The leaf economics spectrum’s morning coffee: plant size-dependent changes in leaf traits and reproductive onset in a perennial tree crop

Background and AimsSize-dependent changes in plant traits are an important source of intraspecific trait variation. However, there are few studies that have tested if leaf trait co-variation and/or trade-offs follow a within-genotype leaf economics spectrum (LES) related to plant size and reproductive onset. To our knowledge, there are no studies on any plant species that have tested whether or not the shape of a within-genotype LES that describes how traits covary across whole plant sizes, is the same as the shape of a within-genotype LES that represents environmentally driven trait plasticity.MethodsWe quantified size-dependent variation in eight leaf traits in a single coffee genotype (Coffea arabica var. Caturra) in managed agroecosystems with different environmental conditions (light and fertilization treatments), and evaluated these patterns with respect to reproductive onset. We also evaluated if trait covariation along a within-genotype plant-size LES differed from a within-genotype environmental LES defined with trait data from coffee growing in different environmental conditions.Key ResultsLeaf economics traits related to resource acquisition – maximum photosynthetic rates (A) and mass-based leaf nitrogen (N) concentrations – declined linearly with plant size. Structural traits – leaf mass, leaf thickness, and leaf mass per unit area (LMA) – and leaf area increased with plant size beyond reproductive onset, then declined in larger plants. Three primary LES traits (mass-based A, leaf N and LMA) covaried across a within-genotype plant-size LES, with plants moving towards the ‘resource-conserving’ end of the LES as they grow larger; in coffee these patterns were nearly identical to a within-genotype environmental LES.ConclusionsOur results demonstrate that a plant-size LES exists within a single genotype. Our findings indicate that in managed agroecosystems where resource availability is high the role of reproductive onset in driving within-genotype trait variability, and the strength of covariation and trade-offs among LES traits, are less pronounced compared with plants in natural systems. The consistency in trait covariation in coffee along both plant-size and environmental LES axes indicates strong constraints on leaf form and function that exist within plant genotypes.     

典型草原围封后羊草地上功能性状对枯落物累积的响应

植物功能性状反映植物适应环境变化过程中在不同器官形态与功能间的资源权衡与分配策略。典型草原围封后枯落物累积导致群落光照、热量和水分的重新分配并改变微环境特征。在此过程中植物地上功能性状将通过怎样的变化来适应新的环境,目前尚不清楚。2015—2017年每年8月对内蒙古地区3种典型草原共有物种羊草（Leymus chinensis）的植株、叶片和茎干功能性状进行了测量与分析。结果表明：枯落物累积显著增加了羊草的植株高度、单株重量、茎叶比和总叶面积;枯落物累积显著增加了羊草的叶片长度、叶片重量、单叶面积、节间长度和茎干重量,这些性状属于敏感性状;枯落物累积对羊草的叶片数量和节间数量无显著影响,相对而言,这些性状属于惰性性状;羊草的单株重量与植株高度、叶片重量呈极显著的正相关关系（P<0.0001）;羊草的植株高度与节间数量、节间长度呈极显著的正相关关系（P<0.0001）。本研究结果从植物地上功能性状的角度阐明了典型草原植物对环境变化的适应方式,可为围封草原的合理管理提供基础数据与理论依据。     

Detection of quantitative trait loci for reproduction and production traits in Large White and French Landrace pig populations (Open Access publication)

A genome-wide scan was performed in Large White and French Landrace pig populations in order to identify QTL affecting reproduction and production traits. The experiment was based on a granddaughter design, including five Large White and three French Landrace half-sib families identified in the French porcine national database. A total of 239 animals (166 sons and 73 daughters of the eight male founders) distributed in eight families were genotyped for 144 microsatellite markers. The design included 51 262 animals recorded for production traits, and 53 205 litter size records were considered. Three production and three reproduction traits were analysed: average backfat thickness (US_M) and live weight (LWGT) at the end of the on-farm test, age of candidates adjusted at 100 kg live weight, total number of piglets born per litter, and numbers of stillborn (STILLp) and born alive (LIVp) piglets per litter. Ten QTL with medium to large effects were detected at a chromosome-wide significance level of 5% affecting traits US_M (on SSC2, SSC3 and SSC17), LWGT (on SSC4), STILLp (on SSC6, SSC11 and SSC14) and LIVp (on SSC7, SSC16 and SSC18). The number of heterozygous male founders varied from 1 to 3 depending on the QTL.     

