The impact of truncating data on the predictive ability for single‐step genomic best linear unbiased prediction

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single‐step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively removed 1 year at a time based on the year an animal was born. For the swine data sets, correlations between corrected phenotypes (Cp) and EBV were used to evaluate the predictive ability on young animals born in 2016–2017. In the simulated data set, keeping data two generations back or greater resulted in no statistical difference (p‐value > 0.05) in the reduction in the true breeding value at generation 15 compared to utilizing all available data. Across swine data sets, removing phenotypes from animals born prior to 2011 resulted in a negligible or a slight numerical increase in the correlation between Cp and EBV. Truncating data is a method to alleviate computational issues without negatively impacting the predictive ability of selection candidate EBV.     

Computing inbreeding coefficients and the inverse numerator relationship matrix in large populations of honey bees

The inbreeding coefficients are considered in breeding decisions, and the inverse numerator relationship matrix A ^?1 is a prerequisite for breeding value estimation. Polyandry and haploid males are among the specifics of relationships between honey bees. Brascamp and Bijma (2014) averaged out the manifold possible relationships among honey bees that appear to have the same parents in a pedigree and assigned a single entry in A to animals that behave as a unit, for example, the workers of a hive. Their methods of calculation connected full‐sibs in the variance matrix of the Mendelian sampling terms D , via nonzero off‐diagonal elements. This impedes the inversion of A and the closely connected calculation of inbreeding coefficients, because efficient algorithms for this task take D to be a diagonal matrix. Memory limitations necessitate their use for large data sets. We adapted the quickest of them to the block diagonal matrix D , that is postulated for the honey bee. To our knowledge, the presented algorithm is the first one that facilitates the method of Brascamp and Bijma (2014) on large data sets.     

In vitro studies of Norwegian Red bovine semen immobilized and cryopreserved in alginate solid gel network

Development of new semen cryopreservation techniques improving sperm survival and ensuring availability of viable spermatozoa for a prolonged time‐period after AI is promising tools to reduce sensitivity of timing of AI and enhance overall fertility. The SpermVital^® technology utilizes immobilization of bull spermatozoa in a solid network of alginate gel prior to freezing, which will provide a gradual release of spermatozoa after AI. The objective of this study was to compare post‐thaw sperm quality and in vitro sperm survival over time of Norwegian Red bull semen processed by the SpermVital^® (SV) technology, the first commercialized production line of SpermVital^® (C) and by conventional procedure applying Biladyl^® extender (B). Post‐thaw sperm motility was not significantly different between SV, C and B semen (p > .05). However, sperm viability and acrosome intactness were higher for SV than C and B semen (p < .05). Small differences in DNA quality were observed (p < .05). Sperm viability after storage in uterus ex vivo was higher for SV than for C semen (p < .05). Furthermore, sperm survival in vitro over time at physiological temperature was significantly higher for SV semen than C semen as well as B semen during the incubation period of 48 hr (p < .05). In conclusion, the SpermVital^® technology is improved and is more efficient in conserving post‐thaw sperm quality and results in higher sperm viability over time in vitro for SV than for C and B semen.     

Effects of five cryoprotectants on proliferation and differentiation‐related gene expression of frozen‐thawed bovine calf testicular tissue

The cryopreservation of testicular tissue is a potential method for preserving male fertility. However, the effect of cryopreservation on bovine calf testicular tissue is scarce. This study investigated the effect of different cryoprotectants on bovine calf testicular tissue at the molecular level. Testicular tissue from ten immature bovine calves (6 months) was collected after slaughter and cryopreserved in an extender containing different concentrations of the following five cryopreservation solutions (CP): bovine serum albumin (BSA) with 5% dimethyl sulfoxide (DMSO), trehalose with 5% DMSO, DMSO and glycerol and ethylene glycol (EG). After 7‐day cryopreservation, the expression levels of three spermatogonial stem cell (SSC)‐related genes, octamer‐4 (OCT4), KIT ligand (MGF/SCF) and kit oncogene (C‐KIT), were investigated by quantitative PCR (qPCR). The cell viability was highest for the tissues preserved with 30 mg/ml BSA (77.82% ± 1.22) and 40 mg/ml trehalose (74.23% ± 1.16) compared with other groups (p < 0.05), and the level of expression of the three genes was highest with 30 mg/ml BSA (p < 0.05). Compared with other CPs, the 30 mg/ml BSA and 40 mg/ml trehalose have the better cryopreserve protection. The 30 mg/ml BSA is the most viable media for the cryopreservation of testicular tissue from cattle.     

Viral skin diseases in the Netherlands

The most common viral skin problems are discussed in the third article in our equine dermatology series.     

肉鸡屠宰加工过程中沙门菌污染定量风险评估

为了构建肉鸡屠宰加工过程中沙门菌污染定量风险评估模型,分析鸡肉中沙门菌的消长变化规律,明确关键风险防控点,采用2015年部分肉鸡屠宰场沙门菌污染监测和调研数据,构建以烫煺后为评估过程起点,包括净膛、清洗预冷和分割传送的模块化过程风险评估模型,以不同分布描述各变量,并通过@RISK软件模拟运行。结果显示,通过构建的模型模拟屠宰加工后终端鸡肉产品中的沙门菌污染量,90%的可能分布在0~9MPN之间,而依据实际监测数据换算为5.3 MPN,说明模型可信。根据过程中各环节的模拟数据,分析了肉鸡携带的沙门菌消长变化,发现预冷后沙门菌污染总量明显下降,但分割传送后污染总量又有所回升。通过拟合的相关系数分析,明确了传送带上的沙门菌是影响终端鸡肉沙门菌污染的最关键风险点。本研究构建的肉鸡屠宰加工全过程沙门菌定量风险评估模型,可为肉鸡屠宰场沙门菌污染的卫生监管和风险管理提供理论依据。     

Influence of the root endophyte Piriformospora indica on the plant water relations,gas exchange and growth of Chenopodium quinoa at limited water availability

This study aimed to evaluate the ability of Piriformospora indica to colonize the root of Chenopodium quinoa and to verify whether this endosymbiont can improve the growth, performance and drought resistance of this species. The study delivered, for the first time, evidence for successful colonization of P. indica in quinoa. Hence, pot experiment was conducted in the greenhouse, where inoculated and non‐inoculated plants were subjected to ample (40%–50% WHC) and deficit (15%–20%WHC) irrigation treatments. Drought adversely influenced the plant growth, leading to decline the total plant biomass by 74%. This was linked to an impaired photosynthetic activity (caused by lower g_s and C_i/C_a ratio; stomatal limitation of photosynthesis) and a higher risk of ROS production (enhanced ETR/A_gross ratio). P. indica colonization improved quinoa plant growth, with total biomass increased by 8% (controls) and 76% (drought‐stressed plants), confirming the growth‐promoting activity of P. indica. Fungal colonization seems to diminish drought‐induced growth hindrance, likely, through an improved water balance, reflected by the higher leaf ψ_w and g_s. Additionally, stomatal limitation of photosynthesis was alleviated (indicated by enhanced C_i/C_a ratio and A_net), so that the threat of oxidative stress was minimized (decreased ETR/A_gross). These results infer that symbiosis with P. indica could negate some of the detrimental effects of drought on quinoa growth, a highly desired feature, in particular at low water availability.