基于系谱和SSR标记的高山杜鹃杂交种亲缘关系分析

该研究对高山杜鹃(Rhododendron L.)的总DNA提取方法进行了改良,然后综合利用高山杜鹃EST数据库和该实验室的马缨杜鹃高通量测序数据,引用已发表文献的SSR引物,从154对SSR引物中筛选出了26对多态性高、重复性好、条带清晰的SSR引物。再从中随机选择10对SSR引物进行荧光标记,对69份不同高山杜鹃的种质进行遗传多样性分析。结果表明,平均有效等位基因数6.959 2个;位点多态性信息含量(PIC)、观测杂合度(HO)、期望杂合度(HE)和Neis基因多样性(H)分别为0.795 2、0.543 5、0.826 5和0.820 2;杂交种间的非加权配对算术平均(UPGMA)聚类结果与其谱系分析结果基本一致,可实现对一些未知来源的育成品种资源进行祖先亲本类型的推测。     

生物信息学软件研究的可视化分析

以Web of Science数据库为数据来源,利用Cite Space和UCINET软件对发表在Nucleic Acids Research期刊上有关生物信息学软件研究的文献做了可视化分析,揭示了该领域的研究力量、作者团队与高被引作者、知识基础、期刊分布、研究热点与前沿,为生物信息学软件的研究和发展提供必要的参考依据。     

Mapplotter——一个输出遗传图谱、图示基因型和QTL曲线图形的软件

分子遗传图谱和ＱＴＬ定位已经在动植物的数量遗传学研究和育种工作中获得广泛应用。现在 ,已经有多种商业化软件或免费软件可以应用于遗传图谱的计算或ＱＴＬ定位。但绝大多数此类软件没有提供图形化输出功能 ,或者只能在Ｍａｃｉｎｔｏｓｈ平台上获得有关遗传图谱 ,图示基因型或ＱＴＬ曲线的图形化输出〔１〕。因此在实际应用中很不方便。遗传图谱计算中应用最广的是Ｍａｐｍａｋｅｒ［２］ 或者是Ｊｏｉｎ ｍａｐ［３］。其中Ｍａｐｍａｋｅｒ可在Ｍａｃｉｎｔｏｓｈ平台上获得图形化输出 ,但在ＰＣ平台上只提供了有限的图形化输出功能。…     

一个控制水稻籽粒长度主效基因--Lk-4(t)的BC2F2群体定位及其遗传效应分析

水稻籽粒大小和形状是影响稻米外观品质和产量的重要影响因素,对控制这些性状基因的定位和克隆有助于弄清籽粒大小基因的表达模式和相应的代谢系统,最终实现该性状的自由调控。运用SSR和CAPs标记对来源于蜀恢527//蜀恢527／小粒回交组合BC2F2群体800隐性长粒单株进行分析,定位了一个控制水稻籽粒长短的基因,Lk-4（t）。对F2和BC2F2群体籽粒大小形状和千粒重的遗传分析表明,回交能将大部分对目的基因效应具有干扰修饰作用的微效基因多态性除去,从而有利于对目的基因型的准确鉴定;在F2和BC2F2群体中只发现两类籽粒长短表现型,即短粒和长粒,并且二者分离比例符合3：1的典型一对等位基因分离比例。这说明群体中籽粒长短变异是受一对基因控制。通过对BC2F2群体中隐性（长粒）单株进行分子标记分析,将这个控制籽粒长短的主效基因定位在3个CAPs标记,P1-EcoRV,P2-SacⅠ和P3-MboⅠ附近。连锁分析表明,Lk-4（t）位于水稻第3染色体着丝粒附近,离标记P1-EcoRⅤ和P2-SacⅠ分别有0．90cM和0．50cM的距离。     

应用CiteSpace对生态学科meta分析的文献计量学和可视化分析

Meta分析是针对一系列独立研究结果进行定量综合分析的方法。从20世纪90年代初开始被应用于生态学的研究中,已经对这一学科的数据汇总方式产生重大影响。为了探究meta分析方法在生态学领域的研究现状及热点,以Web of Science论文核心合集为检索数据库,通过输入关键词检索了1992至2018年之间的论文,并利用Web of Science自带的文献分析工具和Histcite对检索的文献信息进行统计分析,分析了不同年份、国家、期刊、学科基础知识论文的发表和被引情况,用CiteSpace软件对其进行热点分析并绘制了知识图谱。研究发现,我国生态学研究在meta分析方法的改进和利用方面与美国、英国等国家相比尚有差距;使用meta分析方法开展研究越来越多,但研究方向上出现了一些转变,越来越多的研究关注全球变化背景下植物光合作用、物种入侵的机理以及模拟氮循环过程对物候和植被生产力的影响及价值评估的研究,并成为本领域的研究前沿。     

可用于酶分析和杂交分析的DNA的快速分析法

从大量的单个有机体中快速分离DNA的这种能力大大地促进了对这些有机体的基因组的特性的鉴定。特别是应用DNA重组的技术,从含有克隆DNA片段的有机体中快速分离DNA的这种方法大大地促进了对这些克隆的鉴定。这里所叙述的方法是用于从细菌、酵母及组织培养细胞中分离DNA的方法。但是,这些方法是很通用的方法,可以用于从任何有机体中分离DNA。用这些方法得到的DNA制品虽然不是纯的DNA,但是对     

SeqTrace: A Graphical Tool for Rapidly Processing DNA Sequencing Chromatograms

Modern applications of Sanger DNA sequencing often require converting a large number of chromatogram trace files into high-quality DNA sequences for downstream analyses. Relatively few nonproprietary software tools are available to assist with this process. SeqTrace is a new, free, and open-source software application that is designed to automate the entire workflow by facilitating easy batch processing of large numbers of trace files. SeqTrace can identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and end-trim finished sequences. The software features a graphical interface that includes a full-featured chromatogram viewer and sequence editor. SeqTrace runs on most popular operating systems and is freely available, along with supporting documentation, at http://seqtrace.googlecode.com/.     

