The genetic basis of high-latitude adaptation in wild soybean

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A functionally divergent SOC1 homolog improves soybean yield and latitudinal adaptation

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Genetic analysis of the physiological responses to low boron stress in Arabidopsis thaliana

Boron (B) is an essential micronutrient for higher plants. There is wide genetic variation in the response to B deficiency among plant species and cultivars. The objective of this study was to identify quantitative trait loci (QTL) that control B efficiency in natural Arabidopsis accessions. The B efficiency coefficient (BEC) and seed yield under low B conditions (SYLB) were investigated by solution culture in two separate experiments in an Arabidopsis recombinant inbred line (RIL) population. Both of the traits studied exhibited high transgressive variation in the RIL population, and, in total, five and three QTL were identified for BEC and SYLB, respectively. Three of the five QTL, including the QTL, AtBE1-2, that has a large effect on the BEC, were found at the interval of the corresponding QTL for SYLB in both experiments. The close genetic relationship between BEC and SYLB was further confirmed by conditional QTL mapping in the RIL population and unconditional QTL mapping in an AtBE1-2-segregated F(2) population. Epistatic interactions for the tested traits were analysed, and were found to be widespread in the detected QTL of Arabidopsis in the RIL population. Comparison of the QTL interval for B efficiency with reported B-related genes showed that 10 B-related genes, together with one BOR1 homolog (BOR5, At1g74810) were located in the QTL region of AtBE1-2. These results suggest that natural variation in B efficiency in Arabidopsis has a complex molecular basis. They also provide a basis for fine mapping and cloning of the B-efficiency genes, with the ultimate aim of discovering the physiological mechanism of action of the genes.     

大豆蚜对环境的适应及对大豆产量的影响

2009-2010年,以辽东山区大豆主产区岫岩县作为试验点,系统调查了大豆蚜Aphis glycines Matsumura正常型蚜和小型蚜的种群动态,研究了蜡蚧轮枝菌Verticillium lecanii(Zimmerman)Viegas、豆柄瘤蚜茧蜂Lysiphlebus fabarum Marshall、异色瓢虫Harmonia axyridis(Pallas)对大豆蚜正常型蚜和小型蚜的寄生与捕食作用;另外,也研究了降雨对小型蚜和正常型蚜的冲刷作用,以及小型蚜对大豆产量的影响等。研究结果表明,7月上中旬为大豆蚜小型蚜发生初期,7月下旬—8月上旬为小型蚜发生高峰期,2010年小型蚜平均蚜量达10000头/百株以上。此外,通过比较大豆蚜正常型蚜和小型蚜排蜜量,发现正常型蚜与小型蚜在30min内的排蜜频率差异极其显著,正常型蚜排蜜次数明显多于小型蚜。蜡蚧轮枝菌对大豆蚜小型蚜的侵染较正常型低,前者被侵染率低于3%,后者被侵染率高达25%。豆柄瘤蚜茧蜂对正常型蚜的寄生率较小型蚜高,寄生率分别为43.41%和0.58%。异色瓢虫3龄幼虫对正常型蚜和小型蚜的捕食率分别为80.24%和36.36%。降雨对小型蚜冲刷作用明显低于正常型蚜。最后,通过对单株蚜量与单株产量进行单因素方差分析,结果表明,单株小型蚜量对产量影响不显著(F=0.378;df=7,1;P>0.05)。上述研究为明确大豆蚜的发生与为害、小型蚜适应环境的生存机制以及自然天敌对大豆蚜的田间控制作用,进而为大豆蚜的可持续控制提供理论依据。     

