Linkage analysis and integrated software GAPL for pure-line populations derived from four-way and eight-way crosses

Pure lines derived from multiple parents provide abundant variation for genetic study.However,efficient genetic analysis methods and user-friendly software are still lacking.In this study, we developed linkage analysis methods and integrated analysis software for pure-line populations derived from four-way and eight-way crosses.First, polymorphic markers are classified into different categories according to the number of identifiable alleles in the inbred parents.Expected genotypic probability is then derived for each pair of complete markers, and based on them a maximum likelihood estimate(MLE) of recombination frequency is calculated.An EM algorithm is proposed for calculating recombination frequencies in scenarios that at least one marker is incomplete.A linkage map can thus be constructed using estimated recombination frequencies.We describe a software package called GAPL for recombination frequency estimation and linkage map construction in multi-parental pure-line populations.Both simulation studies and results from a reported four-way cross recombinant inbred line population demonstrate that the proposed method and software can build more accurate linkage maps in shorter times than other published software packages.The GAPL software is freely available from www.isbreeding.net and can also be used for QTL mapping in multi-parental populations.

Habitat fragmentation and the population status of rodents in Abayum forest, Ikom, Cross River State, Nigeria

The threat to wildlife population is attributed to various anthropogenic activities. The main objective of this study was to identify the influence of fragment size on the population density of rodents in the study area. Fourteen (14) out of forty (40) fragments existing in the area were randomly sampled. The parameters used for the study were number, size of fragments and the corresponding population distribution of rodents in the study area. Fifty hunters in the area were also interviewed. The fragments were stratified into first, second and third order fragments on the basis of their sizes and randomly selected for the study. Indirect method of wildlife census was carried out through the observation of droppings, trail or tract, burrows, eating habits and noise. Fragment growth rate was 18 to 40 (87.5%) in 7 years. Anthropogenic perturbations in the form of cultivation of permanent cropland, settlement expansion, bush burning, timber exploitation and new settlements in areas previously thinly settled or not accessible to outsiders have resulted in disjointed ecosystems. The population density of rodents correlated with fragment size was highly significant ((P < 0.05) r = 0.9). It was then concluded that fragment size greatly influenced the population and diversity of rodent species. It was recommended that the remaining large fragments in the study area should be protected by law from further fragmentation.

Identifying Genomic Regions Conferring Morphological and Yield-related Traits in Soybean Based On A Four-way Recombinant Inbred Line Population

Improvement of seed yield of soybean(Glycine max(L.)Merr.)is generally achieved by combining morphological and yield-related traits,such as plant height(PH),node number on main stem(NN),pod number per plant(NP),seed number per plant(NS),100-seed weight(HSW)and seed weight per plant(SWPP).Identifying quantitative trait loci(QTLs)for morphological and yield-related traits is therefore important for breeding.In this study,a four-way recombinant inbred line population comprising 160 lines derived from the cross(Kenfeng14×Kenfeng15)×(Heinong48×Kenfeng19)was planted in five different environments and morphological and yield-related trait data were used to identify QTLs by the inclusive composite interval mapping method.Totally 38 QTLs for PH,40 QTLs for NN,26 QTLs for NP,10 QTLs for NS,26 QTLs for HSW and 49 QTLs for SWPP were detected in 125 genomic regions.Single QTLs explained 2.17%-14.60%,2.00%-10.04%,2.37%-9.77%,2.62%-8.61%,0.47%-6.51%and 0.14%-12.39%of the phenotypic variation for PH,NN,NP,NS,HSW and SWPP,respectively.Among these 125 genomic regions,120 were newly associated with morphological and yield-related traits.The results would facilitate the molecular breeding of morphological and yield-related traits in soybean.

Qualitative Properties and Numerical Solution of the Kolmogorov-Fisher Type Biological Population Task with Double Nonlinear Diffusion

In the present work we study the global solvability of the Kolmogorov-Fisher type biological population task with double nonlinear diffusion and qualitative properties of the solution of the task based on the self-similar analysis. In additional, in this paper we consider the model of two competing population with dual nonlinear cross-diffusion.

