快速型黄羽肉鸡饲料利用效率性状的基因组选择研究     

李森  杜永旺  文杰  黄超  陈智武  赵桂苹  郑麦青 《畜牧兽医学报》2021,52(8):2151-2161

旨在探究快速型黄羽肉鸡饲料利用效率性状的遗传参数,评估不同方法所得估计育种值的准确性。本研究以自主培育的快速型黄羽肉鸡E系1 923个个体（其中公鸡1 199只,母鸡724只）为研究素材,采用"京芯一号"鸡55K SNP芯片进行基因分型。分别利用传统最佳线性无偏预测（BLUP）、基因组最佳线性无偏预测（GBLUP）和一步法（SSGBLUP）3种方法,基于加性效应模型进行遗传参数估计,通过10倍交叉验证比较3种方法所得估计育种值的准确性。研究性状包括4个生长性状和4个饲料利用效率性状：42日龄体重（BW42D）、56日龄体重（BW56D）、日均增重（ADG）、日均采食量（ADFI）和饲料转化率（FCR）、剩余采食量（RFI）、剩余增长体重（RG）、剩余采食和增长体重（RIG）。结果显示,4个饲料利用效率性状均为低遗传力（0.08~0.20）,其他生长性状为中等偏低遗传力（0.11~0.35）;4个饲料利用效率性状间均为高度遗传相关,RFI、RIG与ADFI间为中度遗传相关,RFI与ADG间无显著相关性,RIG与ADG间为低度遗传相关。本研究在获得SSGBLUP方法的最佳基因型和系谱矩阵权重比基础上,比较8个性状的估计育种值准确性,SSGBLUP方法获得的准确性分别比传统BLUP和GBLUP方法提高3.85%~14.43%和5.21%~17.89%。综上,以RIG为选择指标能够在降低日均采食量的同时保持日均增重,比RFI更适合快速型黄羽肉鸡的选育目标;采用最佳权重比进行SSGBLUP分析,对目标性状估计育种值的预测性能最优,建议作为快速型黄羽肉鸡基因组选择方法。  相似文献   

一种适用于单胎动物多品种选择的基因组关系矩阵     

张洪志  任端阳  安丽霞  乔利英  刘文忠 《畜牧兽医学报》2021,52(11):3108-3117

旨在提出一种新型基因组关系矩阵并验证其在多品种联合群体中的模拟应用效果。本研究利用QMsim软件模拟牛的表型数据和基因型数据;利用Gmatrix软件构建常规G阵;利用R语言构建新型G阵,新型G阵在常规G阵的基础上,将多品种联合群体的非哈代-温伯格平衡位点考虑在内;利用DMU软件使用“一步”法模型计算基因组估计育种值（estimated genomic breeding value,GEBV）;比较不同情况下使用两种G阵的GEBV预测准确性。结果表明,在不同遗传力及QTL数下,不对新型G阵使用A₂₂阵加权就能达到常规G阵使用A₂₂阵加权时的GEBV预测准确性。在系谱部分缺失时,新型G阵不加权较常规G阵加权时GEBV预测准确性高。证明,在系谱有部分缺失时,新型G阵对多品种GEBV的预测有一定优势。  相似文献   

Ace and ace-like genes of invasive redlegged earth mite: copy number variation,target-site mutations,and their associations with organophosphate insensitivity     

Joshua A. Thia  Paul A. Umina  Ary A. Hoffmann 《Pest management science》2023,79(11):4219-4230

Background

Invasive Australian populations of redlegged earth mite, Halotydeus destructor (Tucker), are evolving increasing organophosphate resistance. In addition to the canonical ace gene, the target gene of organophosphates, the H. destructor genome contains many radiated ace-like genes that vary in copy number and amino acid sequence. In this work, we characterise copy number and target-site mutation variation at the canonical ace and ace-like genes and test for potential associations with organophosphate insensitivity. This was achieved through comparisons of whole-genome pool-seq data from alive and dead mites following organophosphate exposure.

