利用杉木的F1代群体构建遗传连锁图谱

对于杉木 1∶1分离的分子标记位点 ,提出了一种新的构建遗传连锁图谱的策略。通过二点连锁分析 ,任意两个位点的连锁相和重组率可以得到推断和估计。对于一个连锁群中的最优排序 ,采用隐马尔可夫链模型的方法进行多位点的连锁分析。该作图方法比通常林木上所用的“拟测交”作图方法更有效。采用该作图策略 ,利用句容0号无性系 (♀ )×柔叶杉 (♂ )的F1代群体的AFLP分子标记数据重建了句容 0号无性系和柔叶杉的遗传连锁图谱。在句容 0号无性系的连锁图谱中 ,有 10 1个标记分布在 11个连锁群上 ,图谱的总长度为 2 2 82 6cM ,平均图距为 2 2 6cM ,单个连锁群上最多含有 17个标记 ,最少含有 5个标记 ;在柔叶杉的连锁图谱中 ,有 94个标记分布在 11个连锁群上 ,图谱的总长度为 2 5 6 5 8cM ,平均图距为 2 7 3cM ,单个连锁群上最多含有 16个标记 ,最少含有 4个标记。构建的句容 0号无性系和柔叶杉的遗传连锁图谱比原有的图谱分别增加了 2 6个标记和 2 8个标记 ,双亲的图谱共增加了 5 4个AFLP标记 ,使图谱上的分子标记总数达到 195个 ,双亲遗传图谱的跨度均超过了 2 0 0 0cM ,基本上达到了杉木基因组的长度 ,图谱的覆盖率接近于 10 0 %。利用新的作图方法可以较大提高分子标记在图谱上的分辨率 ,得到可认为是     

利用杉木的F1代群体构建遗传连锁图谱

对于杉木11分离的分子标记位点,提出了一种新的构建遗传连锁图谱的策略.通过二点连锁分析,任意两个位点的连锁相和重组率可以得到推断和估计.对于一个连锁群中的最优排序,采用隐马尔可夫链模型的方法进行多位点的连锁分析.该作图方法比通常林木上所用的"拟测交"作图方法更有效.采用该作图策略,利用句容0号无性系(♀)×柔叶杉(♂)的F1代群体的AFLP分子标记数据重建了句容0号无性系和柔叶杉的遗传连锁图谱.在句容0号无性系的连锁图谱中,有101个标记分布在11个连锁群上,图谱的总长度为2 282.6 cM,平均图距为22.6 cM,单个连锁群上最多含有17个标记,最少含有5个标记;在柔叶杉的连锁图谱中,有94个标记分布在11个连锁群上,图谱的总长度为2 565.8 cM,平均图距为27.3 cM,单个连锁群上最多含有16个标记,最少含有4个标记.构建的句容0号无性系和柔叶杉的遗传连锁图谱比原有的图谱分别增加了26个标记和28个标记,双亲的图谱共增加了54个AFLP标记,使图谱上的分子标记总数达到195个,双亲遗传图谱的跨度均超过了2 000 cM,基本上达到了杉木基因组的长度,图谱的覆盖率接近于100%.利用新的作图方法可以较大提高分子标记在图谱上的分辨率,得到可认为是覆盖了整个基因组的遗传连锁框架图.     

生物遗传的连锁和交换

处在同一条染色体的基因在一起遗传的现象称为连锁。由于来自双亲的同源染色体，在性细胞成熟分裂时发生交换而使原来在同一染色体上的基因不再在一起遗传的现象称为交换。连锁和交换是生物界的普遍现象。一个细胞有许多基因，如果它们各个分散，细胞分裂过程中子细胞就不可能准确地获得每个基因，因此连锁对于生命的延续是非常重要的。交换则能使染色体上的基因产生新的组合，是形成生物新类型的原因之一，它和育种工作有密切的关系。交换一般是对等的，但是也有非对等交换。非对等交换可以导致少量染色体重复，重复的染色体片段上的基因经…     

遗传标记作图的通用最大似然模型

作者在构建连锁图谱时,发现Newton-Raphson迭代求解似然方程组,即便纳入合子和配子选择因子,各基因型的估计值仍不能很好的接近实测值,本文提出了一种偏分离遗传标记作图的通用最大似然模型。     

