大型基因组亲缘矩阵求逆算法的优化研究

基因组选择常用的评估方法GBLUP和ssGBLUP都涉及到基因组亲缘矩阵的求逆,而大规模矩阵求逆运算非常耗时。本研究以提高大型基因组亲缘矩阵求逆运算的效率为目的。本研究通过真实数据和模拟数据构建基因组亲缘矩阵,引入Intel MKL矩阵函数,以减少迭代次数(方法1)和重复分块(方法2)两种方式改良分块迭代求逆算法,编程实现算法并在台式电脑和服务器上测试计算时间。结果表明,利用方法1计算4 000×4 000的基因组亲缘矩阵逆矩阵时,与MKL库函数的加速比为0.898。而16 000×16 000矩阵的计算速度为MKL库函数的1.006倍。利用方法2计算4 000×4 000矩阵的运算速度是MKL库函数的1.084倍;而在更大型的128 000×128 000基因组亲缘矩阵求逆运算时,该方法与MKL直接求逆函数的加速比为1.805倍。相比于MKL直接求逆函数,改进后的两种方法在效率上有一定程度的提升。     

可逆矩阵及求逆矩阵的方法

我们学习了逆矩阵并且知道了用伴随矩阵和初等变换法可以求一个可逆阵的逆矩阵。本文将在此基础上,介绍用分块求逆法、二阶矩阵的公式求逆法、利用解线性方程组等来求一个可逆矩阵的逆矩阵。     

求逆矩阵的几种方法

矩阵是线性代数中的主要研究对象与研究工具,而逆矩阵是矩阵理论中的一个非常重要的概念,如何判断一个矩阵是否可逆以及如何求矩阵的逆矩阵就显得非常重要。求逆矩阵方法很多,本文归纳了如下几种:定义法;利用伴随矩阵求逆法;利用伴随矩阵求逆法的推论求逆;利用逆矩阵的性质求逆法;利用矩阵的初等变换求逆;分块对角阵求逆法。     

Gauss-Seidel迭代法求解线性方程组的并行化研究

Gauss-Seidel迭代法在工程计算中具有广泛应用。高维矩阵对线性方程组的求解效率提出了新的要求。本文提出了两种模式下的Gauss-Seidel并行计算方法 ,并对比了在不同矩阵维数下的加速效率,得到了具有较高加速比的并行迭代方法 。     

二倍体栽培紫花苜蓿的起源、繁殖稳定性及其种子和饲草产量

<正> 二倍体栽培紫花苜蓿(Medicago Sativa L.)是应用单倍体育种和选种的方法,在10年间从4倍体栽培紫花苜蓿育成的。培育2倍体紫花苜蓿的目的是为了作种子繁殖及染色体数目稳定性的研究。用4×—2×的杂交方法获得2×单倍体植株,这种单倍体植株虽然相对不育,但在初期可用作母本与2×黄花苜蓿(M.falcata)进行杂交。由此而获得的F_1代杂种是能育的,可作为父本与2×单倍体植株回交。在回交中,各代2倍体栽     

更乐霉素毒性研究(Ⅲ)──鸡毒性试验

本品对伊莎母鸡急性毒性试验,口服、肌注LD50分别为12800、390．84mg／kg．b．w为其治疗量的128、130倍;1日龄伊莎公鸡皮下注射360mg／kg．b．w无死亡;18日龄伊莎公鸡饮水中分别添加GRC0．5、1．5、2．5g/L组,连续饮用86d无毒性反应;16日龄明星肉鸡饲料中分别添加GRC50×10-6、300×10－6、600×10-6组,连续喂饲36d无毒性反应;伊莎蛋鸡于产蛋期饲料中分别添加GRC50×10-6、300×10－6、600×10－6组,连续喂养4个月无毒性反应,不影响孵化率,还可提高产蛋率。取肉、蛋通过高效液相色谱法测定低、中剂量组无残留毒,600×10－6组残留量低于0．1×10－6。     

