木薯种质的遗传多样性评价及高产种质初级筛选

为加强木薯现有选育材料和引进种质的研究利用,本研究以主栽品种SC8和SC205为对照,对142份选育材料和8份瑞士引进新种质进行了16个表型性状的鉴定和EST-SSR标记,分析和评价其遗传多样性;运用主成分分析法挖掘高产木薯种质。分子标记聚类分析表明种质间的遗传相似系数均值为0.652,基于表型性状的聚类遗传相似系数均值为0.186,2种聚类结果之间差异显著,但均表明种质间有一定的遗传差异。2年产量相关性状调查结果差异极显著,表明受环境影响较大。产量相关性状的主成分分析结果表明,C322综合评价表现最好,G74综合评价表现最差,同时,有47份选育材料的综合评价优于2份对照。在今后杂交育种工作中可选择亲缘关系较远且表型差异互补的种质作为杂交亲本,以进一步聚合优良性状,改良不利性状。     

植物功能性状对生态系统服务影响研究进展

全面认识和理解生态系统服务的形成机制是维持其持续供给的前提。植物功能性状直接参与多种生态系统过程, 影响生态系统服务供给, 探讨植物功能性状与生态系统服务的关系是揭示生态系统服务形成机制的重要途径。该文采用系统的文献综述方法, 分析了植物功能性状与生态系统服务关系的研究特点, 总结了影响不同生态系统服务的主要植物功能性状, 阐述了可能的影响途径。结果表明: 植物功能性状与生态系统服务关系研究以草地和森林等自然生态系统为主; 大部分研究集中在生态系统供给服务和支持服务, 包括生物量、净初级生产力、土壤肥力等; 根据植物功能性状对不同生态系统服务的影响程度, 植物功能性状可以聚类为土壤保持服务相关性状、水分循环相关性状、多功能相关性状、产品提供服务与养分循环相关性状以及授粉与生物控制服务相关性状; 并阐述了植物功能性状指标影响不同的生态系统服务途径。围绕植物功能性状对生态系统服务的影响, 今后尚需进一步探讨生态系统多功能性、植物功能性状相关性、气候变化和人类活动不确定性、时空尺度差异等因素对二者关系的影响。     

核桃品种绿岭杂交后代主要性状的遗传分析与优株选择研究

为了培育出矮化、早实、丰产、优质等综合性状优于绿岭的核桃新品种,以绿岭核桃为亲本与辽宁1号、绿早进行杂交,测定了正反交组合374个杂交单株的13个性状,并对其进行了遗传分析,结果表明:杂交后代的表型性状具有较高的遗传多样性,各性状的变异系数均在17%以上,最高达72.40%;而果实相关性状的变异系数除可溶性蛋白质之外,均在20%以下。青皮率和脂肪含量的遗传传递力在4个杂交组合中均大于97%,其遗传受加性效应影响较大。果实相关性状的广义遗传力均在90%以上,说明其在遗传上是比较稳定的,可以在早代进行选择。从杂交后代中初选21个优株,采用主成分分析的方法,对其进行评价和优株选择。结果表明,以性状的累积方差贡献率达到74.3%,确定了4个反映核桃主要性状的主成分;通过计算各单株的综合评价值,在供试的21个优株中,选出了3个综合性状优良的单株,其结果与单株的实际表型相近;并发现短结果枝率、矮化指数和节间长度3个指标能够反映出核桃的矮化优良性状。     

玉米自交系秸秆品质性状鉴定与评价

利用近红外漫反射光谱法,对50份常用普通玉米自交系和50份高油自交系秸秆的中性洗涤纤维(NDF)、酸性洗涤纤维(ADF)、可溶性糖(WSC)和粗蛋白(CP)4个品质性状进行了鉴定评价和相关性分析。结果表明,各品质性状变异较大,各性状自交系间差异均达极显著水平。不同品质性状变异程度不同,其中WSC含量变异最大,变异系数达34.23%。WSC与NDF、ADF极显著负相关,NDF与ADF含量极显著正相关。高油系表现为高WSC、CP和低NDF、ADF含量,总体上高油系秸秆品质优于普通玉米。     

