畜禽遗传评定方法的研究进展

畜禽遗传评定是畜禽育种的重要内容。目前畜禽遗传评定方法中应用最广的是基于表型信息的BLUP动物模型。基因组学的发展和应用产生了大量分子遗传标记,结合分子遗传标记信息的遗传评定方法MBLUP随之产生。MBLUP将成为一种快速有效的畜禽遗传评定方法。本文主要介绍了畜禽遗传评定方法的研究进展和发展趋势。 Abstract:Genetic evaluation is one of the most important components in livestock breeding program.Best linear unbiased prediction (BLUP) Animal Model,which based on phenotypic information,has become the most widely accepted method for genetic evaluation of domestic livestock.Large numbers of molecular genetic markers have been discovered as the development and application of genomics.Some new methods (Marked Assisted BLUP,MBLUP) for genetic evaluation have being developed,which incorporating molecular genetic markers information into genetic evaluation.MBULP will be a rapid and efficient method for genetic evaluation of domestic livestock.The aim of the paper is to introduce the development and current situation of the methods for livestock genetic evaluation.     

InterStoreDB:A Generic Integration Resource for Genetic and Genomic Data

Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research.InterStoreDB is a suite of integrated databases designed to assist in this process.The individual databases are species independent and generic in design,providing access to curated datasets relating to plant populations,phenotypic traits,genetic maps,marker loci and QTL,with links to functional gene annotation and genomic sequence data.Each component database provides access to associated metadata,including data provenance and parameters used in analyses,thus providing users with information to evaluate the relative worth of any associations identified.The databases include CropStoreDB,for management of population,genetic map,QTL and trait measurement data,SeqStoreDB for sequence-related data and AlignStoreDB,which stores sequence alignment information,and allows navigation between genetic and genomic datasets.Genetic maps are visualized and compared using the CMAP tool,and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser.This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal.We demonstrate the value of InterStoreDB as a tool for Brassica research.InterStoreDB is available from:http://www.interstoredb.org     

小麦异交群体连续歧化选择的RAPD分析

利用太谷核不育基因构建的遗传变异丰富的基础群体DNS2,进行了连续5轮歧化选择。本论文从不同的世代中,选择了10个子群体进行RAPD分析。采用7个引物扩增出116个位点,从基因频率和表型带两个角度的分析都表明,群体具有丰富的遗传变异。整个群体总的多态位点百分率达88.79,总杂合度为0.3143。子群体内（间）遗传距离的结果显示：子群体内的遗传差异小于子群体间的遗传差异;各选择子群体与未选群体间都有较大的遗传距离;随着选择轮次的增加,株高选择子群体间的遗传距离逐渐增大;对同一性状进行选择的子群体间世代内（间）平均遗传距离小于对不同性状进行选择的子群体内（间）的遗传距离。RAPD分子聚类结果显示出对同一性状进行选择的子群体聚在一起,反映了对株高选高的选择效果比较明显。 Abstract:A base population was established through multi-parent random crossing by using Taigu dominant male-sterile wheat,and then five cycles of 2-way selection for four quantitative characters were conducted.The dynamic changes of genetic structures in the open-pollinated wheat population were examined by RAPD technique.Seven primers in RAPD analysis amplified 116 sites.The results of gene frequencies and phenotypic bands showed abundant genetic variations existed in the population.The percentage of polymorphic loci was 8879,and the average heterozygosity was 0.3143 in the whole population.The genetic distance of RAPD showed as follows :① The genetic distance within a subpopulation was lower than that between every two subpopulations.② Each subpopulation had considerable divergence compared with unselected population.③ The genetic distances between the subpopulations which were selected for plant height gradually increased accompanied with the selection.④The genetic distance between subpopulations which were selected for the same character was lower than that were selected for different characters both in the same generation and among different generations.The cluster results of RAPD genetic distance demonstrated that the subpopulations selected for the same character going to one cluster.It also showed that the selective effect of increasing plant height was obvious.     