西门塔尔牛、和牛与荷斯坦牛杂种优势预测及实际杂交效果分析

旨在利用覆盖全基因组和性状的特异性SNPs标记预测和牛、西门塔尔牛与荷斯坦牛杂种优势,为牛杂种优势利用和选种选配提供参考依据。本研究分别利用牛Illumina Bovine HD 770 K和GGP Bovine 100 K芯片对464头和牛、1 222头西门塔尔牛和43头荷斯坦牛3个亲本群体进行基因型分型,并通过牛QTLs数据库筛选与目的性状对应的QTLs,对比牛参考基因组映射得到与初生重、周岁重、胴体重性状相关的特异性SNPs;然后构建覆盖全基因组和性状特异性SNPs两种标记状态同源矩阵,通过计算杂交组合亲本间的遗传距离来预测品种间杂种优势,并利用配合力分析验证较优组合的实际杂交效果。结果表明,基于全基因组和性状特异性SNPs计算的各杂交组合遗传距离差异不显著。在全基因组水平上,西门塔尔牛♂×荷斯坦牛♀（S×H）与和牛♂×荷斯坦牛♀（W×H）亲本间杂交组合遗传距离分别为0.346 1和0.338 9;在初生重、周岁重和胴体重性状上,S×H亲本间遗传距离分别为0.343 1、0.348 7和0.336 7,而W×H遗传距离分别为0.337 6、0.340 7和0.329 2;两种SNPs标记计算的遗传距离均为S×H较大,W×H次之。因此,在初生重、周岁重、胴体重性状上,S×H为较优杂交组合。通过分析德系西门塔尔牛♂×荷斯坦牛♀实际杂交群体的配合力,发现10个父系在初生重性状上一般配合力和特殊配合力均为正效应,最高效应值分别达到3.760 9和8.931 2。西门塔尔牛与荷斯坦牛杂交可在初生重、周岁重和胴体重获得较高的杂种优势。     

鸡胚母源抗体对新城疫Lasota毒株繁殖的干扰及克服方法

鸡胚中过高的母源抗体会干扰Lasota毒株的繁殖。本试验结果证明,当母源抗体＞26时种毒（EID50 108.5,HA 210）稀释1×103-5×103倍;母源抗体平均24左右时,种毒稀释5×103-1×104倍;母源抗体降至23左右时,种毒稀释倍数1×104-1×105为宜。按以上方法接种鸡胚,所收毒液效价最高。     

饲养土鸡效益分析

以饲养500只鸡为例,以河南省济源市当地的市场价格和养殖水平为基准,笔者给广大养殖户计算一下饲养土鸡的效益。 从饲养成本上看,饲养土鸡的成本主要包括鸡苗成本、饲料成本及防疫成本。按1只雌鸡苗2元计算,500只鸡苗的成本是1 000元。饲料费用又分为4部分: 育雏前期(0～26日龄)需全价颗粒料160公斤,按饲料价格1.85元/公斤计算,饲料费用为1.85×160=296(元)。 脱温后育雏30天(27～56日龄)饲喂自配全价料,按每只每天饲喂0.06公斤饲料,饲料价格为1.2元/公斤计算,饲料费用为1.2×30×0.06×500=1 080(元)。 育成期94天(57～150日龄…     

杂种藏黄公牛与牦牛杂交的F_1产乳性能测定报告

本文揭示了杂种藏黄公牛（黑×黄）与牦牛杂交的Ｆ１代母犏牛第一胎次的产乳性能,１８３天产奶量６５９３６ｋｇ±４１３４,比对照１组（牦×牦）提高１６５倍;比对照２组（土黄公牛×牦牛）提高０７２倍;乳脂总量３６０７ｋｇ,比对照１组、２组分别提高１２倍、０２倍,建议在川西北牧区牦牛业生产中推广这种种间杂交改良方法。     

Genomic prediction of growth traits for pigs in the presence of genotype by environment interactions using single-step genomic reaction norm model

Economically important traits are usually complex traits influenced by genes, environment and genotype-by-environment (G × E) interactions. Ignoring G × E interaction could lead to bias in the estimation of breeding values and selection decisions. A total of 1,778 pigs were genotyped using the PorcineSNP80 BeadChip. The existence of G × E interactions was investigated using a single-step reaction norm model for growth traits of days to 100 kg (AGE) and backfat thickness adjusted to 100 kg (BFT), based on a pedigree-based relationship matrix (A) or a genomic–pedigree joint relationship matrix (H). In the reaction norm model, the herd-year-season effect was measured as the environmental variable (EV). Our results showed no G × E interactions for AGE, but for BFT. For both AGE and BFT, the genomic reaction norm model (H) produced more accurate predictions than the conventional reaction norm model (A). For BFT, the accuracies were greater based on the reaction norm model than those based on the reduced model without exploiting G × E interaction, with EV ranging from 0.5 to 1, and accuracy increasing by 3.9% and 4.6% in the reaction norm model based on A and H matrices, respectively, while reaction norm model yielded approximately 8.4% and 7.9% lower accuracy for EVs ranging from 0 to 0.4, based on A and H matrices, respectively. In addition, for BFT, the highest accuracy was obtained in the BJLM6 farm for realizing directional selection. This study will help to apply G × E interactions to practical genomic selection.     