植物功能性状与森林生态系统服务的关系研究综述

植物功能性状途径是揭示生物多样性与生态系统服务关系的重要视角,尽管植物功能性状与生态系统服务的关系在单一地点的研究取得突出进展,但对于植物功能性状与生态系统服务的关系仍缺乏整体认识。以森林生态系统为对象,通过系统文献检索及筛选,收集了216篇文献,应用整合分析和二分网络分析等方法,探讨了植物功能性状对森林生态系统服务及其权衡与协同关系的影响。结果表明：植物叶片功能性状关注最多,占研究性状数量的48%,生态系统服务中关注最多是生物量、土壤肥力、病虫害控制和固碳服务;81.1%的植物功能性状与生态系统服务关系组表现为稳定的正向或负向关系,而关联植物功能性状多的生态系统服务（生物量、固碳服务、土壤水分、土壤肥力和病虫害控制）往往与植物功能性状表现为不稳定关系;森林生态系统中存在6组"植物功能性状-生态系统服务簇（简称"性状-服务簇"）：水循环相关的性状-服务簇、土壤保持相关的性状-服务簇、物质生产相关的性状-服务簇、灾害控制相关的性状-服务簇、养分循环相关的性状-服务簇和授粉相关的性状-服务簇,揭示了各性状-服务簇内生态系统服务的权衡或协同关系以及与各性状-服务簇关系密切的植物功能性状。该研究从总体上阐明了植物功能性状与森林生态系统服务关系的研究重点和进展、揭示了植物功能性状对森林生态系统服务影响效应的方向和强度,可为深化森林生态系统服务形成机制认识以及协调生态系统服务权衡关系提供科学依据。     

不同种源厚朴苗期性状变异及主成分分析

基于厚朴（Magnolia officinalis）作为一种传统中药植物及分布区域广、环境异质化程度明显的现象,采用田间种源实验,对分布在中国7个省的14个种源厚朴苗期的生长性状进行了观测分析。结果表明,不同种源厚朴的苗期生长性状差异显著。种源遗传力分析表明,苗高和单株叶面积两个性状的遗传力较高,分别为0.93、0.79,可认为以苗高和单株叶面积为主的种源多性状综合选择改良潜力巨大。相关性分析表明各性状间遗传相关、表型相关、环境相关均存在一定的相关关系,单株叶面积和地上部生长性状的遗传相关程度高于地下部生长性状,表型显著相关的性状组合数量和程度低于遗传相关。厚朴苗期种源选择的首选因子为各生物量及单数叶面积性状,辅助因子为苗高和地径。通过系统聚类分析,初步选定景宁、武夷山、龙胜、开县、城固、宁强及洋县的种源为优良厚朴种源。     

不结球白菜杂种优势及相关分析

以4个不结球白菜不育系与4个父本系以NCⅡ法配制16个杂交组合,研究了16个F1组合的杂种优势表现及其与亲本之间的相关关系,同时对性状间的遗传相关进行分析.结果表明:不结球白菜产量性状杂种优势＞农艺性状杂种优势＞光合性状杂种优势＞品质性状杂种优势.产量性状以超亲优势为主,农艺性状和光合性状以中亲优势为主,品质性状中可溶性糖含量以中亲优势为主, Vc含量和蛋白质含量均为弱的负向优势.亲子相关分析表明,一些性状F1与中亲值、低亲值或高亲值显著相关,因此在亲本选配时,注意亲本差异的同时,中亲值特别是低亲值不能过低,尤其是品质性状.性状间相关分析显示,光合性状与产量性状显著正相关,说明F1高效的光合同化作用是杂种高产的基础.品质性状中,可溶性糖含量与产量显著正相关,但Vc和蛋白质含量与产量负相关,在亲本选配时还应注意二者的协调.     

大麦主要农艺性状的遗传相关剖析

提高产量是大麦育种的最终目标之一。由于产量性状是复杂的数量性状,受多种因素的影响和制约,同时诸因素间又存在着不同程度的相关,某一性状的变化必然导致其它性状的相关改变,这给正确而又有效的选择带来了一定的困难。笔者曾用两个多棱大麦杂交组合和3个二棱大麦杂交组合研究了大麦主要农艺性状的遗传力和遗传进度,对大麦杂种后代的直接选择和处理提出了一些指标^[3], 但未能涉及到各性状间的遗传相关变化。本研究着重分析长江下游大面积推广使用的一些高产二棱大麦新品种主要农艺性状间的遗传相关,进行各性状的通径分析,剖析产生这些相关的原因及估测各性状的相对重要性,为利用这些高产品种作为原始群体,从中选择出更高产品种或某些性状有所改良的新品种提供参考依据。     

杂交水稻加工、外观品质性状间接选择的数学模型研究

利用19个优质杂交水稻品种（组合）,采用双向逐步筛选,求出加工和外观品质性状与产量性状的最优相关子集,建立了品质性状的回归方程,并对子集作了广义相关分析。结果表明千粒重、穗长与糙米率、整精米率、垩白粒率的相关已反映了品质性状与产量性状相关的主要信息（90％以上）,千粒重在21.96～27.64g、穗长在21.18～26.07cm范围内,增大千粒重可提高糙米率,但整米率下降、垩白粒率上升,适当缩短穗长可提高糙米率和整精米率,降低垩白粒率。     