Genetic Analysis of Embryo Production Frequency in Wheat × Maize Cross

A DH population derived from C49S-87/01Y1-1069 was used to study the inheritance of wheat haploid embryo production frequency（EPF） in wheat × maize cross with the mixed major gene and polygene inheritance model of quantitative traits. The results showed that the EPF of wheat × maize cross was controlled by two dominant epistatic genes and polygene with gene effects of 1.95 for the first major gene, 6.69 for the second one and 2.80 for the polygene. The inheritability of major genes was as high as 72.09%, suggesting that the differences in EPF among wheat materials were mainly influenced by genotype. However, non-genetic factors were still important, especially for wheat materials with low EPF.

Mapping novel genetic loci associated with female liver weight variations using Collaborative Cross mice

Background: Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role candidate genes involved directly in the hepatomegaly process and indirectly involved in related diseases etiology.Methods: Liver weight of 506 mice generated from 39 different Collaborative Cross(CC) lines with both sexes at age 20 weeks old was determined using an electronic balance. Genomic DNA of the CC lines was genotyped with high-density single nucleotide polymorphic markers.Results: Statistical analysis revealed a significant(P < 0.05) variation of liver weight between the CC lines, with broad sense heritability(H^2) of 0.32 and genetic coefficient of variation(CV_G) of 0.28. Subsequently, quantitative trait locus(QTL) mapping was performed, and results showed a significant QTL only for females on chromosome 8 at genomic interval 88.61-93.38 Mb(4.77 Mb). Three suggestive QTL were mapped at chromosomes 4, 12 and 13. The four QTL were designated as LWL1-LWL4 referring to liver weight loci 1-4 on chromosomes 8, 4, 12 and 13,respectively.Conclusion: To our knowledge, this report presents, for the first time, the utilization of the CC for mapping QTL associated with baseline liver weight in mice. Our findings demonstrate that liver weight is a complex trait controlled by multiple genetic factors that differ significantly between sexes.

Efficient protocols and methods for high-throughput utilization of the Collaborative Cross mouse model for dissecting the genetic basis of complex traits

The Collaborative Cross(CC)mouse model is a next‐generation mouse genetic reference population(GRP)designated for a high‐resolution quantitative trait loci(QTL)mapping of complex traits during health and disease.The CC lines were generated from reciprocal crosses of eight divergent mouse founder strains composed of five classical and three wild‐derived strains.Complex traits are defined to be controlled by variations within multiple genes and the gene/environment interactions.In this article,we introduce and present variety of protocols and results of studying the host response to infectious and chronic diseases,including type 2 diabetes and metabolic diseases,body composition,immune response,colorectal cancer,susceptibility to Aspergillus fumigatus,Klebsiella pneumoniae,Pseudomonas aeruginosa,sepsis,and mixed infections of Porphyromonas gingivalis and Fusobacterium nucleatum,which were conducted at our laboratory using the CC mouse population.These traits are observed at multiple levels of the body systems,including metabolism,body weight,immune profile,susceptibility or resistance to the development and progress of infectious or chronic diseases.Herein,we present full protocols and step‐by‐step methods,implemented in our laboratory for the phenotypic and genotypic characterization of the different CC lines,mapping the gene underlying the host response to these infections and chronic diseases.The CC mouse model is a unique and powerful GRP for dissecting the host genetic architectures underlying complex traits,including chronic and infectious diseases.

A study of the influence of genetic variance and sex on the density and thickness of the calvarial bone in collaborative cross mice

Background:Bone microarchitecture is affected by multiple genes,each having a small effect on the external appearance.It is thus challenging to characterize the genes and their specific effect on bone thickness and porosity.The purpose of this study was to assess the heritability and the genetic variation effect,as well as the sex effect on the calvarial bone thickness(Ca.Th)and calvarial porosity(%PoV)using the Collaborative Cross(CC)mouse population.Methods:In the study we examined the parietal bones of 56 mice from 9 lines of CC mice.Morphometric parameters were evaluated using microcomputed tomography(μCT)and included Ca.Th and%PoV.We then evaluated heritability,genetic versus environmental variance and the sex effect for these parameters.Results:Our morphometric analysis showed that Ca.Th and%PoV are both significantly different among the CC lines with a broad sense heritability of 0.78 and 0.90,respectively.The sex effect within the lines was significant in line IL111 and showed higher values of Ca.Th and%PoV in females compared to males.In line IL19 there was a borderline sex effect in Ca.Th in which males showed higher values than females.Conclusions:These results stress the complexity of sex and genotype interactions controlling Ca.Th and%PoV,as the skeletal sexual dimorphism was dependent on the genetic background.This study also shows that the CC population is a powerful tool for establishing the genetic effect on these traits.

