Detecting Structure of Haplotypes and Local Ancestry

We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local ancestry of admixed individuals. Our method outperforms competing state-of-the-art methods, particularly for regions of small ancestral track lengths. Applying our method to Mexican samples in HapMap3, we found two regions on chromosomes 6 and 8 that show significant departure of local ancestry from the genome-wide average. A software package implementing the methods described in this article is freely available at http://bcm.edu/cnrc/mcmcmc.     

江浙沪地区汉族人群HLA单体型研究

利用HLA血清学和分子生物学分型方法对江浙沪地区汉族人群166对夫妻进行HLA-A,B和DR B1单体型调查,并分析HLA单体型的分布特征.结果显示,江浙沪地区汉族人群HLA-A2,A11,A24,B13,B46,B60,DRB104,DRB108,DRB109,DRB112和DRB115有较高的频率分布(＞10%).研究中发现HLA-A-B,B-DRB1单体型分别有128条和182条,占理论单体型总数的19.28%(128/664)和27.41%(182/664).其中有18种A-B单体型频率大于0.5%(连锁不平衡参数△＞0),有23种B-DRB1单体型频率大于0.5%(△＞0).A-B-DRB1单体型有351条,占理论单体型总数的52.86%(351/664),其中8种单体型频率大于0.5%(△＞0),A 30-B13-DRB107(4.22 %),A2-B46-DRB109(3.77%),A33-B58-DRB117(3.01%),A33-B58-DRB113.1(1.81%)和A11-B75-DRB112(1.51%)是最常见单体型.江浙沪地区汉族人群HLA单体型有其自身分布特点,遗传特征介于南北汉族之间,在东亚人群中中国汉族群体HLA多态性较为丰富.     

中国人群中STK15基因内两种非同义SNP的连锁不平衡和单体型分析

STK15基因编码一种丝氨酸苏氨酸蛋白激酶,哺乳动物细胞中其过量表达将导致中心体扩增、染色体不稳定和细胞癌变。STK15基因外显子3中有3种非同义单核苷酸多态(SNP),即：91A→T(131F)、169G→A(V571)和311C→T(S104L)。新近研究发现,91A→T与人类肿瘤遗传易感性相关。应用PCR-RFLP技术确定了91A→T(131F)和169G→A(V571)两种SNP在中国人群中的基因型和单体型。采用巢式PCR方法扩增了193例正常个体的DNA样品,通过错配正向巢式内引物引入EcoRⅠ酶切位点。巢式PCR扩增产物用限制性内切酶EcoRⅠ和ACCⅡ双酶切消化,其中EcoRⅠ能酶切91A,AccⅡ能切开169G,用聚丙烯酰胺凝胶电泳银染法鉴定双酶切结果,发现了4种可能的单体型中的3种,其单体型频率分别为：p(91A-169G)=68．65％,p(91T-169A)=10．88％,p(91T-169G)=20．47％,p(91A-169A)=0％;它们组成的6种基因型及频率分别为：91A-169G／91A-169G(46．11％),91A-169G／91T-169A(14．51％),91A-169G／91T-169G(30．57％)．91T-169G／91T-169G(3．11％),91T-169G／91T-169A(4．15％),91T-169A／91T-169A(1．55％)。等位基因及单体型数据分析结果表明,91A→T(131F)和169G→A(V571)之间存在连锁不平衡。     

中国美利奴羊MHC-DRB1 exon2单倍型构建及与布鲁氏菌病易感性关联分析

为研究中国美利奴羊MHC-DRB1基因exon2单倍型与布鲁氏菌易感性的关联性,本实验采用PCR直接测序法对40例布鲁氏菌血清检测阳性和阴性个体MHC-DRB1 exon2的单核苷酸多态性(SNPs)进行检测,而后运用SHEsis在线软件对筛选的SNPs构建单倍型并进行单倍型关联分析.结果显示,在270 bp的序列内共检测到41个SNPs,经Hardy-Weinberg平衡检测筛选出符合条件的SNPs有29个,连锁不平衡发现9个连锁不平衡域,而且每个block中的SNPs两两之间存在强连锁不平衡.单倍型分析显示,由于连锁不平衡存在,仅构建9种单倍型,其中只有Hap8和Hap9两种单倍型在病例-对照组中比较差异有统计学意义(P0.05).     