Important role of genetic drift in rapid polygenic adaptation

We analyzed a model to determine the factors that facilitate or limit rapid polygenic adaptation. This model includes population genetic terms of mutation and both directional and stabilizing selection on a highly polygenic trait in a diploid population of finite size. First, we derived the equilibrium distribution of the allele frequencies of the multilocus model by diffusion approximation. This formula describing the equilibrium allele frequencies as a mutation‐selection‐drift balance was examined by computer simulation using parameter values inferred for human height, a well‐studied polygenic trait. Second, assuming that a sudden environmental shift of the fitness optimum occurs while the population is in equilibrium, we analyzed the adaptation of the trait to the new optimum. The speed at which the trait mean approaches the new optimum increases with the equilibrium genetic variance. Thus, large population size and/or large mutation rate may facilitate rapid adaptation. Third, the contribution of an individual locus i to polygenic adaptation depends on the compound parameter , where is the effect size, the equilibrium frequency of the trait‐increasing allele of this locus, and . Thus, only loci with large values of this parameter contribute coherently to polygenic adaptation. Given that mutation rates are relatively small, this is more likely in large populations, in which the effects of drift are limited.     

Characterizing the contribution of plasticity and genetic differentiation to community‐level trait responses to environmental change

The match between functional trait variation in communities and environmental gradients is maintained by three processes: phenotypic plasticity and genetic differentiation (intraspecific processes), and species turnover (interspecific). Recently, evidence has emerged suggesting that intraspecific variation might have a potentially large role in driving functional community composition and response to environmental change. However, empirical evidence quantifying the respective importance of phenotypic plasticity and genetic differentiation relative to species turnover is still lacking. We performed a reciprocal transplant experiment using a common herbaceous plant species (Oxalis montana) among low‐, mid‐, and high‐elevation sites to first quantify the contributions of plasticity and genetic differentiation in driving intraspecific variation in three traits: height, specific leaf area, and leaf area. We next compared the contributions of these intraspecific drivers of community trait–environment matching to that of species turnover, which had been previously assessed along the same elevational gradient. Plasticity was the dominant driver of intraspecific trait variation across elevation in all traits, with only a small contribution of genetic differentiation among populations. Local adaptation was not detected to a major extent along the gradient. Fitness components were greatest in O. montana plants with trait values closest to the local community‐weighted means, thus supporting the common assumption that community‐weighted mean trait values represent selective optima. Our results suggest that community‐level trait responses to ongoing climate change should be mostly mediated by species turnover, even at the small spatial scale of our study, with an especially small contribution of evolutionary adaptation within species.     

甘蔗—大豆间作对大豆鲜荚产量和农艺性状的影响

为探讨甘蔗-大豆间作模式对大豆鲜荚产量和农艺性状的影响,于2009—2011年连续3年在广州市华南农业大学农场进行大田试验,试验设置2种施氮水平(常规施氮(525kg·hm-2)和减量施氮(300kg·hm-2))和3种种植模式(甘蔗-大豆(1∶1)、甘蔗-大豆(1∶2)、单作大豆)。结果表明:甘蔗-大豆间作(1∶2)模式下,2009年减量施氮水平的大豆鲜荚产量较常规施氮水平提高了33%,2010和2011年不同施氮水平间均无显著差异;甘蔗-大豆间作模式对大豆的单株鲜荚重、多粒荚数和百粒鲜重无显著影响;大豆单株鲜荚重与多粒荚数在不同种植模式下均呈显著相关(P<0.05),在常规施氮间作模式下与大豆单株荚数呈显著相关(P<0.05)。甘蔗-大豆间作没有降低大豆的单株鲜荚产量,也没有对大豆的农艺性状产生负面影响,从增产增收、提高土地生产力来考虑,减量施氮模式下甘蔗-大豆间作具有一定的可行性。     

Divergent response and adaptation of specific leaf area to environmental change at different spatio-temporal scales jointly improve plant survival

Specific leaf area (SLA) is one of the most important plant functional traits. It integrates multiple functions and reflects strategies of plants to obtain resources. How plants employ different strategies (e.g., through SLA) to respond to dynamic environmental conditions remains poorly understood. This study aimed to explore the spatial variation in SLA and its divergent adaptation through the lens of biogeographic patterns, evolutionary history, and short-term responses. SLA data for 5424 plant species from 76 natural communities in China were systematically measured and integrated with meta-analysis of field experiments (i.e., global warming, drought, and nitrogen addition). The mean value of SLA across all species was 21.8 m² kg⁻¹, ranging from 0.9 to 110.2 m² kg⁻¹. SLA differed among different ecosystems, temperature zones, vegetation types, and functional groups. Phylogeny had a weak effect on SLA, but plant species evolved toward higher SLA. Furthermore, SLA responded nonlinearly to environmental change. Unexpectedly, radiation was one of the main factors determining the spatial variation in SLA on a large scale. Conversely, short-term manipulative experiments showed that SLA increased with increased resource availability and tended to stabilize with treatment duration. However, different species exhibited varying response patterns. Overall, variation in long-term adaptation of SLA to environmental gradients and its short-term response to resource pulses jointly improve plant adaptability to a changing environment. Overall SLA-environment relationships should be emphasized as a multidimensional strategy for elucidating environmental change in future research.     

