Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.

An 8-Node Plane Hybrid Element for StructuralMechanics Problems Based on the Hellinger-Reissner Variational Principle

The finite element method (FEM) plays a valuable role in computer modeling and is beneficial to the mechanicaldesign of various structural parts. However, the elements produced by conventional FEM are easily inaccurate andunstable when applied. Therefore, developing new elements within the framework of the generalized variationalprinciple is of great significance. In this paper, an 8-node plane hybrid finite element with 15 parameters (PHQ8-15β) is developed for structural mechanics problems based on the Hellinger-Reissner variational principle.According to the design principle of Pian, 15 unknown parameters are adopted in the selection of stress modes toavoid the zero energy modes.Meanwhile, the stress functions within each element satisfy both the equilibrium andthe compatibility relations of plane stress problems. Subsequently, numerical examples are presented to illustrate theeffectiveness and robustness of the proposed finite element. Numerical results show that various common lockingbehaviors of plane elements can be overcome. The PH-Q8-15β element has excellent performance in all benchmarkproblems, especially for structures with varying cross sections. Furthermore, in bending problems, the reasonablemesh shape of the new element for curved edge structures is analyzed in detail, which can be a useful means toimprove numerical accuracy.

The role of genomic structural variation in the genetic improvement of polyploid crops

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.

Structural Variation Analysis of Mutated Nannochloropsis oceanica Caused by Zeocin Through Genome Re-Sequencing

Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.

Effect of CO_2 on the structural variation of Na_2WO_4/Mn/SiO_2 catalyst for oxidative coupling of methane to ethylene

In this work,the influence of CO2 on the structural variation and catalytic performance of Na2WO4/Mn/Si O2 for oxidative coupling of methane to ethylene was investigated. The catalyst was prepared by impregnation method and characterized by XRD,Raman and XPS techniques. Appropriate amount of CO2 in the reactant gases enhanced the formation of surface tetrahedral Na2WO4 species and promoted the migration of O in MOx,Na,W from the catalyst bulk to surface,which were favorable for oxidative coupling of methane. When the molar ratio of CH4/O2/CO2 was 3/1/2,enriched surface tetrahedral Na2WO4 species and high surface concentration of O in MOx,Na,W were detected,and then high CH4 conversion of 33.1% and high C2H4 selectivity of 56.2% were obtained. With further increase of CO2 in the reagent gases,the content of active surface tetrahedral Na2WO4 species and surface concentration of O in MOx,Na,W decreased,while that of inactive species（Mn WO4 and Mn2O3） increased dramatically,leading to low CH4 conversion and low C2H4 selectivity. It could be speculated that Na2WO4 crystal was transformed into Mn WO4 crystal with excessive CO2 added under the reaction conditions. Pretreatment of Na2WO4/Mn/Si O2 catalyst by moderate amount of CO2 before OCM also promoted the formation of Na2WO4 species.

Structural Variation and Its Influence on the 1/f Noise of a-Si_(1-x)Ru_x Thin Films Embedded with Nanocrystals

The structural variation and its influence on the 1/f noise of a-Si_(1-x)Ru_x thin films are investigated by Raman spectroscopy,transmission electron microscopy, and low frequency noise measurement. The Ru atoms are introduced into the amorphous silicon thin films by rf magnetron co-sputtering. Ru2 Si nanocrystals are found in the as-deposited samples. It is shown that the 1/f noise of the films can be reduced by a slight doping with Ru atoms. Moreover, both the microstructure and the 1/f noise performance of a-Si_(1-x)Ru_x thin films could be improved through a high-temperature annealing treatment.

Structural Variation between the Western and Eastern Kuqa Fold-and-thrust Belt,China:Insights from Seismic Interpretation and Analog Modeling

The Kuqa fold-and-thrust belt exhibits apparent structural variation in the western and eastern zone.Two salt layer act as effective decollements and influence the varied deformation.In this study,detailed seismic interpretations and analog modeling are presented to construct the suprasalt and subsalt structures in the transfer zone of the middle Kuqa and investigate the influence of the two salt layers.The results reveal that the relationship of the two salt layers changes from separated to connected,and then overlapped toward the foreland in the transfer zone.Different structural models are formed in the suprasalt and subsalt units due to the interaction of the two salt layers.The imbricate thrust faults form two broom-like fault systems in the subsalt units.The suprasalt units develop detached folds terminating toward the east in the region near the orogenic belt.Whereas,two offset anticlines with different trends develop at the frontal edge of the lower salt layer and the trailing edge of the upper salt layer,respectively.According to exploration results in this region,the relationship between suprasalt and subsalt structures has an influence on hydrocarbon accumulation.We believe that the connected deformation contains high-risk plays while the decoupled deformation contains well-preserved plays.