A joint analysis to identify loci underlying variation in nematode resistance in three European sheep populations

Gastrointestinal nematode infections are one of the main health/economic issues in sheep industries, worldwide. Indicator traits for resistance such as faecal egg count (FEC) are commonly used in genomic studies; however, published results are inconsistent among breeds. Meta (or joint)‐analysis is a tool for aggregating information from multiple independent studies. The aim of this study was to identify loci underlying variation in FEC, as an indicator of nematode resistance, in a joint analysis using data from three populations (Scottish Blackface, Sarda × Lacaune and Martinik Black‐Belly × Romane), genotyped with the ovine 50k SNP chip. The trait analysed was the average animal effect for Strongyles and Nematodirus FEC data. Analyses were performed with regional heritability mapping (RHM), fitting polygenic effects with either the whole genomic relationship matrix or matrices excluding the chromosome being interrogated. Across‐population genomic covariances were set to zero. After quality control, 4123 animals and 38 991 SNPs were available for the analysis. RHM identified genome‐wide significant regions on OAR4, 12, 14, 19 and 20, with the latter being the most significant. The OAR20 region is close to the major histocompatibility complex, which has often been proposed as a functional candidate for nematode resistance. This region was significant only in the Sarda × Lacaune population. Several other regions, on OAR1, 3, 4, 5, 7, 12, 19, 20 and 24, were significant at the suggestive level.     

植物杀虫剂印楝素对家蚕的毒性测定及解毒方法

测定了植物杀虫剂印楝素(azadirachtin)对家蚕的食下、熏蒸、内吸毒性及安全间隔时间:印楝素对3龄起蚕的致死中浓度(LC50)为202.67×10-6mg/L,致死中量(LD50)为12.56×10-10mg/头,家蚕对印楝素极敏感,但中毒后至死亡的时间较长,一般需3~5d;印楝素在田间常规使用浓度下对家蚕基本无熏蒸毒性;0.5%印楝素乳油2000倍稀释液根灌、喷叶处理,通过桑根或桑叶内吸并在树体内传导的作用极小,即未喷洒到药液的桑叶对家蚕相对安全;印楝素对家蚕的安全间隔时间很长,饲喂0.5%印楝素乳油800、1200、1800和2700倍稀释液处理后的桑叶,间隔30d对3龄蚕的死亡率均在50%以上。蚕用消毒剂消力威(三氯异氰尿酸、碳酸氢钠粉)1000倍和500倍溶液浸渍受印楝素污染的桑叶30min有良好的解毒作用。     

Efficient computation of the genomic relationship matrix and other matrices used in single-step evaluation

Genomic evaluations can be calculated using a unified procedure that combines phenotypic, pedigree and genomic information. Implementation of such a procedure requires the inverse of the relationship matrix based on pedigree and genomic relationships. The objective of this study was to investigate efficient computing options to create relationship matrices based on genomic markers and pedigree information as well as their inverses. SNP maker information was simulated for a panel of 40 K SNPs, with the number of genotyped animals up to 30 000. Matrix multiplication in the computation of the genomic relationship was by a simple 'do' loop, by two optimized versions of the loop, and by a specific matrix multiplication subroutine. Inversion was by a generalized inverse algorithm and by a LAPACK subroutine. With the most efficient choices and parallel processing, creation of matrices for 30 000 animals would take a few hours. Matrices required to implement a unified approach can be computed efficiently. Optimizations can be either by modifications of existing code or by the use of efficient automatic optimizations provided by open source or third-party libraries.     