氮素营养与水分胁迫对大豆产量补偿效应的影响

在大豆营养生长期,对大豆进行不同程度的干旱锻炼,同时改变土壤中的施氮水平,研究大豆产量及其构成因子对干旱胁迫复水的反应机制,为大豆节水增产及抗旱机制的实践探索提供理论依据。水分胁迫强度、历时和氮素营养都对大豆产量及其构成因子的补偿效应产生明显影响,水分胁迫抑制了大豆单株粒数的增长,但可以显著提高百粒重;氮素营养会抑制大豆百粒重的增加,但在一定水分条件下可以显著提高单株籽粒的数量,然而随着水分胁迫程度的加重,单株粒数的增加幅度也会相应减少。虽然氮素营养和水分胁迫使大豆产量构成因子产生补偿效应的阈值范围不同,但二者具有一定的耦合区域,在耦合区域内(水分胁迫时间14d左右、土壤含水量为田间持水量的50%—55%、施氮量在97.5—225kg/hm2之间)单株粒数和百粒重都产生较强的补偿效应,二者的协同作用显著提高了大豆的经济产量,使大豆产量表现出较强的补偿效应。结果表明:氮素营养和适度水分胁迫可以通过不同途径提高大豆植株的生长能力,当二者结合后大豆的补偿生长机制更为复杂,最终表现为水分胁迫提高了大豆的百粒重,而氮素增加了大豆单株粒数,二者协同作用使大豆经济产量显著增加。     

Geographic variation in adaptation at the molecular level: a case study of plant immunity genes

Natural selection imposed by interacting species frequently varies among geographic locations and can lead to local adaptation, where alternative phenotypes are found in different populations. Little is known, however, about whether geographically variable selection acting on traits that mediate species interactions is consistent or strong enough to influence patterns of nucleotide variation at individual loci. To investigate this question, we examined patterns of nucleotide diversity and population structure at 16 plant innate immunity genes, with putative functions in defending plants against pathogens or herbivores, from six populations of teosinte (Zea mays ssp. parviglumis). Specifically, we tested whether patterns of population structure and within-population diversity at immunity genes differed from patterns found at nonimmunity (reference) loci and from neutral expectations derived from coalescent simulations of structured populations. For the majority of genes, we detected no strong evidence of geographically variable selection. However, in the wound-induced serine protease inhibitor (wip1), which inhibits the hydrolysis of dietary proteins in insect herbivores, one population showed unusually high levels of genetic differentiation, very low levels of nucleotide polymorphism, and was fixed for a novel replacement substitution in the active site of the protein. Taken together, these data suggest that wip1 experienced a recent selective sweep in one geographic region; this pattern may reflect local adaptation or an ongoing species-wide sweep. Overall, our results indicate that a signature of local adaptation at the molecular level may be uncommon-particularly for traits that are under complex genetic control.     

QTL mapping and the genetic basis of adaptation: recent developments

Quantitative trait loci (QTL) mapping has been used in a number of evolutionary studies to study the genetic basis of adaptation by mapping individual QTL that explain the differences between differentiated populations and also estimating their effects and interaction in the mapping population. This analysis can provide clues about the evolutionary history of populations and causes of the population differentiation. QTL mapping analysis methods and associated computer programs provide us tools for such an inference on the genetic basis and architecture of quantitative trait variation in a mapping population. Current methods have the capability to separate and localize multiple QTL and estimate their effects and interaction on a quantitative trait. More recent methods have been targeted to provide a comprehensive inference on the overall genetic architecture of multiple traits in a number of environments. This development is important for evolutionary studies on the genetic basis of multiple trait variation, genotype by environment interaction, host–parasite interaction, and also microarray gene expression QTL analysis.     