Tomographic Evaluation of Structural Variations of Nasal Cavity in Various Nasal Pathologies

Objective: The aim of the present study was to evaluate the structural variations of nasal cavity in reference to frequency and types at the key area i.e. the ostiomeatal complex. Materials and Methods: Computed tomography of Paranasal sinuses of 50 patients was studied for clinical suspicion of various sinonasal pathologies. Results: The most commonly encountered anatomical variations in this study were Deviated Nasal Septum in 78% (39 patients), followed by Concha Bullosa in 36% (18 patients), Agger Nasi cell in 18% (nine patients), Pneumatised septum in 12% (six patients), Paradoxical Middle Turbinate and Septated Maxillary Sinus in 10% (five patients each) and Pneumatised Uncinate Process 6% (three patients). In quite a few patients we witnessed more than one variation. Conclusion: The anatomical variations in the nose and ostiomeatal complex are not uncommon, with the most frequent ones involving the nasal septum and the middle turbinate.

SV波斜入射时不同水体模拟方法下超高水头船闸地震反应分析

基于黏弹性人工边界的地震动斜入射方法模拟平面SV波不同角度入射情况,分别采用声固耦合法和附加质量法模拟闸室内水体,研究超高水头船闸闸室位移、应力和塑性损伤等地震反应,对比两种水体模拟方法计算结果的异同。结果表明:(1)整体上,两种方法计算得出的左、右闸墙地震反应结果随入射角度变化的规律基本一致;左闸墙受拉损伤的最大值均出现在入射角15°时,右闸墙受拉损伤的最大值均出现在入射角35°时;地震波入射角度对超高水头船闸动力响应影响较大,设计时应考虑地震波斜入射的影响。(2)当入射角较大时,采用声固耦合法计算的闸墙相对位移极值、主应力极值和受拉损伤结果偏保守的概率更大,对超高水头船闸结构设计来说更为安全。(3)建议两种计算方法相互参考和校核,推荐采用偏安全的结果进行超高水头船闸结构设计。

THE APPLICATIONS OF GENERALIZED VARIATIONAL PRINCIPLES IN NONLINEAR STRUCTURAL ANALYSIS

This paper discusses the generalized variational principles founded by the technique of Lagrangian multipliers in structural mechanics and analyzes the nonlinear statically indeterminate structures. It is assumed that the stress-strain relationship of the materials of structures has the form of namely, the physical equations of structures have the shape of exponential functions. Several examples are given to illustrate the statically indeterminate structures such as the trusses, beams, frames and torsional bars.

Analysis of Intraspecies Diversity of Rice Reveals Variation Patterns of Oryza sativa Basic Leucine Zippers

The basic leucine zipper(bZIP)is an important class of transcription factors in plants,playing a critical role in plant growth and development and responses to biotic and abiotic stress.Due to gene presence/absence variations,it is limited to identify bZIP genes based on the reference genome.Therefore,we performed the bZIP gene family analysis in the rice pan-genome.By employing a rice pan-genome,ninety-four OsbZIPs(72 core genes and 22 variable genes)were identified and divided into 11 groups in a phylogenetic tree.Based upon Ka/Ks values in 33 accessions,OsbZIPs were subjected to different selection pressures during domestication.The analysis of the effects of structural variations(SVs)on gene expression,gene structure,and conserved domains showed that SVs could significantly alter the expression levels of certain OsbZIPs,leading to gene truncation and the emergence of numerous atypical genes.Thirty-four differentially expressed OsbZIPs were identified by analyzing RNA-seq data of the Xanthomonas oryzae pv.oryzae(Xoo)infection susceptible(IR24)and resistant(IRBB67)lines under high temperature,and by counting the number of differentially expressed OsbZIPs in different subgroups.These Osb-ZIPs were found to respond to Xoo infection at an early stage and may not be involved in the mechanism of Xa4 and Xa7 resistance to Xoo.The multiple variation patterns of OsbZIP genes provide new insights into the OsbZIP genes in rice.These results provide new resources and offer new directions for functional studies of OsbZIPs.