武汉市中老年人群口腔健康现况研究

目的 分析武汉市中老年人群口腔健康现况,为中老年人口腔疾病预防和促进口腔健康提供临床依据。方法数据来自武汉市机关单位组织的年度健康体检数据系统中45~95岁人群的口腔检查结果,共1994人。根据世界卫生组织(WHO)《口腔健康调查基本方法》(第5版),重点对龋病、牙周病、牙列缺损、牙列缺失及义齿修复状况等资料进行研究。采用卡方检验和方差分析等统计学方法进行数据分析。结果 1994名研究对象中,男性有1613人(占80.89%),75岁以上老年人有218人(占10.93%),龋均、失牙均数分别为2.68、2.03颗。龋均和失牙均数随着年龄的增加而增加,45~,55~,65~,75~和85~95岁组龋均和失牙均数分别为0.98和0.54,1.82和1.39,3.21和2.48,7.65和6.04,12.65和9.91颗,不同年龄组间差异均有统计学意义(均P<0.01)。失牙修复比例同样随年龄的增加而增加(P<0.01),不同年龄段社区牙周指数(CPI)差异也有统计学意义(P<0.01)。CPI为0的人数在各个年龄段占比随年龄的增加而降低,CPI为2的人数占比大致随年龄的增加而增加(均P<0.01)。结论 武汉市机关中老年体检人群总体口腔健康检查结果与第4次全国口腔健康检查的城市地区相比,整体状况略好。但在高龄人群中,龋病、牙周病、失牙和未修复义齿情况仍较严重,应提高老年人对口腔疾病的预防意识,通过定期口腔检查,及时发现并治疗。同时也应关注高龄老人的义齿修复问题,提高老年人群的生活质量。

基于改进差分进化算法的跨平台武器目标分配方法

现代战争中,跨平台武器单元的协同利用,是合同编队体系的重要内容,作战方式也正由平台级协同向着能力要素级协同转变,这对武器目标分配问题的解决提出了更大挑战。本文将武器单元的最小划分单位细化到能力要素级,以毁伤概率与成本消耗为优化目标,面向多种来袭目标的编队防空场景,提出了跨平台武器目标分配算法。同时,基于混沌映射提出了混沌种群重构(chaotic population reconstruction,CPR)机制,并结合带存档的自适应差分进化(adaptive differential evolution with optional external archive,JADE)算法提出了CPR-JADE算法,利用CPR机制可以帮助算法在解决高维复杂约束问题时跳出局部最优。再将其运用到武器目标分配模型上,实现了对模型的高效求解。最后,通过在多种数据规模下与其他进化优化算法的仿真对比试验分析,验证了所提方法的正确性与有效性。

在流动中走向融合:推动城乡融合发展的实现机制——基于陕西省F县的案例考察

能否在人口快速流动的城乡社会转型发展中加快推进城乡融合发展,是实现农业农村现代化不容忽视的问题。基于城乡融合发展的流动性增强和空间转向的双重基础,通过陕西省F县城乡融合发展实践的案例分析,探究流动情境下城乡融合发展的实现逻辑。研究发现,流动性内嵌于城乡融合发展过程,通过人口流动的表征对传统城乡二元结构带来地域性变化和社会关系转变;在“乡—城”流动、“城—乡”流动和“城乡两栖”的多元人口流动样态下,城乡融合发展实现过程呈现跨域协同机制、关系协调机制和情感维系机制,表现出在流动中走向融合的内在逻辑。推进城乡融合发展,要突破传统二元结构对城乡融合发展研究的单一图解,在流动性引致的城乡社会变迁中,加强城乡物理空间、社会空间和情感空间的融合,进而促进城乡秩序均衡。