Modelling Mechanical Properties in Native and Biomimetically Formed Vascular Grafts

The paper presents a detailed analysis of experimental data in order to characterize the elastic properties of arteries.Suchanalysis would provide a good basis for evaluation of biomimetic vascular grafts.Since the latter needs to exhibit similarproperties of native tissue,it is important to accurately characterize the biomimetic sample in a large range of applied stresses.The stress-strain properties vary according to the specific pathology(e.g.arteriosclerosis,aneurism)and the tissue graft must bechosen correctly.Two models are proposed in this paper on the stress-strain characteristics.An extension for frequency-domainanalysis is provided for one of the models.The comparison between vascular grafts and native tissue for carotid and thoracicarteries in pigs are in good agreement with results from literature.The proposed experimental method offers suitable parametersfor identifying models which characterize both elasticity and stiffness properties of the analyzed tissues(stress-strain).Theproposed models show good performance in characterizing the intrinsic material properties.     

三品系小型猪35个微卫星基因座的遗传学研究

利用35个微卫星基因座对中国三个品系的小型猪（贵州小型香猪、广西巴马小型猪、版纳小耳猪近交系）进行了遗传检测。计算出三个小型猪品系个体样本在35个微卫星基因座的纯合率,并对其进行t检验。计算出各品系的平均杂合度,多态信息含量（PIC）及品系间的遗传距离,并进行了系统聚类。结果表明三个品系的小型猪其基因纯合率均较高,其中版纳小耳猪近交系的基因纯合率最高;PIC和平均杂合度均较低;贵州小型香猪和广西巴马小型猪亲缘关系较近,并均与版纳小耳猪近交系的亲缘关系略远。 Abstract：The polymorphism of 35 microsatellites in the three miniature pig breeds in China(Guizhou miniature pig, Guangxi Bama miniature pig, Banna miniature pig inbred) was analysed. Rates of homozygote for 35 microsatellite loci in three miniature pig breeds were calculated,and t-test for them were performed. Mean heterozygosity and polymorphism information content(PIC) were calculated for all breeds, and genetic distances between these breeds were estimated. The dendrograms were obtained based on genetic distances. The results suggest that rates of homozygote in the three breeds are all high, and that is the highest in Banna miniature pig inbred. The results also suggest that polymorphism information content and mean heterozygosity in all the three breeds are low, and the genetic relationship between Guizhou miniature pig and Guangxi Bama miniature pig is closer than their relationship with Banna miniature pig inbred.     

贵州小型香猪基因组DNA的AFLP检测研究

报道了AFLP标记在研究贵州小型香猪遗传多态性方面的应用和该品系猪个体基因组DNA的AFLP扩增结果,分析了贵州小型香猪的群体遗传结构.实验应用10条AFLP引物,用PstⅠ酶切,对17头猪基因组DNA进行AFLP反应,共获得116个AFLP标记,单引物获得的标记数在2～22间,贵州小型香猪群体相似系数AFLP研究结果为0.866(0.760～0.967),该研究为评价贵州小型香猪的遗传稳定性提供了相关的参数,准确评价尚待和其它品种猪对比研究后确定。 Abstract:We reported the application of AFIP markers to detect genetic polymorphic loci in Guizhou miniaturc pig and their amplified AFLP results.Their genetic construction Of the population was also analysed.TenAFLP primers were used,genomic DNAs from 17 pigs were restrictive by pst I,116 AFLP markers were obtained,the obtaining marker numbers of individual primer were between 2~22.The results indicate as the following:(1)AFLP marker is suitable for analysing genetic polymorphism in pig;(2)The similarty index of population in Guizhou miniaturc pigs was 0.866(0.760~0.967).The study provides a uscful parameter with appraise genetic stability of Guizhou miniature pigs.     