基于SV利率期限结构模型的国债价差研究

利用SV利率期限结构模型,本文选取上海证券交易所和银行间债券市场多个交易日的国债数据,运用遗传算法求解模型参数,得到两个市场的国债收益率曲线。结果表明,使用SV模型拟合出的国债理论价格与实际价格之间误差较小,适用于我国国债市场;在两个市场上相同剩余到期期限的国债收益率之间存在价差,而且价差随着国债的到期期限的增加先变小后变大。可能是由于市场分割、流动性差异和交易机制的不同引起的。

基于构造时间控制的P-SV波静校正方法

由于横波的低速带厚,并且不均匀,加之地表浅层横波速度相对较低,导致P-SV波静校正量大,并且横向变化剧烈。而目前大多数解决该静校正问题的方法都存在一些不足,这里提出了一种简单又易于实现的P-SV波静校正方法。首先,匹配同一层位的PP波和P-SV波同相轴,估计该区的纵、横波速度比γ0值;然后,在PP波和P-SV波共检波点叠加剖面上,利用该γ0值转换PP波构造时间到P-SV波相同构造时间,将该时间应用于P-SV波剖面上;最后,在消除大部分静校正量的P-SV波剖面上作互相关,消除道与道之间较小的时差。经实际数据处理表明,该方法能较好地解决P-SV波静校正问题,使记录质量得到明显提高。

SV模型的变结构研究及应用

探讨 SV模型的诊断分析和变结构建模问题 ,并在扩展 SV模型基础上利用分段建模方法来检测模型结构变化点和分段变化模型的选择 。

PRRSV CH-1a株致弱过程中不同代次病毒结构蛋白基因遗传变异分析

对猪繁殖与呼吸综合征病毒(PRRSV)CH-1a株致弱过程中不同代次病毒(S39、S70、S148、S171)及国内分离株(GD3、JS1、JS5)的结构蛋白基因(ORF2～ORF7)进行了克隆和测序,并与国内外毒株序列进行比较和系统发育进化分析。结果表明,PRRSV CH-1a株各传代毒株和国内分离毒株各个结构蛋白序列均存在不同程度的变异,与GenBank上的登录序列进行了比对,发现GP2～GP5同源性在83.1%～100%,M蛋白同源性在95.4%～100%,N蛋白同源性在87%～100%,其中以GP2、GP3和GP5发生突变几率较大;另外,发现PRRSV CH-1a不同代次病毒GP5的H38突变为Q38(S70),L146突变为Q146(S148),而2006年分离的PRRSV变异毒株由F39突变为I39,而且分离毒株的毒力明显强于经典毒株。进化分析表明,GD3毒株与2006年～2007年分离的毒株以及PRRSV CH-1a株的亲缘关系均较近,处于二者的中间位置。

Analysis of Genetic Variation and Population Structure of Starch Synthesis-related Genes in Indica Rice Cultivars

In this study, 34 molecular markers of starch synthesis-related genes were used to evaluate the genetic variation and population structure of 87 indica rice cultivars from different countries and regions. The results showed that a total of 80 alleles were amplified using 34 primer pairs, with an average of 2.5 alleles per locus. The allele number varied from 2 to 6 among various cultivars. Shannon＇s diversity index of molecular markers varied from 0.303 to 0.796, with an average of 0.539. Polymorphism information content （PIC） varied from 0.084 to 0.658, with an average of 0.295. The genetic similarity coefficients of 87 indica rice cultivars ranged from 0.265 to 0.990, indicating significant genetic differences of starch synthesis-related genes among different cultivars, but the variation frequency of alleles varied among different cultivars. Population structure analysis showed that these 87 indica rice cultivars were divided into three categories. Genetic differences were small within the same category but great among different categories. Moreover, indica rice cultivars with simple genetic components accounted for 39.1% and those with complex genetic background accounted for 60.9%. This study may not only provide theoretical basis for genetic improvement of rice starch quality, but also lay a solid foundation for subsequent association analysis of rice quality-related traits.

翻译与SV提挈句的语用特征

翻译离不开意义转达，而意义的转达有赖于语言的形式转换。翻译的语言形式转换为语用的过程，在这一过程中，SV提挈句以其“适应性”和“关联性”制约原话语内容的转达。SV提挈句的“适应性”和“关联性”为翻译的两个语用特征。

维吾尔语主谓句SV句的语义结构分析

文章以三个平面的理论为指导,透过主谓句SV句挖掘了其深层的内部语义结构关系。

利用SV分量接收函数反演地壳横波速度结构

详细讨论了远震体波SV分量接收函数的特点及其在反演地壳S波速度结构中的优势.与径向接收函数类似,SV分量接收函数可通过对远震体波的SV分量直接反褶积P分量获得.研究分析表明:与径向接收函数相比,SV分量接收函数的振幅随震中距的变化更加稳定,波形简单且突出了对结构最敏感的PS转换波信息.理论数值实验显示:在反演地壳S波速度结构时,SV分量接收函数比径向接收函数具有更好的收敛性.作为实例,利用SV分量接收函数反演方法反演了海拉尔台下的S波速度结构.