GIV: A Tool for Genomic Islands Visualization

A Genomic Islands (GI) is a chunk of DNA sequence in a genome whose origin can be traced back to other organisms or viruses. The detection of GIs plays an indispensable role in biomedical research, due to the fact that GIs are highly related to special functionalities such as disease-causing GIs - pathogenicity islands. It is also very important to visualize genomic islands, as well as the supporting features corresponding to the genomic islands in the genome. We have developed a program, Genomic Island Visualization (GIV), which displays the locations of genomic islands in a genome, as well as the corresponding supportive feature information for GIs. GIV was implemented in C++, and was compiled and executed on Linux/Unix operating systems.

Availability

GIV is freely available for non-commercial use at http://www5.esu.edu/cpsc/bioinfo/software/GIV     

基于WWW与UNIX的核酸序列分析实用软件的开发

讨论了计算机序列分析的工作,介绍了基于WWW和UNIX的核酸序列分析实用软件,其特点是快速,易用,提高了工作效率。     

Gene survival in the Asian wild horse (Equus przewalskii): II. Gene survival in the whole population,in subgroups,and through history

In populations with a known pedigree, exact joint probability distributions of numbers of surviving of genes from each founder can now be calculated for moderately large complex pedigrees (1,000–2,000 individuals and much inbreeding). The usefulness of such calculations is shown by our analysis of gene survival in the Asian wild horse (Equus przewalskii), a species now extinet in the wild with a captive population with 1,516 individuals in the known pedigree (12 generations). We calculate the genetic diversity of subsets of the current population interesting to the North American Species Survival Plan, trace the loss of genetic diversity in this species through its history in captivity, and determine genetically important individuals in the North American population—those with relatively high probabilities of having unique copy genes (genes not found in any other living individual in North America).     

Gene survival in the Asian wild horse (Equus przewalskii): I. Dependence of gene survival in the calgary breeding group pedigree

The joint probability distribution of the number of distinct (not identical by descent) genes from each founder of the Equus przewalskii population that survive in the five horses of the Calgary Zoological Gardens breeding group has been calculated. The dependence structure of this distribution is investigated, and informative marginal distributions are given, among them the distributions of the genetic contributions of each founder to the Calgary horses and the distribution of wild-type genes in these horses. The dependence pattern is found to be complex; there is no substitute for exact calculation of the full joint probability distribution of numbers of surviving genes. Probabilities of gene survival give a more complete summary of the genetic structure of a set of individuals than is provided by more routine measures such as heterozygosity or founder contributions. The feasibility of computing these probabilities for small groups of current individuals descended from few founders via long and complex pedigrees, provides a new approach to assessing such groups, and could be used also in selecting animals to form the founder stock of propagules for future reintroduction programs.     

Analysis of founder representation in pedigrees: Founder equivalents and founder genome equivalents

The concepts of “founder equivalent” and “founder genome equivalent” are introduced to facilitate analysis of the founding stocks of captive or other populations for which pedigrees are available. The founder equivalents of a population are the number of equally contributing founders that would be expected to produce the same genetic diversity as in the population under study. Unequal genetic contributions by founders decrease the founder equivalents, portend greater inbreeding in future generations than would be necessary, and reflect a greater loss of the genetic diversity initially present in the founders. The number of founder genome equivalents of a population is that number of equally contributing founders with no random loss of founder alleles in descendants that would be expected to produce the same genetic diversity as in the population under study. The number of founder genome equivalents is approximately that number of wild-caught animals that would be needed to obtain the same amount of genetic diversity as is in the descendant captive population. Founder equivalents and founder genome equivalents allow comparison of the genetic merits of adding new wild-caught stock vs. further equalizing founder representations in a captive population.     

NAExplor: A Software Tool for Managing and Analyzing Nucleic Acid Structure Files

NAExplor is a software tool for converting coordinates files between the software packages AMBER, CHARMM, and XPLOR. In addition, it manages the conversion of NMR-derived distance restraints information from the MARDIGRAS program into the appropriate file formats used for input in AMBER, CHARMM, and XPLOR. Analyses of H-H distances in nucleic acid structures and calculations of torsion angles for nucleic acid backbone and riboses are also possible.     

Genome-Wide Variation of Cytosine Modifications Between European and African Populations and the Implications for Complex Traits

Elucidating cytosine modification differences between human populations can enhance our understanding of ethnic specificity in complex traits. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at a false discovery rate of 1%. The CpG sites with greater modification levels in European descent were enriched in the proximal regulatory regions, while those greater in African descent were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained primarily by local genetic variation. In addition, a substantial proportion of local modification quantitative trait loci exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interactions could be common. Distinct correlations were observed between gene expression levels and cytosine modifications in proximal regions and gene bodies, suggesting epigenetic regulation of interindividual expression variation. Furthermore, quantitative trait loci associated with population-specific modifications can be colocalized with expression quantitative trait loci and single nucleotide polymorphisms previously identified for complex traits with known racial disparities. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression.