）侵染后的全长转录组数据和RT-qPCR实验对MsGRAS基因家族在响应新疆野苹果抵抗腐烂病菌过程中的表达模式进行分析和验证。结果显示：（1）在新疆野苹果中共鉴定获得83个GRAS基因,涵盖DELLA、LS、SCR、SCL3和DLT等11个亚家族;蛋白结构域预测结果表明,83个MsGRAS蛋白均包含GRAS结构域,其中有4...     

新疆野苹果叶绿体DNA变异与遗传进化分析

利用4对叶绿体DNA引物对来源于新疆巩留、霍城和新源3个地区的242份新疆野苹果种质资源的4个非编码区trn H-psb A、trn S-trn G spacer+intron、trn T-5′trn L和5′trn L-trn F进行了扩增,基于4个叶绿体基因间区的序列变异,从母系遗传的角度评价了遗传变异和不同居群的遗传进化关系。结果表明:4个叶绿体DNA非编码区经测序、拼接、比对和合并之后的片段长度为3812 bp,共有171个多态性变异位点,其中包含6个单一突变位点、16个简约信息位点和149个插入-缺失位点。在242份新疆野苹果种质中,trn H-psb A、trn S-trn G spacer+intron、trn T-5′trn L和5′trn L-trn F区域的变异位点的数量分别为68个、25个、77个和1个,单倍型数量分别为36个、6个、6个和2个,合并之后的叶绿体DNA片段的单倍型为52个。核苷酸多样性和单倍型多样性最高的区域均为trn H-psb A(Hd=0.773,Pi=0.01982),最低的为5′trn L-trn F(Hd=0.025,Pi=0.00002)。242份新疆野苹果种质4个叶绿体DNA区域合并后的遗传多样性较高(Hd=0.806,Pi=0.00291)。Tajima′s D检验中,4个cpDNA区域合并后片段在P0.05水平上显著,4个cpDNA区域整体不遵循中性进化模型,自然选择的压力是新疆野苹果遗传进化的主要动力。新疆野苹果的遗传变异主要存在于居群内部,新疆巩留和新源居群间的遗传距离较近,与霍城居群间遗传距离相对较远,居群间的遗传分化与地理距离相关。3个地区的新疆野苹果各自经历着遗传分化但又存在频繁的基因交流,有向新疆新源的新疆野苹果演化的趋势。     

不同尺度下野大豆种群的遗传分化

为了阐明不同尺度范围内野大豆种群的遗传分化情况,应用随机扩增多态性DNA（RAPD）方法,分别对我国5个纬度8个不同地点的野大豆（Glycine soja)种群及浙江金华地区5个野大豆种群,进行了分子生态学研究。根据RAPD数据计算相似系数及遗传距离并进行聚类分析,发现无论是不同纬度野大豆种群还是金华地区野大豆小种群均存在较高的遗传变异,且不同纬度野大豆种群间的遗传变异与地理纬度有一定正相关。在对金华地区野大豆种群遗传多样怀的研究,利用Shannon指数估算了5个野大豆种群的遗传多样性,发现大部分的遗传变异存在于野大豆种群间（78．5％）,只有少部分的遗传变异存在于种群内。本就此探讨了不同尺度下野大豆种群的遗传多样性与环境因子的关系,并对其成因及维持机制进行了讨论。     

采用RAPD和ISSR标记研究古尔班通古特沙漠东南缘梭梭种群的遗传结构

梭梭(Haloxylon ammodendron(CA Mey.)Bunge)是一种沙漠旱生优势树种,具有重要的生态和经济价值,然而,我们对梭梭种群的遗传多样性和遗传结构所知甚少.本文采用RAPD和ISSR标记对来自古尔班通古特沙漠东南缘的4个天然梭梭种群的遗传多样性和遗传结构进行了检测.5个RAPD引物和8个ISSR引物分别扩增出61和195条带,多态性位点比率分别为83.6%和89.7%,Shannon信息指数分别为0.333和0.367,RAPD和ISSR分析均表明梭梭种群的遗传多样性水平较高.利用分子方差分析(AMOVA)研究梭梭种群的遗传结构,结果表明,大部分遗传变异存在于种群内,通过RAPD分析发现138.2%的遗传变异发生在种群内;通过ISSR分析发现89.4%的遗传变异发生在种群内;而种群间的遗传分化很小.通过RAPD标记没有检测到种群间的遗传分化,ISSR分析表明10.6%的遗传变异发生在种群内.我们推测梭梭种群较高的遗传多样性水平可能源于对异质、高胁迫环境的长期适应,但还需要进一步的研究加以证实.种群间遗传分异低的主要原因是种群间存在强大的基因流.     

采用RAPD和ISSR标记研究古尔班通古特沙漠东南缘梭梭种群的遗传结构

梭梭(Haloxylon ammodendron (CA Mey.) Bunge)是一种沙漠旱生优势树种,具有重要的生态和经济价值,然而,我们对梭梭种群的遗传多样性和遗传结构所知甚少。本文采用RAPD和ISSR标记对来自古尔班通古特沙漠东南缘的4个天然梭梭种群的遗传多样性和遗传结构进行了检测。5个RAPD引物和8个ISSR引物分别扩增出61和195条带,多态性位点比率分别为83.6%和89.7%,Shannon 信息指数分别为0.333和0.367,RAPD和ISSR分析均表明梭梭种群的遗传多样性水平较高。利用分子方差分析(AMOVA)研究梭梭种群的遗传结构,结果表明,大部分遗传变异存在于种群内,通过RAPD分析发现138.2%的遗传变异发生在种群内;通过ISSR分析发现89.4%的遗传变异发生在种群内;而种群间的遗传分化很小。通过RAPD标记没有检测到种群间的遗传分化, ISSR分析表明10.6%的遗传变异发生在种群内。我们推测梭梭种群较高的遗传多样性水平可能源于对异质、高胁迫环境的长期适应,但还需要进一步的研究加以证实。种群间遗传分异低的主要原因是种群间存在强大的基因流。     

重金属污染下曼陀罗种群分化的RAPD分析

将不同空间地段上获得的同一种质但污染年代各不相同的4个曼陀罗材料种子易地种植在同一模拟重金属污染生境中,对这4个曼陀罗种群进行RAPD分析,结果表明,在105个检测位点中发现有78个位点呈多态性。在这些多态位点中未发现与重金属抗性有关的特异性多态DNA片段。S hannon-Weiner指数计算结果表明,在短期污染时间内曼陀罗种群遗传多样性水平降低。随着污染时间的推移,曼陀罗种群逐渐在污染迹地上稳定下来,曼陀罗种群遗传多样性水平有所回升和提高,4个曼陀罗种群遗传多样性由高到低排列顺序为L＞CK＞M＞S。遗传多样性指数表明曼陀罗种群间变异程度远小于种群内的遗传变异。4个种群两两间遗传距离较小,遗传距离最大的种群为L和S,最小的为L和CK种群。因此,在重金属胁迫环境选择下,曼陀罗种群发生了一定程度的分化与微进化,轻高水平的遗传多样性可能是植物适应重金属污染胁迫环境的基础。     

动物种群遗传多态性研究中的PCR技术

基因组DNA的变异是种群遗传多态性研究的基础。PCR技术可以在反应管内经济快速地扩增特定DNA序列,在动物种群遗传多态性研究中的应用主要包括三个方面：(1)种群遗传多态位点的检测;(2)基因定位或利用已经定位的单拷贝基因设计染色体位点特异的分子标记;(3)与DNA测序技术相结合,高效经济地获取特定基因座位的全部遗传变异。     

非生物胁迫下植物表观遗传变异的研究进展

植物在整个生命过程中固着生长,不能主动躲避外界不良环境的危害,需要通过自身的防御机制来抵御和适应外界胁迫,而表观遗传修饰在调控植物应对不良环境胁迫中起重要作用。该文从DNA甲基化、组蛋白修饰、染色质重塑和非编码RNA等方面进行了综述,主要阐述了近年来国内外有关非生物胁迫下植物的表观遗传变化,以期为利用表观遗传变异提高植物的抗胁迫能力提供参考。     

承德大窝铺不同海拔与群落类型天然油松种群遗传多样性

利用ISSR技术分析了河北承德大窝铺3个不同海拔、4个不同群落类型的油松天然种群的遗传多样性与遗传分化,探讨了天然油松种群遗传多样性与主要生态因子的关系.结果表明:天然油松种群具有较高的遗传多样性,13个筛选出的随机引物共检测出180个位点,总多态位点比率分别达到73.33％和91.11％.海拔影响油松种群的遗传多样性,中海拔( 1070～1130 m)高于高海拔(1230 ～1350 m)和低海拔(910 ～970 m)(多态位点比率分别为63.33％、51.67％和59.44％);群落类型与种群的基因组结构变异之间存在一定的内在联系.遗传变异多来自种群内部(分别为90.45％和75.22％),种群分化不明显;群落类型对天然油松种群间遗传变异和基因交流(Gst为0.248,Nm为1.517)的影响高于海拔对其影响(Gst为0.095,Nm为4.738).可以认为,群落类型对大窝铺天然油松种群遗传分化有较大影响.     

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modelling [SEM] and generalized dissimilarity modelling [GDM]) to quantify the relationship of genomic variation (6,830 single nucleotide polymorphisms [SNPs]) with climate and geography, among 140 wild accessions. RDA, SEM and GDM each identified environment as explaining more genomic variation than geography, suggesting that local adaptation to heterogeneous abiotic habitats may be an important source of genetic diversity in this species. Environmental factors describing temporal variation in precipitation and evaporative demand explained the most SNP variation among accessions, indicating that these forces may represent key selective agents. Lastly, by studying how SNP–environment associations vary throughout the genome (44,064 SNPs), we mapped the location and investigated the functions of loci putatively contributing to climatic adaptations. Together, our findings indicate an important role for selection imposed by the abiotic environment in driving genomic differentiation between populations.     

Using connectivity to identify climatic drivers of local adaptation

Understanding the climatic drivers of local adaptation is vital. Such knowledge is not only of theoretical interest but is critical to inform management actions under climate change, such as assisted translocation and targeted gene flow. Unfortunately, there are a vast number of potential trait–environment combinations, and simple relationships between trait and environment are ambiguous: representing either plastic or evolved variation. Here, we show that by incorporating connectivity as an index of gene flow, we can differentiate trait–environment relationships reflecting genetic variation vs. phenotypic plasticity. In this way, we rapidly shorten the list of trait–environment combinations that are of significance. Our analysis of an existing data set on geographic variation in a tropical lizard shows that we can effectively rank climatic variables by the strength of their role in local adaptation. The promise of our method is a rapid and general approach to identifying the environmental drivers of local adaptation.     

Life span variation in 13 Drosophila species: a comparative study on life span,environmental variables and stress resistance

Recently, heterogeneity of the environment has been suggested as an important player in the evolution of life span variation. Established ageing theories propose that life span variation is the result of coevolution with other traits, such as stress resistance. This study aimed to compare these alternative hypotheses by examining the relationship between four environmental variables and different types of stress resistance traits with life span in 13 Drosophila species originating from tropical, subtropical and temperate environments (ecotypes). Average life span was found to differ significantly both between species and sexes, but only male life span correlated with the environment and cold resistance. While controlling for phylogeny, the environmental variable precipitation seasonality and resistance against cold‐induced stress explained most variation in male life span. Furthermore, male life span varied between species in a manner represented by environmental variables linked to the different ecotypes, such that tropical species lived longer and were less cold resistant. The current results suggest that general mechanisms underlying stress resistance and life span are unlikely. In addition, our results point to the environment independently shaping variation in life span and cold resistance rather than genetic interactions.     

Quantifying effects of environmental and geographical factors on patterns of genetic differentiation

Elucidating the factors influencing genetic differentiation is an important task in biology, and the relative contribution from natural selection and genetic drift has long been debated. In this study, we used a regression-based approach to simultaneously estimate the quantitative contributions of environmental adaptation and isolation by distance on genetic variation in Boechera stricta, a wild relative of Arabidopsis. Patterns of discrete and continuous genetic differentiation coexist within this species. For the discrete differentiation between two major genetic groups, environment has larger contribution than geography, and we also identified a significant environment-by-geography interaction effect. Elsewhere in the species range, we found a latitudinal cline of genetic variation reflecting only isolation by distance. To further confirm the effect of environmental selection on genetic divergence, we identified the specific environmental variables predicting local genotypes in allopatric and sympatric regions. Water availability was identified as the possible cause of differential local adaptation in both geographical regions, confirming the role of environmental adaptation in driving and maintaining genetic differentiation between the two major genetic groups. In addition, the environment-by-geography interaction is further confirmed by the finding that water availability is represented by different environmental factors in the allopatric and sympatric regions. In conclusion, this study shows that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, which only produced a gradual, clinal pattern of genetic variation. These findings emphasize the importance of environmental selection in shaping patterns of species-wide genetic variation in the natural environment.     