茄子果实相关农艺性状全基因组关联分析研究进展与展望

茄子是重要的园艺作物,也是茄科植物中种植最广泛的蔬菜之一。茄子果实相关农艺性状是一种复杂的数量性状,传统育种选育效率低、周期长。高通量测序技术与生物信息学技术的快速发展,使得全基因组关联分析(genome-wide association study, GWAS)在解析茄子果实相关复杂农艺性状的遗传规律方面展现出巨大的应用前景。本文对全基因组关联分析在茄子的果形、果色等果实相关农艺性状中的研究进展进行了综述;针对茄子数量性状遗传研究中普遍存在的“丢失遗传力”(missing heritability)问题,从4个GWAS策略在茄子果实相关农艺性状研究中的应用热点出发,提出了未来茄子GWAS的发展对策;并结合当前茄子遗传改良的实践需求,展望了GWAS策略在茄子分子育种领域的广阔应用前景。本文为今后利用GWAS解析各种茄子果实相关性状的遗传基础以及选育符合消费者需求的果实材料提供了理论依据和参考。     

A statistical model for under- or overdispersed clustered and longitudinal count data

We propose a likelihood-based model for correlated count data that display under- or overdispersion within units (e.g. subjects). The model is capable of handling correlation due to clustering and/or serial correlation, in the presence of unbalanced, missing or unequally spaced data. A family of distributions based on birth-event processes is used to model within-subject underdispersion. A computational approach is given to overcome a parameterization difficulty with this family, and this allows use of common Markov Chain Monte Carlo software (e.g. WinBUGS) for estimation. Application of the model to daily counts of asthma inhaler use by children shows substantial within-subject underdispersion, between-subject heterogeneity and correlation due to both clustering of measurements within subjects and serial correlation of longitudinal measurements. The model provides a major improvement over Poisson longitudinal models, and diagnostics show that the model fits well.     

物种与科属的数量关系——以中国鸟类为例

许多研究表明,物种与高级分类阶元在数量上密切相关,这种关系在地区物种数量预测中具有很高的应用价值。应用中国不同地理类型(保护区、行政区和动物地理亚区)的鸟类物种名录,研究物种与科属的数量相关关系和频次分布规律,结果表明(1)物种与高级分类阶元在数量上有着极显著相关关系(P<0.01),其中物种—属的相关关系要显著于物种—科,且在对数、乘幂、指数和线数4种模型中,用乘幂模型拟合最好;(2)物种在科属间的频次分布具有规律性(P<0.05),随着物种数/科属的增加,频次迅速减少,在4种模型中,乘幂模型拟合最好,属的规律性较科显著。根据以上结果,物种与科属间的数量强相关关系与物种数量在科属间有规律的频次分布有关。     

拟南芥花粉管与柱头互作的乙醇代谢耦合模型

依据拟南芥公开的代谢途径数据库,构建了基于酶与酶的拟南芥代谢网络模型。利用拟南芥花粉管与柱头互作过程中的转录组数据,挖掘出花粉管与柱头在互作过程中的特异表达基因,进一步将特异表达的酶基因匹配到已构建的拟南芥代谢网络中,根据网络拓扑模型中的节点(酶)之间的共表达关联性,最后给出了一个拟南芥花粉管与柱头互作的乙醇代谢耦合模型。     

A Statistical Model for Estimation of Fish Density Including Correlation in Size,Space, Time and between Species from Research Survey Data

Trawl survey data with high spatial and seasonal coverage were analysed using a variant of the Log Gaussian Cox Process (LGCP) statistical model to estimate unbiased relative fish densities. The model estimates correlations between observations according to time, space, and fish size and includes zero observations and over-dispersion. The model utilises the fact the correlation between numbers of fish caught increases when the distance in space and time between the fish decreases, and the correlation between size groups in a haul increases when the difference in size decreases. Here the model is extended in two ways. Instead of assuming a natural scale size correlation, the model is further developed to allow for a transformed length scale. Furthermore, in the present application, the spatial- and size-dependent correlation between species was included. For cod (Gadus morhua) and whiting (Merlangius merlangus), a common structured size correlation was fitted, and a separable structure between the time and space-size correlation was found for each species, whereas more complex structures were required to describe the correlation between species (and space-size). The within-species time correlation is strong, whereas the correlations between the species are weaker over time but strong within the year.     

