The estimation of genomic relationships using breedwise allele frequencies among animals in multibreed populations

Different approaches of calculating genomic measures of relationship were explored and compared with pedigree relationships (A) within and across base breeds in a crossbreed population, using genotypes for 38,194 loci of 4,106 Nordic Red dairy cattle. Four genomic relationship matrices (G) were calculated using either observed allele frequencies (AF) across breeds or within-breed AF. The G matrices were compared separately when the AF were estimated in the observed and in the base population. Breedwise AF in the current and base population were estimated using linear regression models of individual genotypes on breed composition. Different G matrices were further used to predict direct estimated genomic values using a genomic BLUP model. Higher variability existed in the diagonal elements of G across breeds (standard deviation = 0.06, on average) compared with A (0.01). The use of simple observed AF across base breeds to compute G increased coefficients for individuals in distantly related populations. Estimated breedwise AF reduced differences in coefficients similarly within and across populations. The variability of the current adjusted G matrix decreased from 0.055 to 0.035 when breedwise AF were estimated from the base breed population. The direct estimated genomic values and their validation reliabilities were, however, unaffected by AF used to compute G when estimated with a genomic BLUP model, due to inclusion of breed means in the model. In multibreed populations, G adjusted with breedwise AF from the founder population may provide more consistency among relationship coefficients between genotyped and ungenotyped individuals in an across-breed single-step evaluation.     

Polymorphism and parent-of-origin effects on gene expression of CAST, leptin and DGAT1 in cattle

This study aimed to investigate differential allele expression (DAE) and polymorphism and parent-of-origin effects on expression of genes related to beef traits. CAST, related to meat tenderness, and DGAT1 and leptin, related to fat deposition, were evaluated. In bovine fetal tissues CAST was expressed twice as much (P < 0.05) in muscle of homozygous GG than in heterozygous AG. Leptin was expressed about one-tenth as much (P < 0.05) in heterozygous TpCm (allele T of paternal origin and allele C of maternal origin) than in homozygous CC. No DAE was observed. The evidence of polymorphism effect on expression of CAST and parent-of-origin effect on leptin contributes to a better understanding of events controlling the expression of genes of economic interest in cattle. Furthermore, if the parent-of-origin effects observed in fetal tissues are confirmed in adult tissues and associated to phenotypic variation, this parental origin criterion may be considered in marker-assisted selection of beef traits.     

Index conditions of resolution

1 Introduction Automated reasoning mechanisms[1,2] are widely used, for example to solve constraint satisfaction prob- lems. The exploration of e?cient automated reasoning strategies is therefore important. If more strategies are incorporated into such mechanisms, resolution based deduction becomes stricter. This results in the gen- eration of a lower number of unuseable clauses. Un- fortunately however, some strategies are incompatible with each other. For example, deletion strategy can dest…     

考虑线路可用裕度问题的配电网多目标馈线规划

针对配电网线路布局与通道资源利用之间存在的矛盾,研究了配电网馈线规划的多目标模型,在考虑线路投资成本和网络损耗的同时,建立了可用裕度模型。针对该多目标模型提出了一种适用于配电网馈线规划的删除路径算法,并结合不同的网络复杂程度对算法中的K进行了函数拟合,最后通过逼近理想解排序法优选出最优方案。结果表明,考虑可用裕度模型的馈线布局方案可为下一个阶段的馈线规划尽可能的留有建设余地。     

Short communication: Multivariate outlier detection for routine Nordic dairy cattle genetic evaluation in the Nordic Holstein and Red population

It is of practical importance to ensure the data quality from a milk-recording system before use for genetic evaluation. A procedure was developed for detection of multivariate outliers based on an approximation for Mahalanobis distance and was implemented in the Nordic Holstein and Red population. The general target of this procedure is based on the Nordic Cattle Genetic Evaluation yield model, which is a 9-trait model for milk, protein, and fat in the first 3 lactations. The procedure is based on the phenotypic correlation structure as a function of days in milk (DIM) and on computation of trait means and standard deviations within a production year, lactation, and DIM. For each record in the data, a Mahalanobis distance value was computed based on the trait mean and the covariance matrix for the actual production year, lactation, and DIM. A set of cutoff values, ranging from 10 to 100 with steps of 10, for discarding multivariate outliers was investigated. Prediction accuracy was calculated as the Pearson correlations between estimated breeding values predicted by full data set and estimated breeding values predicted by reduced data set for cows without records in the reduced data set and with 1 or more records deleted due to the editing rules on Mahalanobis distance. The results showed that, averaged over all scenarios, gains of 0.005 to 0.048 on prediction accuracy have been obtained by deleting the multivariate outliers. The improvements were more profound for progeny of young bulls compared with progeny of proven bulls. It is easy to implement this multivariate outlier-detection procedure in the routine genetic evaluation for different dairy cattle breeds; however, an optimal cutoff value for Mahalanobis distance needs to be defined to achieve an acceptable compromise between genetic evaluation accuracy and data deletion.     