不同木本植物功能型当年生小枝功能性状差异

为探讨不同植物功能型之间小枝功能特征的差异,在重庆金佛山和缙云山分别采集20和26个木本植物,选择当年生的小枝测定其叶片和枝条性状。结果表明:1)叶片厚度表现为:落叶植物<常绿植物,乔木<灌木;单叶面积和叶片总面积表现为:落叶植物>常绿植物,乔木>灌木;不同植物功能型间小枝的叶片数量均无显著差异。2)落叶植物和乔木的小枝横截面积、小枝长度和小枝干重均显著高于常绿植物和灌木,不同植物功能型间小枝密度无显著差异。3)与常绿植物和灌木相比,落叶植物和乔木有较高的展叶效率(单位长度小枝支撑的叶片面积),小枝的出叶强度(单位长度小枝支撑的叶片数)无显著差异。4)在小枝水平上,常绿植物比落叶植物投入更多的生物量到叶片。     

质量性状和数量性状含义的辨析

植物或动物的性状一般分为质量性状和数量性状,而实际上,许多性状并不是绝对的质量性状或数量性状,而是同时受到一个或少数几个主基因和或数量性状多基因的控制.因此,在遗传学教学中,有必要对此类性状进行分析.为加深学生对此类性状的遗传及这两个概念的理解,通过性状次数分布图分析,结合最新的遗传学研究成果,对之进行了分析和讨论.     

梭梭和骆驼刺对干旱的适应策略差异

该研究目的在于揭示干旱荒漠中2个优势种梭梭(Haloxylon ammodendron)和骆驼刺(Alhagi sparsifolia)是否在适应干旱的策略上存在差异。在新疆艾比湖自然保护区内自然形成的干旱胁迫梯度上,首先测量梭梭和骆驼刺的3类功能性状(叶、光合和水力性状);其后分析性状随干旱梯度的变化,性状在两个物种之间的差别,两物种应对干旱胁迫时所采用策略的差异性。结果显示:梭梭和骆驼刺的功能性状在干旱梯度上的变化存在不同。除干物质含量外,其余10个功能性状在梭梭和骆驼刺间均存在显著差异,但在干旱梯度与物种的共同作用下,梭梭与骆驼刺之间性状差异呈现缩小趋势。Pearson相关分析表明,骆驼刺显著相关的性状仅有10对,而梭梭有15对。主成分分析可将梭梭11个功能性状分为与植物抗旱能力有关的2个典型性状组合类别,即干旱胁迫-碳获取组和抗干旱胁迫组。但对骆驼刺,很难划分出与抗旱有关的性状组合。该研究结果表明,相较梭梭,骆驼刺具有更强的耐旱能力,属于保守型物种,性状之间联系不显著,但梭梭的性状之间联系紧密,它利用各种性状之间的权衡和补偿关系尽可能地减小干旱胁迫。该研究揭示了干旱荒漠中不同生...     

植物性状研究的机遇与挑战:从器官到群落

植物性状(Plant trait)或植物功能性状(Plant functional trait)通常是指植物对外界环境长期适应与进化后所表现出的可量度、且与生产力优化或环境适应等密切相关的属性。近几十年来,植物性状研究在性状-生产力、性状-养分、性状间相互关系、性状-群落结构维持等方面取得了卓越成就。然而,由于大多数性状调查都是以植物群落内优势种或亚优势种为对象,使其在探讨群落尺度的性状-功能关系、性状数据如何用于改进或优化模型、性状数据如何与遥感连接等问题时,存在空间尺度和量纲不匹配的极大挑战。为了破解上述难题,亟需发展新的、基于单位土地面积的群落性状(Community trait)概念体系、数据源和计算方法等,推动植物性状数据与快速发展的宏观生态学新技术(遥感、模型和通量观测等)相结合,既拓展了植物性状研究范畴,又可推动其更好地服务于区域生态环境问题的解决。所定义的群落性状(如叶片氮含量、磷含量、比叶面积、气孔密度、叶绿素含量等),是在充分考虑群落内所有物种的性状实测数据,再结合比叶面积、生物量异速生长方程和群落结构数据等,推导而成的基于单位土地面积的群落性状。受测试方法的影响,传统的直接算术平均法或相对生物量加权平均法所获得的群落水平的植物性状(如叶片氮含量g/kg或%),虽然可以有效地探讨群落结构维持机制,由于无法实现对群落性状在量纲上向单位土地面积转换,使它很难与模型和遥感数据相匹配。基于单位土地面积的群落性状,可在空间尺度匹配(或量纲匹配)的前提下实现个体水平测定的植物性状数据与生态模型和遥感观测相联系,更好地探讨区域尺度下自然生态系统结构和功能的关系及其对全球变化的响应与适应。同时,它也可更好地建立群落水平的性状-功能的定量关系(非物种水平),为更好地探讨自然群落结构维持机制和生产力优化机制提供了新思路。     