Evaluation of the utility of diagonal elements of the genomic relationship matrix as a diagnostic tool to detect mislabelled genotyped animals in a broiler chicken population

This study explored distributions of diagonal elements of genomic relationship matrix (G), evaluated the utility of G as a diagnostic tool to detect mislabelled animals in a genomic dataset and evaluated the effect of mislabelled animals on the accuracy of genomic evaluation. Populations of 10 000 animals were simulated with 60 000 SNP varying in allele frequency at each locus between 0.02 and 0.98. Diagonal elements of G were distributed with a single peak (mean = 1.00 ± 0.03) and ranged from 0.84 through 1.36. Mixed populations were also simulated: 7 000 animals with frequencies of second alleles ranging from 0.02 through 0.98 were combined with 1750 or 7000 animals with frequencies of second alleles ranging from 0.0 through 1.0. The resulting distributions of diagonal elements of G were bimodal. Body weight at 6 weeks was provided by Cobb-Vantress for broiler chickens, of which 3285 were genotyped for 57 636 SNP. Analysis used a combined genomic and pedigree relationship matrix; G was scaled using current allele frequencies. The distribution of diagonal elements was multimodal and ranged from 0.54 to 3.23. Animals with diagonal elements >1.5 were identified as coming from another chicken line or as having low call rates. Removal of mislabelled animals increased accuracy by 0.01. For the studied type of population, diagonal elements of G may be a useful tool to help identify mislabelled animals or secondary populations.     

几种农药对桑椹小粒性菌核病的防治效果试验

桑椹菌核病是果用桑树的重要病害,为高效、安全控制该病对桑果生产的危害,进行了大田农药防治筛选试验。结果表明,70%甲基托布津可湿性粉剂500倍液、50%多菌灵-硫磺粉剂500倍液和1 000倍液对桑椹小粒性菌核病具有较好的防治效果,且对桑叶和桑椹无明显药害;70%甲基托布津粉剂1 000倍液、25%吡唑醚菌酯乳油1 500倍和3 000倍液以及40%嘧霉胺粉剂1 000倍液也有一定的防治效果。     

Sampling efficiency for species composition assessments using the wheel-point method in a semi-arid savanna

A pilot survey to determine the sampling efficiency of the wheel-point method, using the nearest plant method, to assess species composition (using replicate similarity related to sampling intensity, and total sampling time) was conducted on three plot sizes (20 × 20m, 30 × 30m, 40 × 40m) at two sites in a semi-arid savanna. Total sampling time included the time to demarcate a plot. A 40 × 40m plot had the highest precision and repeatability (number of point observations required to achieve a stated asymptotic value), and was followed by a 20 × 20m plot. These relationships were consistent across sites. A 40 × 40m plot recorded the highest sampling times due to the time required to demarcate a plot. A 20 × 20m plot was the most efficient. A model to assist in making decisions regarding a suitable plot and sample size, and for planning and budgeting of vegetation monitoring programs was developed. Future surveys should include a Monte-Carlo data simulation as an adjunct to data collection.     

牛瑟氏泰勒虫不同靶基因PCR检测方法的比较

为筛选出检测牛瑟氏泰勒虫更为特异、敏感的PCR方法,本试验以牛瑟氏泰勒虫p23和p33基因、HSP70基因及18S rRNA基因为靶基因进行PCR检测,并从其敏感性、特异性和临床样本检出率等方面进行了比较。结果显示,4种靶基因引物对牛瑟氏泰勒虫的检测均有较高的特异性,当牛瑟氏泰勒虫基因组DNA浓度为127 ng/μL时,p23、p33、HSP70及18S rRNA4种基因的最小检测量分别为1×105、1×105、1×104和1×106copies/μL;检测临床样本阳性检出率分别为30.19%(16/53)、39.62%(21/53)、47.17%(25/53)和54.72%(29/53)。表明以18SrRNA基因为靶基因的PCR方法从敏感性和临床检出率上明显优于其他3种基因。     

Effects of short period frequent milking on milk yield and udder health in Turkish Saanen goats

The major purpose of this study was to investigate whether increasing milking frequency for a short period (21 days) increases milk yield and milk components and improves udder health throughout lactation in Turkish Saanen goats. Two groups were formed (control, n = 14, treatment, n = 14); balanced by parity, bodyweight and birth type to make them homogenous. Feeding and management practices were the same for both groups. The treatment group was milked four times a day (4×) for 21 days after weaning whereas the control group was milked twice a day (2×). All the animals were milked twice daily thereafter. The pyronin methyl green stain method was used to estimate the somatic cell count (SCC), which is an indication of udder health. This method provided a count that excluded RNA and background noise while including cells with DNA. Repeated measures analyses indicated that overall differences between the 2× and 4× groups were significant for the morning, evening and total test day milk yields, in that values for the 4× group were increased 14.7, 8.8 and 12.1%, respectively. Differences between the groups for SCC were not significant. The results of this study indicate that increasing milking frequency to 4×, even for a short time (21 days), increases overall milk yield throughout lactation in dairy goats.