南京都市圈跨市日常人口流动影响因素及其空间效应研究

跨市日常人口流动逐渐成为衡量都市圈一体化水平的重要因素,其不仅受到本地社会经济环境的影响,也受到邻近地区发展的空间效应影响,但目前对其影响因素及空间效应的讨论相对较少。因此,文章对其影响因素及其空间效应进行研究。研究发现:①南京都市圈跨市日常人口流动规模和节点控制力分别形成了以南京市为核心向外围扩散和以边界区域为核心沿主要交通走廊分布的空间格局。②其分布具有空间依赖性,流动规模主要体现在周边区域对空间单元的随机冲击,节点控制力主要体现在周边区域中介作用提升对本区域的空间溢出作用。③影响其空间格局的因素较为复杂,流动规模受到公服设施、交通建设、经济社会属性多种类型的因素影响,而节点控制力则主要与公服设施、交通建设相关。研究进一步丰富了日常人口流动的研究内容,既从空间效应维度对其形成机制进行补充,也为跨区域人口流动引导体系的构建提供了依据。

中国居民心理与行为调查研究:理念、实践与展望

为使研究者全面了解中国居民心理与行为调查研究(PBICR),本文从四个方面介绍其背景和特色。在设计理念上,PBICR聚焦中国人群的心理健康与健康行为的诸多方面,充分考虑时效性与高效性,秉承数据开放与数据共享初衷,以大样本、多中心、重复性、全国性横断面设计搭建高质量数据库,促进数据挖掘与交流合作;在调查实施上,PBICR采用人口规模成比例、多阶段抽样与配额抽样相结合的抽样方法,以面对面实地调查获取数据并严格质量控制,保证样本代表性与可靠性;在成果产出上,因PBICR研究内容涵盖丰富、更新接轨国际热点,可满足多样化变量数据研究需求,既往研究结果在公共卫生、管理学、传播学、心理学等多个领域具有较高影响力;展望未来,PBICR将逐步完成从总库到分库的数据库建设,关注特殊人群与全球广泛地区,增添追踪性调查与生物医学数据研究视角,拥有更大研究潜力,通过总体布局多层面驱动中国居民心理与行为健康研究。

追踪调查中的样本更新问题研究——部分国际追踪调查的实践经验总结及思考

社会科学研究中,经常需要对样本成员进行长期甚至终身追访,以揭示现象的变化和发展规律、有效识别现象间的因果关系,同时估计截面总体特征也是关注的重点。追踪调查数据在研究变量变化规律、识别变量间因果关系等方面具有显著优势,在社会科学研究中得到广泛应用。然而,随着追访轮次的增加,受无回答和样本成员死亡的影响,追踪样本会出现样本损耗、低年龄组代表性不足等问题。此外,由于移民和新生总体的加入,截面总体不断变化。因此,利用追踪样本估计截面总体会面临潜在的偏差,包括无回答偏差和涵盖偏差。为了减少这些偏差,国际上多数追踪调查项目均定期或不定期从总体或子总体中抽取更新样本,并将其和追踪样本整合起来,以估计截面总体特征,即对追踪样本进行样本更新。尽管我国追踪调查项目取得一定发展,但国内却鲜有文献对此问题进行讨论。本文通过梳理部分国际知名追踪调查的抽样设计方案和技术文档,对样本更新的总体范围、更新频率、更新样本的抽取方法、追踪样本和更新样本整合方法的实践经验进行归纳和总结,并指出潜在的问题及需要加强研究的方向,为我国追踪调查实践提供经验和理论上的支撑。

Mathematical formalization of the process of crossing individuals of different populations within the framework of the quasispecies model

This paper presents a mathematically formalized description of the process of crossing individuals of different populations as a break of the first kind of functional dependencies of the population state vector components.In this case,the validity of the quasispecies model as a model of population development was assumed.The practical interpretation of a mathematically formalized description is considered on the example of an artificial population of Lymantria dispar.The results of the work can be used to assess the development parameters of both natural and artificial populations.