八个树种叶水力性状对水分条件的响应及其驱动因素

树木叶片的水力效率和安全性会对水分条件的改变做出一定的响应, 进而影响树木的生长和分布, 然而叶导水率(K_leaf)和叶水力脆弱性(P₅₀)对不同水分条件的响应模式及其影响因素尚不清楚。该研究选取了晋西北关帝山和黑茶山两种水分条件下的8种树种, 测量其水力性状、叶片导管和形态性状, 比较两地不同树种的K_leaf和P₅₀的变化, 分析叶片水力效率和安全性之间的权衡关系, 并探讨叶片水力性状在不同树种及水分条件下的响应模式及其驱动因素。结果表明: 对同一树种而言, 湿润的关帝山叶最大导水率(K_max)和P₅₀均高于干旱的黑茶山; 对同一地区而言, 从在高水分条件下生长的树种到在易干旱环境生长的树种, K_max和P₅₀均逐渐下降。K_max、P₅₀、膨压丧失点水势(TLP)之间均存在显著相关关系。两地叶片P₅₀与导管密度、导管塌陷预测值((t/b)³)、叶片厚度、比叶质量显著正相关, 与导管直径、叶面积显著负相关, 不同树种的K_leaf和P₅₀与叶导管性状的关系大于叶形态性状。同一树种的关帝山到黑茶山P₅₀变化量(δP₅₀)与比叶质量和叶干物质含量在两地的变化量显著正相关, 同一树种δP₅₀与叶形态性状变化量的关系大于与叶导管性状的。以上结果表明: 随着水分条件变差, 叶片水力效率降低, 水力安全性提高, 不同树种叶片水力效率与安全性之间存在一定的权衡关系, 不同树种叶水力性状的差别受叶导管性状影响的程度大于受叶形态性状的影响, 同一树种叶水力安全性对水分条件变化的响应主要依靠叶形态性状的驱动, 树木在提高自身叶水力安全的同时增加了叶构建的碳投资。     

Phylogeny-based assignment of functional traits to DNA barcodes outperforms distance-based,in a comparison of approaches

The full potential for using DNA barcodes for profiling functional trait diversity has yet to be determined in plants and animals; thus, we outline a general framework for quantifying functional trait diversity of insect community DNA and propose and assess the accuracy of three methods for achieving this. We built a novel dataset of traits and DNA barcodes for wild bees in China. An informatics framework was developed for phylogeny-based integration of these data and prediction of traits for any subject barcodes, which was compared with two distance-based methods. For Phylogenetic Assignment, we additionally conducted a species-level analysis of publically available bee trait data. Under the specimen-level dataset, the rate of trait assignment was negatively correlated with distance between the query and the nearest trait-known reference, for all methods. Phylogenetic Assignment was found to perform best under several criteria; particularly, it had the lowest false-positive rate (rarely returning a state prediction where success was unlikely; where the distance from query to the nearest reference was high). For a wider range of compiled traits, conservative life-history traits showed the highest rates of assignment; for example, sociality was predicted with confidence at 53%, parasitism at 44% and nest location at 33%. As outlined herein, automated trait assignment might be applied at scale to either barcodes or metabarcodes. With further compilation and databasing of DNA barcode and trait data, the rate and accuracy of trait assignment is expected to increase to the point of being a widely viable and informative approach.     

The traits of “trait ecologists”: An analysis of the use of trait and functional trait terminology

Trait and functional trait approaches have revolutionized ecology improving our understanding of community assembly, species coexistence, and biodiversity loss. Focusing on traits promotes comparability across spatial and organizational scales, but terms must be used consistently. While several papers have offered definitions, it remains unclear how ecologists operationalize “trait” and “functional trait” terms. Here, we evaluate how researchers and the published literatures use these terms and explore differences among subdisciplines and study systems (taxa and biome). By conducting both a survey and a literature review, we test the hypothesis that ecologists’ working definition of “trait” is adapted or altered when confronting the realities of collecting, analyzing and presenting data. From 486 survey responses and 712 reviewed papers, we identified inconsistencies in the understanding and use of terminology among researchers, but also limited inclusion of definitions within the published literature. Discrepancies were not explained by subdiscipline, system of study, or respondent characteristics, suggesting there could be an inconsistent understanding even among those working in related topics. Consistencies among survey responses included the use of morphological, phonological, and physiological traits. Previous studies have called for unification of terminology; yet, our study shows that proposed definitions are not consistently used or accepted. Sources of disagreement include trait heritability, defining and interpreting function, and dealing with organisms in which individuals are not clearly recognizable. We discuss and offer guidelines for overcoming these disagreements. The diversity of life on Earth means traits can represent different features that can be measured and reported in different ways, and thus, narrow definitions that work for one system will fail in others. We recommend ecologists embrace the breadth of biodiversity using a simplified definition of “trait” more consistent with its common use. Trait‐based approaches will be most powerful if we accept that traits are at least as diverse as trait ecologists.     

