利用简化的SDS法提取杨树基因组DNA   总被引：5，自引：0，他引：5  

郝会海  李燕玲  杜志军  杜克久 《河北林果研究》2006,21(4):363-366

以杨树组培苗幼嫩叶片为材料,在室温下采用简化的SDS法快速制备其基因组DNA,并对制备DNA过程中的影响因子进行了初步研究。结果表明,采用此方法制备的基因组DNA在数量和纯度上可以满足聚合酶链式反应(PCR)的要求。另外,DNA提取缓冲液中添加一定浓度的PVP、β-巯基乙醇,有利于DNA提取。  相似文献   

漾濞核桃叶片基因组DNA的两种提取方法效果比较   总被引：10，自引：2，他引：10  

杨恩  陈少瑜  张雨  范志远  习学良 《西部林业科学》2005,34(4):72-75

以漾濞核桃不同生长期的叶片为材料，采用高盐低pH法和改良CTAB法作提取其基因组DNA的效果比较实验。通过琼脂糖凝胶电泳、紫外分光光度计和RAPD扩增对所提取的DNA样品进行检测，比较所得DNA的产量、质量，认为从漾濞核桃不同发育时期叶片中获得DNA的提取效果不同。4种叶样以冬芽和新叶的效果为好，老叶最差；用两种提取方法从叶片中得到的DNA产量和质量有所不同，高盐低pH法提取的DNA纯度高，但是产量较低；而改良CTAB法则相反，产量高，纯度低。  相似文献   

貉源犬瘟热病毒CDV-ZC株分离鉴定、全基因测序与分析     

戴秀美  常维山  张永兵  王敏  王蕾  郭树源 《中国兽医学报》2015,35(5):711-717

应用非洲绿猴肾细胞(Vero)从山东省诸城市疑似犬瘟热(canine distemper,CD)感染貉的肝脏、脾脏、肺脏等组织病料的研磨上清液中分离出1株病毒。分离株经Vero细胞传至第4代出现典型的细胞病变效应(CPE),经毒力测定、血清学、RT-PCR检测及测序、回归动物试验证明为犬瘟热病毒(Canine distemper virus,CDV),命名为CDV诸城分离株(CDV-ZC)。采用RT-PCR方法分段克隆分离株的全基因序列并测序,测序成功的各序列依次拼接得到全基因序列并进行序列比对。结果表明,CDV-ZC株全基因(KJ994343)与标准美洲型犬瘟热强毒株A75/17核苷酸同源性高达96.5%,而与疫苗株Onderstepoort、CDV3等亲缘关系较远,同源性为91.6%~92.0%。血凝素(H)基因序列分析表明,CDV-ZC株与国内野毒株LN(13)2、GP株等以及日本野毒株UENO、HAMA等共同归属于Asia-1型,在H蛋白信号淋巴细胞激活因子(SLAM)受体结合区即542~544位增加了1个潜在N-连接糖基化位点(N-X-S/T)。致病性强毒株CDV-ZC的成功分离及全基因序列测定加深了我们对当前中国CDV流行株遗传变异情况的了解,为CD的有效预防、诊断及控制提供理论依据。  相似文献   

Is the use of formulae a reliable way to predict the accuracy of genomic selection?     

S. Brard  A. Ricard 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(3):207-217

We studied four formulae used to predict the accuracy of genomic selection prior to genotyping. The objectives of our study were to investigate the impact of the parameters of each formula on the values of accuracy calculated using these formulae, and to check whether the accuracies reported in the literature are in agreement with the formulae. First, we computed the marginal distribution of accuracy (by integration) for each parameter of all four formulae: heritability h², reference population size T, number of markers M and number of effective segments in the genome M_e. Then, we collected 145 accuracies and corresponding parameters reported in 13 publications on genomic selection (mainly in dairy cattle), and performed analysis of variance to test the differences between observed and predicted accuracy with effects of formulae and parameters. The variation of accuracy for different values of each parameter indicated that two parameters, T and M_e, had a significant impact and that considerable differences existed between the formulae (mean accuracies differed by up to 0.20 point). The results of our meta‐analysis showed a big formula effect on the accuracies predicted using each formula, and also a significant effect of the value obtained for M_e calculated from N_e (effective population size). Each formula can therefore be demonstrated to be optimal depending on the assumption used for M_e. In conclusion, no rules can be applied to predict the reliability of genomic selection using these formulae.  相似文献   

The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs          下载免费PDF全文

T. Aasmundstad  I. Andersen‐Ranberg  Ø. Nordbø  T. Meuwissen  O. Vangen  E. Grindflek 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(5):386-391

The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76 683 animals, of which 4933 animals are genotyped. The heritabilities for front leg conformation, stayability, osteochondrosis and arched back, estimated using the traditional pedigree, were found to be between 0.12 and 0.29. When using the combined genomic and pedigree relationship matrix, the heritabilities were between 0.14 and 0.36. The results show that the combined relationship matrix can be used for the estimation of (co)variance components, and that the predictive ability of the model in this study marginally increases with the inclusion of genomic information.  相似文献   

Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study          下载免费PDF全文

B.O. Fragomeni  D.A.L. Lourenco  S. Tsuruta  Y. Masuda  I. Aguilar  I. Misztal 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(5):340-345

The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix ( G ) is replaced by an approximation of G ^?1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G ^?1 and the approximated G ^?1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G ^?1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.  相似文献   

Genomic best linear unbiased prediction method reflecting the degree of linkage disequilibrium          下载免费PDF全文

M. Nishio  M. Satoh 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(5):357-365

The degree of linkage disequilibrium (LD) between markers differs depending on the location of the genome; this difference biases genetic evaluation by genomic best linear unbiased prediction (GBLUP). To correct this bias, we used three GBLUP methods reflecting the degree of LD (GBLUP‐LD). In the three GBLUP‐LD methods, genomic relationship matrices were conducted from single nucleotide polymorphism markers weighted according to local LD levels. The predictive abilities of GBLUP‐LD were investigated by estimating variance components and assessing the accuracies of estimated breeding values using simulation data. When quantitative trait loci (QTL) were located at weak LD regions, the predictive abilities of the three GBLUP‐LD methods were superior to those of GBLUP and Bayesian lasso except when the number of QTL was small. In particular, the superiority of GBLUP‐LD increased with decreasing trait heritability. The rates of QTL at weak LD regions would increase when selection by GBLUP continues; this consequently decreases the predictive ability of GBLUP. Thus, the GBLUP‐LD could be applicable for populations selected by GBLUP for a long time. However, if QTL were located at strong LD regions, the accuracies of three GBLUP‐LD methods were lower than GBLUP and Bayesian lasso.  相似文献   

Impact of relationships between test and training animals and among training animals on reliability of genomic prediction          下载免费PDF全文

X. Wu  M.S. Lund  D. Sun  Q. Zhang  G. Su 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(5):366-375

One of the factors affecting the reliability of genomic prediction is the relationship among the animals of interest. This study investigated the reliability of genomic prediction in various scenarios with regard to the relationship between test and training animals, and among animals within the training data set. Different training data sets were generated from EuroGenomics data and a group of Nordic Holstein bulls (born in 2005 and afterwards) as a common test data set. Genomic breeding values were predicted using a genomic best linear unbiased prediction model and a Bayesian mixture model. The results showed that a closer relationship between test and training animals led to a higher reliability of genomic predictions for the test animals, while a closer relationship among training animals resulted in a lower reliability. In addition, the Bayesian mixture model in general led to a slightly higher reliability of genomic prediction, especially for the scenario of distant relationships between training and test animals. Therefore, to prevent a decrease in reliability, constant updates of the training population with animals from more recent generations are required. Moreover, a training population consisting of less‐related animals is favourable for reliability of genomic prediction.  相似文献   

Estimates of genetic variance and variance of predicted genetic merits using pedigree or genomic relationship matrices in six Brown Swiss cattle populations for different traits          下载免费PDF全文

A. Loberg  J. W. Dürr  W.F. Fikse  H. Jorjani  L. Crooks 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(5):376-385

The amount of variance captured in genetic estimations may depend on whether a pedigree‐based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree‐based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population‐trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree‐based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree‐based relationship matrix. The ratio of the genomic to pedigree‐based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress.  相似文献   

呕吐毒素降解菌A4的分离及降解特性研究     

于阳光  胡俊强  王刚  高红侠  邱涵  张宇航  刘馨  史建荣  徐剑宏 《农业环境科学学报》2022,41(12):2648-2659

为了给呕吐毒素（DON）污染的谷物和饲料脱毒提供菌株资源,本研究从赤霉病污染区域的小麦田采集土壤样品,通过富集培养,分离筛选到一株DON降解菌,通过形态、16S rDNA、gyrB基因序列对降解菌进行菌种鉴定,液相色谱串联质谱和核磁共振鉴定降解产物,明确其降解途径和解毒机制,通过菌株生长特性、降解特性和基因组间差异分析比较DON降解菌A4、A8和A16之间的差异。结果表明：分离筛选获得DON降解菌A4,该菌能在10 h内降解9.7 μg·mLP＞-1P＞ DON,降解率高达97%。经鉴定,A4为德沃斯氏菌（Devosia sp.）。A4通过降解DON为3-keto-DON进行脱毒。A4的最适生长温度为35℃,最适NaCl浓度为2%,其耐热性和耐盐性优于菌株A8和A16。A4的最适降解温度为35℃、最适降解pH为8.0,其降解速率高于菌株A8和A16。通过平均核苷酸相似度（ANI）分析,A4与A8和A16之间的ANI分别为81.54%和77.87%,均低于95%,因此属于不同种的菌株。研究表明,筛选得到的新型DON脱毒菌株A4具有良好的抗逆性,为DON的污染控制提供了新的降解菌资源。  相似文献