生物遗传的代数结构

本文根据生物遗传的内在规律，在多基因座配子中构造了一类运算，阐明了生物遗传具有交换的R-代数的数学结构，从而使遗传问题可用代数方法解决。文中，利用这种代数所得到的因子频率定理，具有比Hardy-Weinberg平衡定律更为广泛的意义。同时，作为这种代数应用的例子，讨论了在连锁条件下群体基因型频率的计算问题，得到了一系列有意义的结果。     

三点自交法和两点最大似然法构建水稻F2群体分子标记连锁图谱的比较

根据连锁遗传的原理,列出了三点自交法和两点自交最大似然(ML)法估算显性标记遗传距离的具体步骤和算法,将水稻F2群体含香味基因Aro及其连锁的RFLP数据转变为显性标记数据后,用上述两种方法构建的连锁图谱与用MAPMAKER软件计算共显性数据得到的图谱排序相同、标记间距离相近．但是标记数据存在较大程度偏分离时,由三点自交法构建的图谱中标记间图距有增大趋势．作者为提高作图精确性,简化计算过程,讨论了三点自交法对估算重组值的影响及其在分子标记作图中的应用价值,并建议将共显性标记转变为显性标记时进行两次自交ML法估算。     

林木全同胞群体的多位点连锁分析

多位点连锁分析是构建人类以及动植物的遗传连锁图谱的关键步骤之一。但是由于林木遗传背景的复杂性,多位点连锁分析在林木的全同胞群体中还没有得到应用．本文将多位点连锁分析应用到林木的F1代全同胞群体中．对于全同胞群体的任意分离比的两个位点,给出了在不同的连锁相下从一个位点到另一个位点的转移概率矩阵．对于给定的一列标记位点,考虑了不同分离比位点以及两位点间的连锁相信息,采用隐马尔可夫链模型计算极大似然函数和相邻位点间的重组率．本文的方法有助于构建完整的高密度的林木遗传连锁图谱．     

学习"三点测验"应注意的几个问题

三点测验是普通遗传学的学习难点,正确理解这部分内容中出现的新概念是克服难点的关键。下面就相关问题进行讨论。１　区别交换率与重组率概念重组率：杂合体在形成配子时,非等位基因之间重新组合产生重组合类型配子的频率,等于杂合体测交后代中重组合类型个体占测交后代总数的百分率。在连锁遗传中,重组率是指位于同源染色体上的非等位基因之间发生重新组合产生的重组合类型配子的百分率。交换率：同源非姊妹染色单体上两个基因之间发生交换的频率。在连锁遗传中,同源非姊妹染色单体之间对等片段在减数分裂前期Ⅰ的交换,使其所携带的…     

基于F2群体的香菇遗传图谱构建及其在QTL定位中的应用

以171个F2双核体菌株为作图群体,通过相互配对的2个单核体的基因型推断双核体基因型,构建了第一张基于双核体群体的香菇遗传图谱。该图谱包含分布于15个连锁群的459个标记,覆盖长度为989.7cM,平均标记间隔为2.2cM。此外,以此双核体群体作为表型分离群体,定位了6个与香菇双核体菌丝生长速度相关的QTLs,位于5个连锁群上。采用全同胞单核体随机交配策略,易于构建相对大的双核体群体,用于连锁图构建和QTL定位。研究表明,在食用菌连锁图谱构建及QTL定位研究中,利用F2群体,可能为提高遗传作图效率,解决作图群体与表型分离群体间不一致问题提供新的途径。     

连锁值——表述基因连锁强度的新参数

在遗传学中,同一染色体上基因之间的连锁强度是用交换率表示的.一般而言,交换率越高,基因连锁强度越低.但交换率不是基因连锁强度的最方便的量度,因为利用交换率来计算具有连锁交换现象的杂交后代分离比例时,必须区分相引组和相斥组两种不同的亲本交配情形.在相引组,一个亲本具有两个显性性状,另一个亲本具有两个隐性性状;在相斥组,两个亲本各具有一个显性性状和一个隐性性状。这两种情形下的配子比例和F_2分     