Joint oligogenic segregation and linkage analysis using bayesian Markov chain Monte Carlo methods

One of the most challenging areas in human genetics is the dissection of quantitative traits. In this context, the efficient use of available data is important, including, when possible, use of large pedigrees and many markers for gene mapping. In addition, methods that jointly perform linkage analysis and estimation of the trait model are appealing because they combine the advantages of a model-based analysis with the advantages of methods that do not require prespecification of model parameters for linkage analysis. Here we review a Markov chain Monte Carlo approach for such joint linkage and segregation analysis, which allows analysis of oligogenic traits in the context of multipoint linkage analysis of large pedigrees. We provide an outline for practitioners of the salient features of the method, interpretation of the results, effect of violation of assumptions, and an example analysis of a two-locus trait to illustrate the method.     

Genetic analysis of the temperament of Nellore cattle using linear and threshold models

Temperament is an important trait for the management and welfare of animals and for reducing accidents involving people who work with cattle. The present study aimed to estimate the genetic parameters related to the temperament score (T) and weaning weight (WW) of Nellore cattle, reared in a beef cattle breeding program in Brazil. Data were analyzed using two different two-trait statistical models, both considering WW and T: (1) a linear-linear model in which variance components (VCs) were estimated using restricted maximum likelihood; and (2) a linear-threshold model in which VCs were estimated via Bayesian inference. WW was included in the analyses of T to minimize any possible effects of sequential selection and to allow for estimation of the genetic correlation between these two traits. The heritability estimates for T were 0.21±0.003 (model 1) and 0.26 (model 2, with a 95% credibility interval (95% CI) of 0.21 to 0.32). The estimated genetic correlations between WW and T were of a moderate magnitude (−0.33±0.01 (model 1) and −0.34 (95% CI: −0.40, −0.28, model 2). The genetic correlations between the estimated breeding values (EBVs) obtained for the animals based on the two models were high (>0.92). The use of different models had little influence on the classification of animals based on EBVs or the accuracy of the EBVs.     

长白山温带森林不同演替阶段群落功能性状的空间变化

群落构建机制研究是生态学研究的热点。长白山自然保护区拥有完整的原始阔叶红松林生态系统, 近年来随着物种多样性丧失愈发严重, 对该地区开展群落构建机制研究显得尤为重要。该研究以长白山不同演替阶段的3块5.2 hm ²固定监测样地(次生杨桦林、次生针阔混交林、原始椴树红松林)为研究对象, 通过采集样地内主要树种的6个关键功能性状(叶面积、比叶面积、叶片厚度、叶氮含量、叶磷含量、最大树高), 分析不同空间尺度下(5 m × 5 m, 10 m × 10 m, 20 m × 20 m, 30 m × 30 m, 40 m × 40 m, 50 m × 50 m和60 m × 60 m)及不同演替阶段群落性状空间值的变化, 结合零模型的模拟结果对长白山温带森林演替过程中的群落构建机制进行讨论。结果表明: 种库大小对于研究结果具有重要影响。在较大的种库下, 环境过滤作用影响显著。而在样地水平进行研究时, 演替早期和中期, 群落性状空间值与零模型模拟值无显著差异, 在演替的晚期, 群落性状空间值显著高于零模型模拟值。结合多个群落功能多样性指数分析发现, 环境过滤和竞争作用共同决定该地区顶级群落的物种组成。在演替早期大量物种迁入, 群落内物种间存在强烈的资源竞争, 而随着演替进行, 部分物种逐渐被竞争排除出群落, 群落中的物种呈现明显的生态位分化, 竞争作用是维持物种共存的主要机制。     

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: I. egg production traits

A genome scan was performed to detect chromosomal regions that affect egg production traits in reciprocal crosses between two genetically and phenotypically extreme chicken lines: the partially inbred line New Hampshire (NHI) and the inbred line White Leghorn (WL77). The NHI line had been selected for high growth and WL77 for low egg weight before inbreeding. The result showed a highly significant region on chromosome 4 with multiple QTL for egg production traits between 19.2 and 82.1 Mb. This QTL region explained 4.3 and 16.1% of the phenotypic variance for number of eggs and egg weight in the F₂ population, respectively. The egg weight QTL effects are dependent on the direction of the cross. In addition, genome‐wide suggestive QTL for egg weight were found on chromosomes 1, 5, and 9, and for number of eggs on chromosomes 5 and 7. A genome‐wide significant QTL affecting age at first egg was mapped on chromosome 1. The difference between the parental lines and the highly significant QTL effects on chromosome 4 will further support fine mapping and candidate gene identification for egg production traits in chicken.     