东北边境口岸城市人口收缩特征及影响因素

以东北地区设立边境口岸的25个县级行政区域为研究对象,采用ARCGIS空间分析和SPSS数理统计相结合的方法,分析城市人口收缩的时空特征及影响因素。研究表明:一是在2001-2020年二十年的时间里,76%的东北边境口岸城市发生人口收缩,表现为短期内存在部分增长,长期态势以收缩为主,且后期收缩现象较为明显。二是根据回归结果显示,发生人口收缩的城市存在以下三个共性问题:交通便捷度较差、口岸贸易水平不高和口岸经济产生的带动效应有限。三是医疗和教育条件不能满足居民更高生活标准的要求,地方财政收入比较少,城市居住体验感降低,也是导致人口流失的重要方面。

从香港地区安老需求探讨大湾区跨境养老的建设重点

自回归祖国以来,香港特区政府陆续推出了多项跨境福利措施,旨在支持香港地区居民在内地安度晚年。尽管有这些措施,选择到内地养老的港人并不多,主要的原因是医疗及其他福利的可移植性和衔接问题还未能很好解决,影响港人北上养老的意愿。随着香港地区与内地经济的深度融合,尤其是大湾区的地理与人力资源的优势不断彰显,预示着未来港人在内地生活及养老将成为趋势,为了向政策制定者提供客观及实用的建议,本文通过综合分析香港地区、内地和海外文献、相关政策文件、媒体报导及持份者观点等数据,探讨港人到内地养老的推拉因素,并提出推进跨境养老发展建议。

跨文化视域下应对老龄化挑战:德国养老服务体系对不断优化我国养老事业的启示

发展进入新时代,合理应对人口老龄化挑战已成为国家经济增长和可持续发展的关键。党中央将应对人口老龄化视为国家战略,加快了老年社会保障、养老服务、健康支撑体系建设。党的二十大报告强调实施积极应对人口老龄化国家战略,推动全体老年人享有基本养老服务,重视养老服务高质量发展。本文以外语人的跨文化视角研究中德两国养老服务,提供优化方案,包括服务体系建设、医疗护理体系等。目的是为提升中国养老服务品质探索更具特色的优化路线。

马氏珠母贝不同地理种群内自繁和种群间杂交子一代主要性状的比较

为了培育马氏珠母贝新品种,开展了不同地理种群内自繁和种群间杂交的工作,获得了3个自繁群体和3个杂交群体,BB1、DD1和SS1分别来自北海野生种群(BW)、大亚湾野生种群(DW)和三亚野生种群(SW)自繁一代;BD1、BS1和DS1分别来自BW与DW、BW与SW以及DW与SW杂交一代。运用方差分析对6个子一代群体的5个主要性状(壳长、壳宽、壳厚、总体重和壳重)进行了比较,3个杂交群体未表现出杂种优势。但获得的6个群体将成为进一步选育的基本群体。子一代的变异性增加为进一步选育奠定了基础。

三疣梭子蟹(Portunus trituberculatus)不同地理种群内自繁和种群间杂交子一代生长性状的比较

采用不同地理种群体内自繁和种群间杂交的方法,进行了自繁和杂交子一代生长性状的比较研究。结果表明,80日龄时的杂交子一代在各项指标都表现出一定的杂种优势(0.24%—13.50%),LS在这5个性状中都高于ZL。100日龄时杂交子一代表现出的杂种优势有所下降,杂种优势率在-0.88%—4.13%之间,甲长表现出杂种劣势。120日龄时杂交子一代的杂种优势范围为-1.91%—4.37%,甲长、甲宽表现出杂种劣势。可见不同杂交组合、不同性状、不同时间表现出的杂种优势有显著差异。ANOVA分析表明:80日龄、100日龄、120日龄时,5个生长性状在群体之间存在极显著差异。实验结果表明:三疣梭子蟹4个杂交子一代在生长性状上存在一定程度的杂种优势,可见种内群体间杂交是培育三疣梭子蟹优良新品系的重要方法之一。