Synaptonemal complexes in insects

The synaptonemal complex (SC) is the key nuclear element formed in meiotic prophase I to join 2 homologous chromosomes at the pachytene bivalent. It is a highly conserved structure that is universally present in eukaryotes. The SC is presented as a tripartite protein structure, which consists of 2 lateral elements and a central region. In insects, the central region is particularly distinct and highly ordered. This made it possible to describe the fine structure of the central region and propose a model of its architecture. Chromatid DNA is arranged in chromatin loops extending radially from the SC. The loops appear to consist of a basic chromatin fiber with a diameter of 20–30 nm. In many insect species, synaptonemal polycomplexes occur in postpachytene cells. They represent one of the possible ways of SC degradation. Another process, which occurs beyond pachytene, is the formation of proteinaceous chromatid axis, the silver-stained chromatid core. Based on results in insect models, the chromatid cores have been related to the structure and formation of the SC. Research on insect models significantly contributed to understanding individual steps of the SC formation and temporal sequence of chromosome pairing. These include the formation of lateral elements of the SC, pairing initiation, interlocking of chromosomes, and synapsis of homologous chromosomes. Attention is also given to non-homologous pairing, including synaptic adjustment, correction of pairing, and pairing of sex chromosomes. In the next section, chiasmatic and achiasmatic modes of meiosis are compared with respect to the SC formation. In the chiasmatic mode, the SCs display recombination nodules that are believed to mediate the process of recombination. These nodules were discovered in insects, and indirect evidence for their role comes from insects. Two different examples of achiasmatic meiosis, occurring in the heterogametic sex of several insect orders, are given: one involves the SC formation, whereas in the other, SCs are absent. Finally, the potential of SC karyotyping for analysis of the insect genome is discussed.     

Monte Carlo simulations on marker grouping and ordering

Four global algorithms, maximum likelihood (ML), sum of adjacent LOD score (SALOD), sum of adjacent recombinant fractions (SARF) and product of adjacent recombinant fraction (PARF), and one approximation algorithm, seriation (SER), were used to compare the marker ordering efficiencies for correctly given linkage groups based on doubled haploid (DH) populations. The Monte Carlo simulation results indicated the marker ordering powers for the five methods were almost identical. High correlation coefficients were greater than 0.99 between grouping power and ordering power, indicating that all these methods for marker ordering were reliable. Therefore, the main problem for linkage analysis was how to improve the grouping power. Since the SER approach provided the advantage of speed without losing ordering power, this approach was used for detailed simulations. For more generality, multiple linkage groups were employed, and population size, linkage cutoff criterion, marker spacing pattern (even or uneven), and marker spacing distance (close or loose) were considered for obtaining acceptable grouping powers. Simulation results indicated that the grouping power was related to population size, marker spacing distance, and cutoff criterion. Generally, a large population size provided higher grouping power than small population size, and closely linked markers provided higher grouping power than loosely linked markers. The cutoff criterion range for achieving acceptable grouping power and ordering power differed for varying cases; however, combining all situations in this study, a cutoff criterion ranging from 50 cM to 60 cM was recommended for achieving acceptable grouping power and ordering power for different cases.     

Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach

Quantitative trait loci (QTL) affecting the phenotype of interest can be detected using linkage analysis (LA), linkage disequilibrium (LD) mapping or a combination of both (LDLA). The LA approach uses information from recombination events within the observed pedigree and LD mapping from the historical recombinations within the unobserved pedigree. We propose the Bayesian variable selection approach for combined LDLA analysis for single-nucleotide polymorphism (SNP) data. The novel approach uses both sources of information simultaneously as is commonly done in plant and animal genetics, but it makes fewer assumptions about population demography than previous LDLA methods. This differs from approaches in human genetics, where LDLA methods use LA information conditional on LD information or the other way round. We argue that the multilocus LDLA model is more powerful for the detection of phenotype–genotype associations than single-locus LDLA analysis. To illustrate the performance of the Bayesian multilocus LDLA method, we analyzed simulation replicates based on real SNP genotype data from small three-generational CEPH families and compared the results with commonly used quantitative transmission disequilibrium test (QTDT). This paper is intended to be conceptual in the sense that it is not meant to be a practical method for analyzing high-density SNP data, which is more common. Our aim was to test whether this approach can function in principle.     