山葡萄UDP-葡萄糖:类黄酮5-O-葡萄糖基转移酶(5GT)等位基因的克隆与分析

山葡萄中大量的双糖苷花色苷严重影响山葡萄酒品质,而5GT是合成双糖苷花色苷的关键酶。研究不同葡萄品种间5GT等位基因的差异,为抑制双糖苷花色苷的合成奠定基础,对提高山葡萄酒的品质有重要意义。本研究克隆了‘赤霞珠’、‘左山一’、‘哈桑’和‘左红一’中的5GT等位基因,并用软件对其进行了序列分析和生物信息学分析,共获得了7个5GT等位基因,均位于葡萄9号染色体上,分别编码297~464个氨基酸。序列分析结果表明,4个5GT等位基因由于基因突变可能丧失了5GT功能;7个5GT等位基因均没有信号肽,属于GT1家族中的5GT亚家族。不同葡萄品种中的5GT等位基因存在一定差异,推测这7个5GT等位基因中可能只有3个5GT可以合成双糖苷花色苷。     

Possible roles of vacuolar H+-ATPase and mitochondrial function in tolerance to air-drying stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains

Yeasts used in bread making are exposed to air-drying stress during dried yeast production processes. To clarify the genes required for air-drying tolerance, we performed genome-wide screening using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 278 gene deletions responsible for air-drying sensitivity. These genes were classified based on their cellular function and on the localization of their gene products. The results showed that the genes required for air-drying tolerance were frequently involved in mitochondrial functions and in connection with vacuolar H(+)-ATPase, which plays a role in vacuolar acidification. To determine the role of vacuolar acidification in air-drying stress tolerance, we monitored intracellular pH. The results showed that intracellular acidification was induced during air-drying and that this acidification was amplified in a deletion mutant of the VMA2 gene encoding a component of vacuolar H(+)-ATPase, suggesting that vacuolar H(+)-ATPase helps maintain intracellular pH homeostasis, which is affected by air-drying stress. To determine the effects of air-drying stress on mitochondria, we analysed the mitochondrial membrane potential under air-drying stress conditions using MitoTracker. The results showed that mitochondria were extremely sensitive to air-drying stress, suggesting that a mitochondrial function is required for tolerance to air-drying stress. We also analysed the correlation between oxidative-stress sensitivity and air-drying-stress sensitivity. The results suggested that oxidative stress is a critical determinant of sensitivity to air-drying stress, although ROS-scavenging systems are not necessary for air-drying stress tolerance.     

Glutaredoxin Interacts with GR and AhpC to Enhance Low-Temperature Tolerance of Antarctic Psychrophile Psychrobacter sp. ANT206

Glutaredoxin (Grx) is an important oxidoreductase to maintain the redox homoeostasis of cells. In our previous study, cold-adapted Grx from Psychrobacter sp. ANT206 (PsGrx) has been characterized. Here, we constructed an in-frame deletion mutant of psgrx (Δpsgrx). Mutant Δpsgrx was more sensitive to low temperature, demonstrating that psgrx was conducive to the growth of ANT206. Mutant Δpsgrx also had more malondialdehyde (MDA) and protein carbonylation content, suggesting that PsGrx could play a part in the regulation of tolerance against low temperature. A yeast two-hybrid system was adopted to screen interacting proteins of 26 components. Furthermore, two target proteins, glutathione reductase (GR) and alkyl hydroperoxide reductase subunit C (AhpC), were regulated by PsGrx under low temperature, and the interactions were confirmed via bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP). Moreover, PsGrx could enhance GR activity. trxR expression in Δpsgrx, Δahpc, and ANT206 were illustrated 3.7, 2.4, and 10-fold more than mutant Δpsgrx Δahpc, indicating that PsGrx might increase the expression of trxR by interacting with AhpC. In conclusion, PsGrx may participate in glutathione metabolism and ROS-scavenging by regulating GR and AhpC to protect the growth of ANT206. These findings preliminarily suggest the role of PsGrx in the regulation of oxidative stress, which could improve the low-temperature tolerance of ANT206.     

广义自缩序列的线性复杂度

周期与线性复杂度的稳定性是衡量周期序列伪随机性质的一个重要指标.本文在给出广义自缩序列的线性复杂度的上界之后,借助伽罗瓦域中的若干理论,分析了该类序列的线性复杂度的稳定性,包括广义自缩序列在单符号插入、删除变换和少量符号替换操作下的线性复杂度的变化情况,给出了变化后序列的线性复杂度的具体表达式.