Song complexity is associated with habitat quality in an upland passerine

Understanding the influence of intrinsic (genetic and morphological) and extrinsic (geographical, environmental and social) factors on the performance and spatial differentiation of sexual signals, such as bird song, can help identify behavioural indicators of individual quality, habitat degradation and social environment. We used the Iberian Bluethroat Luscinia svecica azuricollis, a migratory bird that breeds in fragmented landscapes dominated by shrublands, as a case study to: (1) assess how a set of acoustic indicators of song performance are driven by intrinsic and extrinsic factors; and (2) contrast deterministic (adaptations to the environmental context and morphological constraints) vs. stochastic (differentiation by geographical isolation) explanations for song differentiation patterns. We explored acoustic indicators of song performance (spectral, temporal and song complexity) in relation to parameters related to genetic structure, body size, habitat type, habitat quality (assessed through a spatially explicit modelling approach) and social context (population abundance and songbird community composition). Then, we explored the contribution of genetic, geographical and environmental dissimilarity to song diversification across space. Our results highlight an association of song spectral variables with genetic structure and a significant connection between song complexity and duration with habitat quality. We found no relationship between social features and acoustic variables, or between song differentiation and genetic or geographical distances. There was, however, a correlation between song differentiation and environmental dissimilarity. We recommend the consideration of song complexity as an indicator of habitat quality.     

Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss)

Organisms typically show evidence of adaptation to features within their local environment. However, many species undergo long‐distance dispersal or migration across larger geographic regions that consist of highly heterogeneous habitats. Therefore, selection may influence adaptive genetic variation associated with landscape features at residing sites and along migration routes in migratory species. We tested for genomic adaptation to landscape features at natal spawning sites and along migration paths to the ocean of anadromous steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin. Results from multivariate ordination, gene–environment association and outlier analyses using 24,526 single nucleotide polymorphisms (SNPs) provided evidence that adaptive allele frequencies were more commonly associated with landscape features along migration paths than features at natal sites (91.8% vs. 8.2% of adaptive loci, respectively). Among the 45 landscape variables tested, migration distance to the ocean and mean annual precipitation along migration paths were significantly associated with adaptive genetic variation in three distinct genetic groups. Additionally, variables such as minimum migration water temperature and mean migration slope were significant only in inland stocks of steelhead that migrate up to 1,200 km farther than those near the coast, indicating regional differences in migratory selective pressures. This study provides novel approaches for investigating migratory corridors and some of the first evidence that environment along migration paths can lead to substantial divergent selection. Consequently, our approach to understand genetic adaptation to migration conditions can be applied to other migratory species when migration or dispersal paths are generally known.     

Adaptation to the laboratory environment in Drosophila subobscura

Adaptation to a novel environment is expected to have a number of features. Among these is a temporal increase in fitness and some or all of its components. It is also expected that additive genetic variances for these fitness characters will fall. Finally, it is expected that at least some additive genetic correlations will decrease, from positive toward negative values. In a study of several life‐history variables in a Drosophila subobscura population sampled from the wild and then cultured in the laboratory, we did not find any such longitudinal trends over the first 29 generations. However, a temporal comparison (over 14 generations) of the later generations of this laboratory‐adapted population with a new population, derived from a more recent wild‐caught sample, indicated clearly that laboratory adaptation was nonetheless occurring. This study suggests the need for extensive replication and control in studies of the features of adaptation to a novel environment.     

Fitness and adaptation in a novel environment: effect of inbreeding, prior environment, and lineage

Abstract. The ability of populations to undergo adaptive evolution depends on the presence of genetic variation for ecologically important traits. The maintenance of genetic variation may be influenced by many variables, particularly long-term effective population size and the strength and form of selection. The roles of these factors are controversial and there is very little information on their impacts for quantitative characters. The aims of this study were to determine the impacts of population size and variable versus constant prior environmental conditions on fitness and the magnitude of response to selection. Outbred and inbred populations of Drosophila melanogaster were maintained under benign, constant stressful, and variably stressful conditions for seven generations, and then forced to adapt to a novel stress for seven generations. Fitness and adaptability were assayed in each replicate population. Our findings are that: (1) populations inbred in a variable environment were more adaptable than those inbred in a constant environment; (2) populations adapted to a prior stressful environment had greater fitness when reared in a novel stress than those less adapted to stress; (3) inbred populations had lower fitness and were less adaptable than the outbred population they were derived from; and (4) strong lineage effects were detectable across environments in the inbred populations.     

Exploring genomic variation associated with drought stress in Picea mariana populations

Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype‐by‐environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.     

Adaptive landscape genetics: pitfalls and benefits

Landscape genetics offers a promising framework for assessing the interactions between the environment and adaptive genetic variation in natural populations. A recent workshop held at the University of Neuchatel brought together leading experts in this field to address current insights and future research directions in adaptive landscape genetics. Considerable amounts of genetic and/or environmental data can now be collected, but the forthcoming challenge is to do more with such manna. This requires a markedly better understanding of the genetic variation that is adaptive and prompts for advances in information management together with the development of a balance between theory and data. Moreover, showing the links between landscapes and adaptive genetic variation will ultimately move the field beyond association studies.