Comparison of four direct algorithms for computing inbreeding coefficients

One widely used measure in genetic analyses of livestock species is the inbreeding coefficient. Computation costs of inbreeding coefficients are of importance for large populations. Very recently, a ‘direct’ method for computing inbreeding coefficients was modified using a relatively efficient method to construct lists of ancestors in which the integrity of chronological order within each ancestral path is kept. Using simulated data, the computational efficiency of the recently modified algorithm was investigated by comparing it with three other algorithms – the original direct algorithm, its previously modified algorithm and another direct algorithm. The recently modified algorithm became considerably faster than the original algorithm and its previous modification when the number of generations increased, and it was fast relative to the other direct algorithm when the average number of generations and family size were not large. When only animals born in the most recent year were evaluated with the knowledge of inbreeding coefficients for their ancestors, the recently modified algorithm outperformed the other algorithms, indicating its possible advantage in updating situations.     

Emerging and re-emerging viruses of the honey bee (Apis mellifera L.)

Until the late 1980s, specific viral infections of the honey bee were generally considered harmless in all countries. Then, with the worldwide introduction of the ectoparasite mite Varroa destructor, beekeepers encountered increasing difficulties in maintaining their colonies. Epidemiological surveys and laboratory experiments have demonstrated that the newly acquired virulence of several viruses belonging to the family Dicistroviridae (acute bee paralysis virus, Kashmir bee virus and Israeli acute paralysis virus) in Europe and the USA had been observed in relation with V. destructor acting as a disseminator of these viruses between and within bee colonies and as an activator of virus multiplication in the infected individuals: bee larvae and adults. Equal emphasis is given to deformed wing virus (DWV) belonging to the Iflaviridae. Overt outbreaks of DWV infections have been shown to be linked to the ability of V. destructor to act not only as a mechanical vector of DWV but also as a biological vector. Its replication in mites prior to its vectoring into pupae seemed to be necessary and sufficient for the induction of a overt infection in pupae developing in non-viable bees with deformed wings. DWV in V. destructor infested colonies is now considered as one of the key players of the final collapse. Various approaches for combating bee viral diseases are described: they include selection of tolerant bees, RNA interference and prevention of new pathogen introduction. None of these approaches are expected to lead to enhanced bee-health in the short term.     

Networks of inbreeding coefficients in a selected population of rabbits

The correlation between pedigree and genomic-based inbreeding coefficients is usually discussed in the literature. However, some of these correlations could be spurious. Using partial correlations and information theory, it is possible to distinguish a significant association between two variables which is independent from associations with a third variable. The objective of this study is to implement partial correlations and information theory to assess the relationship between different inbreeding coefficients using a selected population of rabbits. Data from pedigree and genomic information from a 200K SNP chip were available. After applying filtering criteria, the data set comprised 437 animals genotyped for 114,604 autosomal SNP. Fifteen pedigree- and genome-based inbreeding coefficients were estimated and used to build a network. Recent inbreeding coefficient based on runs of homozygosity had 9 edges linking it with different inbreeding coefficients. Partial correlations and information theory approach allowed to infer meaningful associations between inbreeding coefficients and highlighted the importance of the recent inbreeding based on runs of homozygosity, but a good proxy of it could be those pedigree-based definitions reflecting recent inbreeding.     

陇东地区不同生境下蜜蜂的种类及其生态分布

通过对陇东地区不同生境下蜜蜂种类的系统调查,共鉴定出该地区的蜜蜂物种有32种,隶属蜜蜂科7属,其中甘肃省新记录4种,甘肃省特有种3种.同时介绍了这些物种的分布区域、活动时期和发生概况,对揭示、保护、利用当地的蜜蜂资源具有积极的指导作用.     