中国汉族人群MASP2基因单核苷酸多态性的连锁不平衡和单体型分析

目的：探讨中国汉族人群甘露糖结合凝集素相关的丝氨酸蛋白酶（MASP2）基因单核苷酸多态性（SNP）的连锁不平衡和单体型,为相关研究提供更为详实的数据。方法：选取30例广州汉族无关个体,用重新测序的方法进行MASP2基因SNP的发掘,构建连锁不平衡（LD）模式,与HapMap公布的其他4个人群数据相比,并选择4个标签SNP（tagSNP）在232例北京汉族个体和291例广州汉族个体中分析MASP2的多态性和单体型。结果和结论：对MASP2的重测序共检测出16个SNP,LD分析显示来自中国不同地区人群的LD模式基本相同,与来自美国和日本的人群存在差异;北京和广州地区汉族人群tagSNP的等位基因和基因型频率分布不存在显著差异。     

Polymorphism identification in the goat KITLG gene and association analysis with litter size

This study reported the analysis of KIT ligand (KITLG) gene polymorphisms in 681 goats of three breeds: Xinong Saanen (SN), Guanzhong (GZ), and Boer (BG). In addition, the study identified three allelic variants: g.769T>C and g.817G>T in SN and GZ breeds, and g.9760G>C in the three goat breeds. The g.769T>C and g.817G>T loci were closely linked (r² > 0.33). All the single nucleotide polymorphism loci were in Hardy–Weinberg disequilibrium (P < 0.05). Significant associations were found for litter size with all three loci. Therefore, these results suggest that the KITLG gene is a strong candidate gene affecting litter size in goats.     

Haplotype Frequency Distribution and Linkage Disequilibrium Analysis of Single Nucleotide Polymorphisms at the Human FMO3 Gene Locus

We analyzed flavin-containing monooxygenase 3 (FMO3) polymorphisms, haplotype structure, and linkage disequilibrium (LD) in 256 Han Chinese and 50 African-American individuals to compare their haplotype frequencies and LD with other world populations. For the Han Chinese, genotyping of three haplotype tag single nucleotide polymorphisms (E158K, V257M, and E308G) was performed by polymerase chain reaction (PCR)-restriction fragment length polymorphism. For the African-Americans, genotyping of all coding exons was performed by modified PCR-single strand conformational polymorphism. Haplotype frequencies, LD, and evolutionary rates were inferred and estimated computationally. There were significant differences in haplotype frequency distribution and LD pattern among Han Chinese, African-Americans, and other world populations. Four major haplotypes of Han Chinese were EVE, KVE, EME, and EVG. Two major haplotypes of African-Americans were EVE and KVE. We found that sites 158 and 257 are in significant LD in both populations. This is the first report comparing FMO haplotypes and LD of Han Chinese with African-Americans. The data presented here justify further pharmacogenetic studies for potentially optimizing recommended drug dosages and evaluating relationships with disease processes.     

Haplotype structure and copy number polymorphism of the beta‐defensin 7 genes in diverse chicken breeds

Beta‐defensins is a family of avian peptides related to the innate immune system. Copy number variation was recently reported for the avian beta‐defensin 7 gene (AvBD7) between the highly inbred Leghorn and Fayoumi lines. Here, we examined copy number variants in 35 different chicken breeds and found that 31 of them have at least the same representation of the duplicated AvBD7 allele. We also found haplotypes upstream of the AvBD6 regions that are strongly linked to the AvBD7 duplication. We observed a strong linkage disequilibrium spanning of the upstream region of the AvBD6 gene, with two SNPs being flanking markers to detect duplication of the AvBD7.     

Linkage disequilibrium structures in cattle and their application to breed identification testing

We examined the extent of linkage disequilibrium (LD) block lengths in four breed populations: Japanese Black, Angus, Hereford and Holstein. Three chromosomal regions in which QTL were previously mapped in Japanese Black populations were scanned with 84 microsatellite markers. The estimated LD lengths in these four purebred populations varied from 535 to 683 kb, which is much shorter than the values reported previously. Our findings suggest that QTL can be mapped in sub-centimorgan regions in these populations using an LD-mapping method. We also developed breed identification methods to distinguish Japanese Black from Angus, Hereford, Holstein and F₁ animals (Japanese Black × Holstein) respectively using the haplotypic frequencies of a pair of markers in the breed populations. After assessing the distributions of posterior probabilities to be Japanese Black, we obtained several pairs of markers that completely distinguished Japanese Black from the other breeds. We also obtained several combinations of six markers that completely distinguished Japanese Black animals from F₁ animals.     

Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle

The objective of this study was to quantify the extent of linkage disequilibrium (LD) on bovine chromosomes 19 and 29 and to study the pattern of selection signatures in beef and dairy breeds (Angus and Holstein) of Bos taurus. The extent of LD was estimated for 370 and 186 single nucleotide polymorphism markers on BTA19 and 29 respectively using the square of the correlation coefficient (r(2)) among alleles at pairs of loci. A comparison of the extent of LD found that the decline of LD followed a similar pattern in both breeds. We observed long-range LD and found that LD dissipates to background levels at a locus separation of about 20 Mb on both chromosomes. Along each chromosome, patterns of LD were variable in both breeds. We find that a minimum of 30 000 informative and evenly spaced markers would be required for whole-genome association studies in cattle. In addition, we have identified chromosomal regions that show some evidence of selection for economically important traits in Angus and Holstein cattle. The results of this study are of importance for the design and application of association studies.     