Bayesian models for the analysis of genetic structure when populations are correlated

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.     

Estimating correlation coefficient between two variables with repeated observations using mixed effects model

We estimate the correlation coefficient between two variables with repeated observations on each variable, using linear mixed effects (LME) model. The solution to this problem has been studied by many authors. Bland and Altman (1995) considered the problem in many ad hoc methods. Lam, Webb and O'Donnell (1999) solved the problem by considering different correlation structures on the repeated measures. They assumed that the repeated measures are linked over time but their method needs specialized software. However, they never addressed the question of how to choose the correlation structure on the repeated measures for a particular data set. Hamlett et al. (2003) generalized this model and used Proc Mixed of SAS to solve the problem. Unfortunately, their method also cannot implement the correlation structure on the repeated measures that is present in the data. We also assume that the repeated measures are linked over time and generalize all the previous models, and can account for the correlation structure on the repeated measures that is present in the data. We study how the correlation coefficient between the variables gets affected by incorrect assumption of the correlation structure on the repeated measures itself by using Proc Mixed of SAS, and describe how to select the correlation structure on the repeated measures. We also extend the model by including random intercept and random slope over time for each subject. Our model will also be useful when some of the repeated measures are missing at random.     

Fluorescence correlation spectroscopy of finite-sized particles

A theory is presented to study fluorescence correlation spectroscopy for particles with size comparable to the beam waist of the observation volume. Analytical correlation curves are derived for some experimentally interesting particle geometries. It is found that the finiteness of the particle generally decreases the value of the correlation amplitude and increases the correlation time compared to a point particle model. Furthermore, not only the size but also the distribution of fluorophores affects the shape of the correlation function. This is experimentally demonstrated with surface and internally labeled fluorescent spheres. In addition, experiments are performed on fluorescent spheres of different radii to validate the model by comparing the results to theoretical predictions.     

A new model for calculating muscle forces from electromyograms

A muscle model is described that uses electromyogram (EMG), muscle length and speed of contraction to predict muscle force. Physiological parameters are the Hill constants and the shape of the twitch response to a single stimulus. The model was incorporated in a jaw model of the rabbit and tested by predicting the bite force produced by the jaw muscles during mastication. The time course of the calculated force appeared to match the bite force, measured in vivo by a strain gauge, applied to the bone below the teeth. The variation in peak strain amplitude from cycle to cycle correlated with the variation predicted by the model. The peak amplitude of the integrated EMGs of individual jaw muscles showed an average correlation with peak strain of 0.41. Use of the sum of the available peak amplitudes, weighted according to their effect upon the bite force increased the correlation to 0.46; the model predicted bite forces showed a correlation of 0.57 with the strain. The increase in correlation was statistically significant. The muscle forces were calculated using a minimum number of easily obtainable constants.     

Delayed Protein Synthesis Reduces the Correlation between mRNA and Protein Fluctuations

Recent experimental results indicate that, in single Escherichia coli cells, the fluctuations in mRNA level are uncorrelated with those of protein. However, a basic two-stage model for prokaryotic gene expression suggests that there ought to be a degree of correlation between the two. Therefore, it is important to investigate realistic modifications of the basic model that have the potential to reduce the theoretical level of the correlation. In this work, we focus on translational and reporter maturation delay, reporting that its introduction into the two-stage model reduces the cross correlation between instantaneous mRNA and protein levels. Our results indicate that the experimentally observed sample correlation coefficient between mRNA and protein levels may increase if the protein measurements are shifted back in time by the value of the delay.     

A Probit Latent Class Model with General Correlation Structures for Evaluating Accuracy of Diagnostic Tests

Summary Traditional latent class modeling has been widely applied to assess the accuracy of dichotomous diagnostic tests. These models, however, assume that the tests are independent conditional on the true disease status, which is rarely valid in practice. Alternative models using probit analysis have been proposed to incorporate dependence among tests, but these models consider restricted correlation structures. In this article, we propose a probit latent class model that allows a general correlation structure. When combined with some helpful diagnostics, this model provides a more flexible framework from which to evaluate the correlation structure and model fit. Our model encompasses several other PLC models but uses a parameter‐expanded Monte Carlo EM algorithm to obtain the maximum‐likelihood estimates. The parameter‐expanded EM algorithm was designed to accelerate the convergence rate of the EM algorithm by expanding the complete‐data model to include a larger set of parameters and it ensures a simple solution in fitting the PLC model. We demonstrate our estimation and model selection methods using a simulation study and two published medical studies.