Generalized linear mixed models for mapping multiple quantitative trait loci

Many biological traits are discretely distributed in phenotype but continuously distributed in genetics because they are controlled by multiple genes and environmental variants. Due to the quantitative nature of the genetic background, these multiple genes are called quantitative trait loci (QTL). When the QTL effects are treated as random, they can be estimated in a single generalized linear mixed model (GLMM), even if the number of QTL may be larger than the sample size. The GLMM in its original form cannot be applied to QTL mapping for discrete traits if there are missing genotypes. We examined two alternative missing genotype-handling methods: the expectation method and the overdispersion method. Simulation studies show that the two methods are efficient for multiple QTL mapping (MQM) under the GLMM framework. The overdispersion method showed slight advantages over the expectation method in terms of smaller mean-squared errors of the estimated QTL effects. The two methods of GLMM were applied to MQM for the female fertility trait of wheat. Multiple QTL were detected to control the variation of the number of seeded spikelets.     

多个典范性状的综合优化研究

本文运用系统优化原理,利用综合的手段,研究了育种目标约束下多个数量性状表现型向量与基因型向量的典范相关,提出了综合典范性状的数学模型．综合典范性状是Ｓ个遗传力较大的典范性状在育种目标约束下遗传力极大化的线性组合．综合典范性状作为选择指标,选择效率高,提高了多目标育种决策的科学性和预见性．     

Ecogeochemistry potential in deep time biodiversity illustrated using a modern deep-water case study

The fossil record provides the only direct evidence of temporal trends in biodiversity over evolutionary timescales. Studies of biodiversity using the fossil record are, however, largely limited to discussions of taxonomic and/or morphological diversity. Behavioural and physiological traits that are likely to be under strong selection are largely obscured from the body fossil record. Similar problems exist in modern ecosystems where animals are difficult to access. In this review, we illustrate some of the common conceptual and methodological ground shared between those studying behavioural ecology in deep time and in inaccessible modern ecosystems. We discuss emerging ecogeochemical methods used to explore population connectivity and genetic drift, life-history traits and field metabolic rate and discuss some of the additional problems associated with applying these methods in deep time.     

云南甘蔗品种表型性状的遗传多样性分析

为了提高云南甘蔗品种资源的利用效率,为甘蔗遗传育种亲本的选择、杂交组合配制提供理论指导,本研究从18个质量性状和5个数量性状对73份云南甘蔗品种和27份中国历年主栽甘蔗品种(不包括云南选育的主栽品种)的遗传变异、遗传多样性、聚类关系等开展了研究。结果表明:云南甘蔗品种芽形、曝光后节间颜色、曝光前节间颜色、芽沟和57号毛群的多样性十分丰富;而数量性状的遗传变异主要来自叶片宽度和株高;相似性系数和聚类分析表明品种的相似性处于中等水平,可分成2个大类群4个亚类群及20个小类群,主成份分析表明云南甘蔗品种和中国历年主栽品种可划分为3个明显的基因库,与聚类分析结果基本一致。     

大别山野生川榛坚果主要性状分析及评价

本研究以大别山地区96份川榛种质资源为基础材料,采用概率分级和因子分析的方法,评价了川榛坚果16项数量性状和9项质量性状指标。结果表明:川榛坚果数量性状的变异较为丰富,变异幅度在5.49%~111.18%,其中与产量直接相关的壳仁间隙(111.18%)、果仁质量(32.61%)、坚果质量(32.22%)、出仁率(26.60%)及壳腰厚度(25.46%)性状变异较大。经K-S检验表明,供试性状除了果仁形状指数(P=0.007)和壳仁间隙(P=0.003)2项指标外,其他14项性状指标均符合正态分布。因子分析法提取了坚果大小因素、坚果出仁率因素及坚果饱满度因素,初步构建川榛坚果性状综合评价指标。上述研究为川榛坚果性状的评价、描述和质量等级的建立提供参考依据。