Prediction of response to marker-assisted and genomic selection using selection index theory

Selection index methods can be used for deterministic assessment of the potential benefit of including marker information in genetic improvement programmes using marker-assisted selection (MAS). By specifying estimates of breeding values derived from marker information (M-EBV) as a correlated trait with heritability equal to 1, it was demonstrated that marker information can be incorporated in standard software for selection index predictions of response and rates of inbreeding, which requires specifying phenotypic traits and their genetic parameters. Path coefficient methods were used to derive genetic and phenotypic correlations between M-EBV and the phenotypic data. Methods were extended to multi-trait selection and to the case when M-EBV are based on high-density marker genotype data, as in genomic selection. Methods were applied to several example scenarios, which confirmed previous results that MAS substantially increases response to selection but also demonstrated that MAS can result in substantial reductions in the rates of inbreeding. Although further validation by stochastic simulation is required, the developed methodology provides an easy means of deterministically evaluating the potential benefits of MAS and to optimize selection strategies with availability of marker data.     

Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters

Accuracy of prediction of estimated breeding values based on genome-wide markers (GEBV) and selection based on GEBV as compared with traditional Best Linear Unbiased Prediction (BLUP) was examined for a number of alternatives, including low heritability, number of generations of training, marker density, initial distributions, and effective population size (Ne). Results show that the more the generations of data in which both genotypes and phenotypes were collected, termed training generations (TG), the better the accuracy and persistency of accuracy based on GEBV. GEBV excelled for traits of low heritability regardless of initial equilibrium conditions, as opposed to traditional marker-assisted selection, which is not useful for traits of low heritability. Effective population size is critical for populations starting in Hardy-Weinberg equilibrium but not for populations started from mutation-drift equilibrium. In comparison with traditional BLUP, GEBV can exceed the accuracy of BLUP provided enough TG are included. Unfortunately selection rapidly reduces the accuracy of GEBV. In all cases examined, classic BLUP selection exceeds what was possible for GEBV selection. Even still, GEBV could have an advantage over traditional BLUP in cases such as sex-limited traits, traits that are expensive to measure, or can only be measured on relatives. A combined approach, utilizing a mixed model with a second random effect to account for quantitative trait loci in linkage equilibrium (the polygenic effect) was suggested as a way to capitalize on both methodologies.     

苇状羊茅与多年生黑麦草内生真菌菌丝基因组DNA提取的优化及PCR初步检测

感染内生真菌的禾草在牧草和草坪业上具有重要的生态和经济意义，家畜采食感染Neotyphodium coenophialum和N.lolii的苇状羊茅和多年生黑麦草会发生中毒。本研究收集天津口岸1998年以来进境的部分苇状羊茅和多年生黑麦草种子，对经镜检确认带有内生真菌的种子进行分离培养，对疑似菌株的菌丝用改进的Moiler等方法进行基因组DNA抽提，测定浓度及纯度，对照原方法，DNA的纯度有较大提高，浓度略有上升。Tubulin2基因的引物IS1-IS3扩增结果显示为单一的条带，结合形态学和序列比对，分离培养得到的菌株可以基本确定为N．coenophialum和N。lolii。根据Genbank中N.coenophialum和N.lolii的NC25基因序列设计出引物F1-R1，扩增得到能区分开N.coenophialum和N．lolii的单一条带（相差160bp），建立了N．coenophialum和N．lolii的PCR检测方法，结果准确可靠。     

猪繁殖与呼吸障碍综合征病毒基因芯片检测技术的建立与优化

根据猪繁殖与呼吸综合征病毒（PRRSV）的核衣壳蛋白编码基因序列设计了一对特异性引物P1／P2。扩增出大小为294bp的目的片段；再针对这个基因片段。设计合成4条寡核苷酸探针。其中反向引物的5’端用荧光素Cy3标记。以荧光标记不对称PCR技术为基础。通过将单链PCR产物与芯片杂交实现对PRRSV的检测。建立PRRSV的基因芯片检测方法。利用该方法对39份猪组织样品进行检测。与RT—PCR检测方法相比。本方法具有良好的特异性和敏感性。试验结果表明用该方法快速检测病料组织中PRRSV是可行的，对该病的进行快速诊断和分子流行病学调查具有重要意义。     

棕榈藤基因组DNA提取及RAPD反应条件探索

棕榈藤(rattan)是棕榈科(Palmae Juss．)藤本植物，属棕榈科省藤亚科(Calamoideae)省藤族(Calameae)植物，包括13属600余种，主要分布于热带地区。棕榈藤是热带森林宝库中的多用途植物资源，具有很高的经济价值和开发前景，是仅次于木材和竹材的重要林产品，其中黄藤(Daemonorops margaritae(Hance)Seccari)和单叶省藤(Calamus simplicifolius Wei)是我国大面积栽培的2个重要藤种。     

利用简化的SDS法提取杨树基因组DNA

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。     

漾濞核桃叶片基因组DNA的两种提取方法效果比较

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。     

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

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.     

The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs

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.