MIXED MODEL APPROACHES FOR ESTIMATING GENETIC VARIANCES AND COVARIANCES

The limitations of methods for analysis of variance(ANOVA)in estimating genetic variances are discussed. Among the three methods(maximum likelihood ML, restricted maximum likelihood REML, and minimum norm quadratic unbiased estimation MINQUE)for mixed linear models, MINQUE method is presented with formulae for estimating variance components and covariances components and for predicting genetic effects. Several genetic models, which cannot be appropriately analyzed by ANOVA methods, are introduced in forms of mixed linear models. Genetic models with independent random effects can be analyzed by MINQUE(1)method whieh is a MINQUE method with all prior values setting 1. MINQUE(1)method can give unbiased estimation for variance components and covariance components, and linear unbiased prediction (LUP) for genetic effects. There are more complicate genetic models for plant seeds which involve correlated random effects. MINQUE(0/1)method, which is a MINQUE method with all prior covariances setting 0 and all prior variances setting 1, is suitable for estimating variance and covariance components in these models. Mixed model approaches have advantage over ANOVA methods for the capacity of analyzing unbalanced data and complicated models. Some problems about estimation and hypothesis test by MINQUE method are discussed.     

小麦异交群体选择分化的RAPD分析

用RAPD分子标记技术及数量遗传分析手段对小麦异交群体趋异选择4代得到的各子群体的遗传关系进行了分析,并对两种结果进行了相关分析。采用11个引物扩增出134个位点,RAPD分析结果表明,群体具有丰富的遗传变异,整个群体的多态位点百分率达0.8134,杂合度达0.3006;子群体间遗传分化较小,相对基因分化系数Gst为0.2310,固定指数平均0.2120,标准遗传距离为0.1044±0.048,表明遗传变异多数来自群体之内。而数量遗传分析发现,选择性状进展都与预期方向相符,主成分遗传距离大部分达显著水平,说明选择使群体发生了相当程度的分化。对两种遗传距离进行聚类分析表明,二种信息间关系各类群成员多不一致。其原因可能在于：数量性状是人工选择的目标,RAPD是基因组随机序列的扩增,二者之间的相关与引物选择有关。 Abstract：The genetic relations of some subpopulations in the fourth generation of selection in outbreeding population of winter wheat were examined by RAPD techniques and quantitative analysis. The correlations of the two results were examined.For RAPD analysis, 11 primers were adopted, and 134 sites were amplified. The results showed that abundant genetic variations existed in the populations. In the whole population, the percentage of polymorphic sites (P) is 0.8134, and the averaged heterozygosity is 0.3006. However,genetic differentiation among subpopulations is small. The relative gene differentiation (Gst) is 0.2310,fixed index averages 0.2120, and the standard genetic distance between subpopulations is 0.1044±0.048.All above shows that most of the genetic variations existed within populations.The cluster results from RAPD analysis and principal component distances showed that similarity relations were only found in small part of the subpopulations. The reason for the results may be that the genes concerned for quantitative traits are selected directly,while the genes involved in RAPD analysis are only random samples of the whole genomes.     

CDS: a fold-change based statistical test for concomitant identification of distinctness and similarity in gene expression analysis

The problem of identifying differential activity such as in gene expression is a major defeat in biostatistics and bioinformatics.Equally important,however much less frequently studied,is the question of similar activity from one biological condition to another.The foldchange,or ratio,is usually considered a relevant criterion for stating difference and similarity between measurements.Importantly,no statistical method for concomitant evaluation of similarity and distinctness currently exists for biological applications.Modem microarray,digital PCR(dPCR),and Next-Generation Sequencing(NGS) technologies frequently provide a means of coefficient of variation estimation for individual measurements.Using fold-change,and by making the assumption that measurements are normally distributed with known variances,we designed a novel statistical test that allows us to detect concomitantly,thus using the same formalism,differentially and similarly expressed genes(http://cds.ihes.fr).Given two sets of gene measurements in different biological conditions,the probabilities of making type I and type II errors in stating that a gene is differentially or similarly expressed from one condition to the other can be calculated.Furthermore,a confidence interval for the fold-change can be delineated.Finally,we demonstrate that the assumption of normality can be relaxed to consider arbitrary distributions numerically.The Concomitant evaluation of Distinctness and Similarity(CDS) statistical test correctly estimates similarities and differences between measurements of gene expression.The implementation,being time and memory efficient,allows the use of the CDS test in high-throughput data analysis such as microarray,dPCR,and NGS experiments.Importantly,the CDS test can be applied to the comparison of single measurements(N:1) provided the variance(or coefficient of variation) of the signals is known,making CDS a valuable tool also in biomedical analysis where typically a single measurement per subject is available.