Results

A combination of increased copy number and target-site mutations at the canonical ace was associated with organophosphate insensitivity in H. destructor. Resistant populations were segregating for G119S, A201S, F331Y at the canonical ace. A subset of populations also had copy numbers of canonical ace > 2, which potentially helps overexpress proteins carrying these target-site mutations. Haplotypes possessing different copy numbers and target-site mutations of the canonical ace gene may be under selection across H. destructor populations. We also detected some evidence that increases in copy number of radiated ace-like genes are associated with organophosphate insensitivity, which might suggest potential roles in sequestration or breakdown of organophosphates.

Conclusion

Different combinations of target-site mutations and (or) copy number variation in the canonical ace and ace-like genes may provide non-convergent ways for H. destructor to respond to organophosphate selection. However, these changes may only play a partial role in organophosphate insensitivity, which appears to have a polygenic architecture. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.  相似文献   

Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm     

Fernando Brito Lopes  Fernando Baldi  Ludmilla Costa Brunes  Marcos Fernando Oliveira e Costa  Eduardo da Costa Eifert  Guilherme Jordão Magalhães Rosa  Raysildo Barbosa Lobo  Cláudio Ulhoa Magnabosco 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2023,140(1):1-12

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner–Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.  相似文献   

牛基因组DNA两种提取方法的比较研究   总被引：3，自引：0，他引：3  

程金华  朱化彬  王栋  郝海生  杨波 《畜牧兽医学报》2006,37(9):874-877

研究哺乳动物基因组DNA的水煮抽提法，并将传统的酚仿抽提法和水煮法进行比较，水煮法即通过对细胞的煮沸和冷却，使细胞破裂、蛋白变性，从而获得用于PCR扩增的模板DNA的方法。通过电泳分析和PCR扩增检测了所提取基因组DNA的完整性、可行性。检测时采用3对引物对2种方法提取的DNA进行了PCR扩增，同时对冷冻保存的基因组DNA也进行了扩增检测。结果表明：水煮法提取基因组DNA是一种快速、简便、经济、高效的方法。  相似文献   

用改进的酚-氯仿法提取鱼类基因组DNA效果的分析     

马洪雨  郭金峰  岳永生 《家畜生态》2006,(2)

提取鱼类基因组DNA的研究报道并不多见,效果也各有差异。本文以泰山螭霖鱼、东平湖鲤鱼、东平湖鲫鱼为材料,采用改进的酚-氯仿法提取基因组DNA,并进行了紫外分光光度、琼脂糖凝胶电泳、微卫星PCR扩增等方法的鉴定。结果表明,本方法提取的基因组DNA浓度在0.9μg/μL~3.25μg/μL之间,A260/A280比值在1.79~1.87之间,电泳条带整齐明亮,适合微卫星PCR扩增,且整个操作过程使用试剂较少,简单易行。  相似文献   

Prediction of response to marker-assisted and genomic selection using selection index theory   总被引：1，自引：0，他引：1  

J. C. M. Dekkers 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2007,124(6):331-341

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.  相似文献   

Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters   总被引：2，自引：1，他引：2  

W.M. Muir 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2007,124(6):342-355

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.  相似文献   

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     

廖芳  刘跃庭  崔铁军  黄国明  罗家凤  尹旭芳 《植物检疫》2006,20(5):265-268

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。  相似文献   

猪圆环病毒复制与转录模式研究进展     

琚春梅 《动物医学进展》2007,28(4):68-72

猪圆环病毒(PCV)是一种单股、环状DNA病毒,有两种血清型,其中PCV-2是引起断奶仔猪多系统衰竭综合征的重要病原,给世界养猪业造成了巨大的经济损失.文章主要从PCV-1和PCV-2的基因组结构、复制起始区的结构与功能、复制相关蛋白的结构与功能、转录图谱、各转录物的剪接方式及主要转录物的转录效率等方面进行了综述,同时也对二者的复制与转录模式的异同点进行了比较.这些结果对PCV-1和PCV-2毒力差异的分子机制研究具有一定的借鉴意义,同时可为抗PCV药物的研发提供一定的理论依据.  相似文献