Mechanism of bacterial adaptation to low temperature

Survival of bacteria at low temperatures provokes scientific interest because of several reasons. Investigations in this area promise insight into one of the mysteries of life science —namely, how the machinery of life operates at extreme environments. Knowledge obtained from these studies is likely to be useful in controlling pathogenic bacteria, which survive and thrive in cold-stored food materials. The outcome of these studies may also help us to explore the possibilities of existence of life in distant frozen planets and their satellites.     

The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana

The capacity to tolerate freezing temperatures limits the geographical distribution of many plants, including several species of agricultural importance. However, the genes involved in freezing tolerance remain largely unknown. Here, we describe the variation in constitutive freezing tolerance that occurs among worldwide accessions of Arabidopsis thaliana. We found that although plants from high latitudes tend to be more freezing tolerant than plants from low latitudes, the environmental factors that shape cold adaptation differ across the species range. Consistent with this, we found that the genetic architecture of freezing tolerance also differs across its range. Conventional genome‐wide association studies helped identify a priori and other promising candidate genes. However, simultaneously modelling climate variables and freezing tolerance together pinpointed other excellent a priori candidate genes. This suggests that if the selective factor underlying phenotypic variation is known, multi‐trait mixed models may aid in identifying the genes that underlie adaptation.     

Neutral adaptation of the genetic code to double-strand coding

Summary We lay new foundations to the hypothesis that the genetic code is adapted to evolutionary retention of information in the antisense strands of natural DNA/RNA sequences. In particular, we show that the genetic code exhibits, beyond the neutral replacement patterns of amino acid substitutions, optimal properties by favoring simultaneous evolution of proteins encoded in DNA/RNA sense-antisense strands. This is borne out in the sense-antisense transformations of the codons of every amino acid which target amino acids physicochemically similar to each other. Moreover, silent mutations in the sense strand generate conservative ones in its antisense counterpart and vice versa. Coevolution of proteins coded by complementary strands is shown to be a definite possibility, a result which does not depend on any physical interaction between the coevolving proteins. Likewise, the degree to which the present genetic code is dedicated to evolutionary sense-antisense tolerance is demonstrated by comparison with many randomized codes. Double-strand coding is quantified from an information-theoretical point of view.     

Triangulating the genetic basis of adaptation to multifarious selection

Understanding how natural populations adapt to their local environments is a major research theme for ecological genomics. This endeavour begins by sleuthing for shared genetic similarities among unrelated natural populations sharing adaptive traits to documented selective pressures. When the selective pressures have low dimensionality, and the genetic response is localized to a few genes of major effect, this detective work is relatively straightforward. However, in the real world, populations face a complex mixture of selective pressures and many adaptive responses are the result of changes in quantitative traits that have a polygenic genetic basis. This complex relationship between environment and adaptation presents a significant challenge. How can we begin to identify drivers of adaptation in natural settings? In this issue of Molecular Ecology, Orsini et al. (2012) take advantage of the biological attributes of the freshwater microcrustacean Daphnia ( Fig. 1 ) to disentangle multidimensional selection’s signature on the genome of populations that have repeatedly evolved adaptive responses to isolated selective pressures including predation, parasitism and anthropogenic changes in land use. Orsini et al. (2012) leverage a powerful combination of spatially structured populations in a geographic mosaic of environmental stressors, the historical archive of past genotypes preserved in lake‐bottom sediments and selection experiments to identify sets of candidate genomic regions associated with adaptation in response to these three environmental stressors. This study provides a template for future investigation in ecological genomics, combining multiple experimental approaches with the genomic investigation of a well‐studied ecological model species.

Figure 1 Open in figure viewer PowerPoint Adult Daphnia magna carrying a resting egg in the brood pouch. The water flea Daphnia is a renowned ecological model system and rapidly developing as an ecological and environmental genomics model species. Photo credit Joachim Mergeay.     