工蜂幼虫,蛹对小鼠T淋巴细胞转化功能的影响

用工蜂幼虫、蛹、蜂王幼虫分别灌喂小鼠１２天后，通过Ｔ淋巴细胞转化试验发现，工蜂幼虫、蛹与蜂王幼虫一样，均可显著提高小鼠的Ｔ淋巴细胞转化功能。结果表明，工蜂幼虫、蛹在提高机体免疫功能方面，与蜂王幼虫有同样的药理作用。     

Performance of pedigree and various forms of marker-derived relationship coefficients in genomic prediction and their correlations

In recent years, with development and validation of different genotyping panels, several methods have been proposed to build efficient similarity matrices among individuals to be used for genomic selection. Consequently, the estimated genetic parameters from such information may deviate from their counterpart using traditional family information. In this study, we used a pedigree-based numerator relationship matrix ( A ) and three types of marker-based relationship matrices () including two identical by descent, that is and and one identical by state, as well as four Gaussian kernel () similarity kernels with different smoothing parameters to predict yet to be observed phenotypes. Also, we used different kinship matrices that are a linear combination of marker-derived IBD or IBS matrices with A, constructed as , where the weight () assigned to each source of information varied over a grid of values. A Bayesian multiple-trait Gaussian model was fitted to estimate the genetic parameters and compare the prediction accuracy in terms of predictive correlation, mean square error and unbiasedness. Results show that the estimated genetic parameters (heritability and correlations) are affected by the source of the information used to create kinship or the weight placed on the sources of genomic and pedigree information. The superiority of GK -based model depends on the smoothing parameters (θ) so that with an optimum θ value, the GK -based model statistically yielded better performance (higher predictive correlation, lowest MSE and unbiased estimates) and more stable correlations and heritability than the model with IBD, IBS or kinship matrices or any of the linear combinations.     

蜂群分蜂行为研究进展

蜜蜂是多雄性真社会性昆虫,分蜂是这个庞大家族繁衍的重要手段,它们通过信息素和蜂舞来传递信息.群内工蜂是由不同亚家庭的全同胞姐妹和半同胞姐妹组成,它们在分蜂过程中扮演着不同的角色[1].它们自我组织如此有序,分工如此高效是十分值得我们深入研究的.     

Estimation of inbreeding depression on female fertility in the Finnish Ayrshire population

Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low‐density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (F_PH), runs of homozygosity (F_ROH) and pedigree (F_PED). Phenotypic records were available for 13,712 animals including non‐return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows. Average F_PED was 0.02, F_ROH 0.06 and F_PH 0.63. A correlation of 0.71 was found between F_PED and F_ROH, 0.66 between F_PED and F_PH and 0.94 between F_ROH and F_PH. Pedigree‐based inbreeding coefficients did not show inbreeding depression in any of the traits. However, when F_ROH or F_PH was used as a covariate, significant inbreeding depression was observed; a 10% increase in F_ROH was associated with 5 days longer IFL0 and IFL1, 2 weeks longer IFL3 and 3 days longer ICF2 compared to non‐inbred cows.     

温皮和水分对洋槐蜂蜜和龙眼蜂蜜屯导车的彩响

通过电导率仪检测温度和水分对洋槐和龙眼蜂蜜电导率的变化情况。结果表明：不同品种蜂蜜的电导率不一样;向蜂蜜里添加水分后,蜂蜜的电导率明显提高,并且随着温度升高而加大,电导率随温度变化符合线性相关。而且在同一温度下,蜂蜜的电导率与水的添加量也成线性相关。     

Estimation of ancestral inbreeding effects on stillbirth,calving ease and birthweight in German Holstein dairy cattle

In this study, the effect of different measurements of ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models were used to estimate the effect of ancestral inbreeding, and the estimated regression coefficient of phenotypic data on different measurements of ancestral inbreeding was used to quantify the effect of ancestral inbreeding. The first model included only one measurement of inbreeding, whereas the second model included the classical inbreeding coefficients and one alternative inbreeding coefficient. The third model included the classical inbreeding coefficients, the interaction between classical inbreeding and ancestral inbreeding, and the classical inbreeding coefficients of the dam. Phenotypic data for this study were collected from February 1998 to December 2008 on three large commercial milk farms. During this time, 36 477 calving events were recorded. All calves were weighed after birth, and 8.08% of the calves died within 48 h after calving. Calving ease was recorded on a scale between 1 and 4 (1 = easy birth, 4 = surgery), and 69.95, 20.91, 8.92 and 0.21% of the calvings were scored with 1, 2, 3 and 4, respectively. The average inbreeding coefficient of inbred animals was 0.03, and average ancestral inbreeding coefficients were 0.08 and 0.01, depending on how ancestral inbreeding was calculated. Approximately 26% of classically non‐inbred animals showed ancestral inbreeding. Correlations between different inbreeding coefficients ranged between 0.46 and 0.99. No significant effect of ancestral inbreeding was found for calving ease, because the number of animals with reasonable high level of ancestral inbreeding was too low. Significant effects of ancestral inbreeding were estimated for birthweight and stillbirth. Unfavourable effects of ancestral inbreeding were observed for birthweight. However, favourable purging effects were estimated for stillbirth, indicating that purging could be partly beneficial for genetic improvement of stillbirth.     