Linkage between the loci for transferrin and ceruloplasmin in pigs

Summary. Evidence for genetic linkage between the loci for transferrin ( Tf ) and ceruloplasmin ( Cp ) in pigs was presented. The results were based on a study of a single sire family comprising 35 informative offspring. No recombinants were observed. The recombination frequency was estimated to be in the range of 0 to 8%. This indicated that the recombination frequency between Tf and Cp loci in pigs may be much lower than that reported previously between these two loci in cattle and in human.     

Protein variation in Adh and Adh-related in Drosophila pseudoobscura. Linkage disequilibrium between single nucleotide polymorphisms and protein alleles

A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.     

Close linkage between the albumin and Gc loci in the horse

Evidence for close linkage between the structural loci for albumin and Gc protein in the horse was presented. A recombination frequency (c) of 0.009 ± 0.006 (95 % confidence limits: 0.001 < c < 0.032) was estimated. These results were based on a study of a large sire family comprising 223 offspring from informative matings. No evidence of linkage disequilibrium was observed in one horse population studied.     

Integrating genetic linkage maps with pachytene chromosome structure in maize

Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1). all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2). each RN corresponds to one crossover, and (3). the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r(2) = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.     

Recombination patterns reveal information about centromere location on linkage maps

Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres – an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half‐tetrad analyses. We validate the method on a linkage map for sockeye salmon (Oncorhynchus nerka) with known centromeric regions. Further tests suggest that the method will work well in other salmonids and other eukaryotes. However, the method performed weakly when applied to a male linkage map (rainbow trout; O. mykiss) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations, our method should work well for high‐density maps in species with strong recombination interference and will enrich many existing and future mapping resources.     

The search for heterogeneity in insulin-dependent diabetes mellitus (IDDM): linkage studies, two-locus models, and genetic heterogeneity

One hundred families with insulin-dependent diabetes mellitus (IDDM) were analyzed for linkage with 27 genetic markers, including HLA, properdin factor B (BF), and glyoxalase 1(GLO) on chromosome 6, and Kidd blood group (Jk) on chromosome 2. The linkage analyses were performed under several different genetic models. An approximate correction for two-locus linkage analysis was developed and applied to four markers. Two different heterogeneity tests were implemented and applied to all the markers. One, the Predivided-Sample Test, utilizes various criteria thought to be relevant to genetic heterogeneity in IDDM. The other, the Admixture Test, looks for heterogeneity without specifying a prior how the sample should be divided. Results continued to support linkage of IDDM with three chromosome 6 markers: HLA, BF, and GLO. The total lod score for Kidd blood group, under the recessive model with 20% penetrance, is 1.63--down 1.2 from the 2.83 reported by us earlier. The only other marker whose lod score exceeded 1.0 under any model was pancreatic amylase (AMY2). The two-locus correction, which involved lowering the penetrance values used in the analysis, affected estimates of theta (recombination fraction) but did not markedly change the lod scores themselves. There was little evidence for heterogeneity within any of the lod scores, under either the Predivided-Sample Test or the Admixture Test.     

The effect of undetected recombination on genealogy sampling and inference under an isolation‐with‐migration model

Many methods for fitting demographic models to data sets of aligned sequences rely upon an assumption that the data have a branching coalescent history without recombination within regions or loci. To mitigate the effects of the failure of this assumption, a common approach is to filter data and sample regions that pass the four‐gamete criterion for recombination, an approach that allows data to run, but that is expected to detect only a minority of recombination events. A series of empirical tests of this approach were conducted using computer simulations with and without recombination for a variety of isolation‐with‐migration (IM) model for two and three populations. Only the IMa3 program was used, but the general results should apply to related genealogy‐sampling‐based methods for IM models or subsets of IM models. It was found that the details of sampling intervals that pass a four‐gamete filter have a moderate effect, and that schemes that use the longest intervals, or that use overlapping intervals, gave poorer results. A simple approach of using a random nonoverlapping interval returned the smallest difference between results with and without recombination, with the mean difference between parameter estimates usually less than 20% of the true value (usually much less). However, the posterior probability distributions for migration rates were flatter with recombination, suggesting that filtering based on the four‐gamete criterion, while necessary for methods like these, leads to reduced resolution on migration. A distinct, alternative approach, of using a finite sites mutation model and not filtering the data, performed quite poorly.