Testing for adaptation to climate in Arabidopsis thaliana: a calibrated common garden approach

BACKGROUND AND AIMS: A recent method used to test for local adaptation is a common garden experiment where analyses are calibrated to the environmental conditions of the garden. In this study the calibrated common garden approach is used to test for patterns of adaptation to climate in accessions of Arabidopsis thaliana. METHODS: Seedlings from 21 accessions of A. thaliana were planted outdoors in College Park, MD, USA, and development was monitored during the course of a growing season. ANOVA and multiple regression analysis were used to determine if development traits were significant predictors of plant success. Previously published data relating to accessional differences in genetic and physiological characters were also examined. Historical records of climate were used to evaluate whether properties of the site of origin of an accession affected the fitness of plants in a novel environment. KEY RESULTS: By calibrating the analysis to the climatic conditions of the common garden site, performance differences were detected among the accessions consistent with a pattern of adaptation to latitude and climatic conditions. Relatively higher accession fitness was predicted by a latitude and climatic history similar to that of College Park in April and May during the main growth period of this experiment. The climatic histories of the accessions were better predictors of performance than many of the life-history and growth measures taken during the experiment. CONCLUSIONS: It is concluded that the calibrated common garden experiment can detect local adaptation and guide subsequent reciprocal transplant experiments.     

Cryptic genetic variation and adaptation to waterlogging in Caledonian Scots pine,Pinus sylvestris L.

Local adaptation occurs as the result of differential selection among populations. Observations made under common environmental conditions may reveal phenotypic differences between populations with an underlying genetic basis; however, exposure to a contrasting novel environment can trigger release of otherwise unobservable (cryptic) genetic variation. We conducted a waterlogging experiment on a common garden trial of Scots pine, Pinus sylvestris (L.), saplings originating from across a steep rainfall gradient in Scotland. A flood treatment was maintained for approximately 1 year; physiological responses were gauged periodically in terms of photochemical capacity as measured via chlorophyll fluorescence. During the treatment, flooded individuals experienced a reduction in photochemical capacity, F_v/F_m, this reduction being greater for material originating from drier, eastern sites. Phenotypic variance was increased under flooding, and this increase was notably smaller in saplings originating from western sites where precipitation is substantially greater and waterlogging is more common. We conclude that local adaptation has occurred with respect to waterlogging tolerance and that, under the flooding treatment, the greater increase in variability observed in populations originating from drier sites is likely to reflect a relative absence of past selection. In view of a changing climate, we note that comparatively maladapted populations may possess considerable adaptive potential, due to cryptic genetic variation, that should not be overlooked.     

Range margin populations show high climate adaptation lags in European trees

How populations of long‐living species respond to climate change depends on phenotypic plasticity and local adaptation processes. Marginal populations are expected to have lags in adaptation (i.e. differences between the climatic optimum that maximizes population fitness and the local climate) because they receive pre‐adapted alleles from core populations preventing them from reaching a local optimum in their climatically marginal habitat. Yet, whether adaptation lags in marginal populations are a common feature across phylogenetically and ecologically different species and how lags can change with climate change remain unexplored. To test for range‐wide patterns of phenotypic variation and adaptation lags of populations to climate, we (a) built model ensembles of tree height accounting for the climate of population origin and the climate of the site for 706 populations monitored in 97 common garden experiments covering the range of six European forest tree species; (b) estimated populations' adaptation lags as the differences between the climatic optimum that maximizes tree height and the climate of the origin of each population; (c) identified adaptation lag patterns for populations coming from the warm/dry and cold/wet margins and from the distribution core of each species range. We found that (a) phenotypic variation is driven by either temperature or precipitation; (b) adaptation lags are consistently higher in climatic margin populations (cold/warm, dry/wet) than in core populations; (c) predictions for future warmer climates suggest adaptation lags would decrease in cold margin populations, slightly increasing tree height, while adaptation lags would increase in core and warm margin populations, sharply decreasing tree height. Our results suggest that warm margin populations are the most vulnerable to climate change, but understanding how these populations can cope with future climates depend on whether other fitness‐related traits could show similar adaptation lag patterns.