Rates of inbreeding and genetic diversity in Iranian Holstein Cattle

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1 048 572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non‐founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non‐founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co‐ancestry and inbreeding, which would lead to better handling of the effective population size.     

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.     

Role of selection and inbreeding on the incidence of cutaneous malignant melanoma in Sinclair swine

Summary This paper reports the quantitative analysis of the historical database of a herd of Sinclair swine affected by cutaneous malignant melanoma. The herd was under partial and non-systematic selection for melanoma susceptibility (animals having at least one tumour during the first 6 weeks of life). Weighted selection differentials for the number of tumours at birth and the number of tumours at 6 weeks were generally positive and between −0.43 and 4.76 tumours for the number of tumours at 6 weeks. Estimates of the heritability for number of tumours at birth and at 6 weeks using 1934 animals were 0.27 (±0.03) and 0.25 (±0.03), respectively. The estimate of the genetic correlation between these two traits was 0.95 (±0.03). Genetic trends were positive for the number of tumours at birth and at 6 weeks. In spite of positive selection differentials and a moderate heritability, there was a negative phenotypic trend in the number of tumours. Natural selection might be acting in a direction opposite to artificial selection in the Sinclair herd. The slopes of the regression of the number of tumours at birth, at 6 weeks, and melanoma susceptibility on individual inbreeding coefficients were non-significant, indicating no evidence of dominance. The number of live-born pigs was lower in litters from parents susceptible to the disease (p < 0.01).     

HPLC指纹图谱在蜂蜜种类识别中的应用研究

本文主要介绍了指纹图谱技术在蜂蜜种类识别和蜂蜜活性物质研究中的应用，并提出了我国开展蜂蜜指纹图谱研究的意义。     

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

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.     

雄蜂精液采集量与季节环境变化关系的研究

经过对雄蜂精液采集量随季节变化的规律以及与其有关的环境因子方面的研究,结果表明雄蜂精液采集量与季节变化密切相关,意大利雄蜂与卡尼鄂拉雄蜂的采精量也表现出一定的差异;雄蜂精液采集量与外界温度、降水量、蜜粉源以及蜂群群势等生态因子相关。     

天然成熟蜜与非成熟蜜质价比研究

选择22个群势相当、蜂群结构相似的继箱群，按群势大小随机分成两组，一组生产天然成熟蜜，一组生产非成熟蜜，记录试验蜂群的群势、产蜜量、产浆量。结果表明：天然成熟蜜试验组（A组）的取蜜量平均为11552g，非成熟蜜试验组（B组）的平均取蜜量为28961g，B组的取蜜量是A组的2．51倍，t检验表明，P〈0．01，差异极显著；测定两组蜂蜜的含糖量，天然成熟蜜在80％（41度）以上，而非成熟蜜在36度左右，计算取糖量为：A组9309g，B组15649g；B组的取糖量是A组的1．68倍，P〈0．01，差异极显著；产浆量为：A组707g，B组691g，P〉0．05，差异不显著；群势下降率的平均值为：A组21％，B组23％，P〉0．05，差异不显著。结论，从蜂蜜的产量方面考虑，天然成熟蜜的价格应该是非天然成熟蜜的2．5倍。     

分子亲缘系数矩阵的EXCEL计算程序

本文通过VBA语言编程，实现了分子亲缘系数矩阵及其逆阵计算的程序设计，提高了数据处理的准确性。尤其是该程序借助于已在国内广泛使用的Excel，使广大基层技术人员采用最佳线性无偏预测(BLUP)法进行家畜育种值评定更加方便可行。