Novel strategies to mine alcoholism-related haplotypes and genes by combining existing knowledge framework

High-throughout single nucleotide polymorphism detection technology and the existing knowledge provide strong support for mining the disease-related haplotypes and genes. In this study, first, we apply four kinds of haplotype identification methods (Confidence Intervals, Four Gamete Tests, Solid Spine of LD and fusing method of haplotype block) into high-throughout SNP genotype data to identify blocks, then use cluster analysis to verify the effectiveness of the four methods, and select the alcoholism-related SNP haplotypes through risk analysis. Second, we establish a mapping from haplotypes to alcoholism-related genes. Third, we inquire NCBI SNP and gene databases to locate the blocks and identify the candidate genes. In the end, we make gene function annotation by KEGG, Biocarta, and GO database. We find 159 haplotype blocks, which relate to the alcoholism most possibly on chromosome 1∼22, including 227 haplotypes, of which 102 SNP haplotypes may increase the risk of alcoholism. We get 121 alcoholism-related genes and verify their reliability by the functional annotation of biology. In a word, we not only can handle the SNP data easily, but also can locate the disease-related genes precisely by combining our novel strategies of mining alcoholism-related haplotypes and genes with existing knowledge framework. Supported by the National Natural Science Foundation of China (Grant Nos. 30570424, 60601010 and 30600367), the National High-Tech Research and Development Program of China, (Grant No.2007AA02Z329), the Key Science and Technology Program of Heilongjiang Province(Grant No.GB03C602-4), Natural Science Foundation of Heilongjiang Province (Grant No. F2008-02), Youth Science Foundation of Harbin Medical University (Grant No. 060045) and Science Foundation of Heilongjiang Province Education Department (Grant Nos. 11531113 and 1152hq28).     

Patterns and Causes of Signed Linkage Disequilibria in Flies and Plants

Most empirical studies of linkage disequilibrium (LD) study its magnitude, ignoring its sign. Here, we examine patterns of signed LD in two population genomic data sets, one from Capsella grandiflora and one from Drosophila melanogaster. We consider how processes such as drift, admixture, Hill–Robertson interference, and epistasis may contribute to these patterns. We report that most types of mutations exhibit positive LD, particularly, if they are predicted to be less deleterious. We show with simulations that this pattern arises easily in a model of admixture or distance-biased mating, and that genome-wide differences across site types are generally expected due to differences in the strength of purifying selection even in the absence of epistasis. We further explore how signed LD decays on a finer scale, showing that loss of function mutations exhibit particularly positive LD across short distances, a pattern consistent with intragenic antagonistic epistasis. Controlling for genomic distance, signed LD in C. grandiflora decays faster within genes, compared with between genes, likely a by-product of frequent recombination in gene promoters known to occur in plant genomes. Finally, we use information from published biological networks to explore whether there is evidence for negative synergistic epistasis between interacting radical missense mutations. In D. melanogaster networks, we find a modest but significant enrichment of negative LD, consistent with the possibility of intranetwork negative synergistic epistasis.     

Prediction of identity by descent probabilities from marker-haplotypes

The prediction of identity by descent (IBD) probabilities is essential for all methods that map quantitative trait loci (QTL). The IBD probabilities may be predicted from marker genotypes and/or pedigree information. Here, a method is presented that predicts IBD probabilities at a given chromosomal location given data on a haplotype of markers spanning that position. The method is based on a simplification of the coalescence process, and assumes that the number of generations since the base population and effective population size is known, although effective size may be estimated from the data. The probability that two gametes are IBD at a particular locus increases as the number of markers surrounding the locus with identical alleles increases. This effect is more pronounced when effective population size is high. Hence as effective population size increases, the IBD probabilities become more sensitive to the marker data which should favour finer scale mapping of the QTL. The IBD probability prediction method was developed for the situation where the pedigree of the animals was unknown (i.e. all information came from the marker genotypes), and the situation where, say T, generations of unknown pedigree are followed by some generations where pedigree and marker genotypes are known.     

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r(2) ≥ 0.3) in both traditional and village chickens at pairwise marker distances of ~10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling ~75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions.     

SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci

In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses of linkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large number of samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study with high efficiency. The platform has been well evaluated by several sets of real data.     

Genome-wide variation in the human and fruitfly: a comparison

Average levels of nucleotide diversity are ten-fold lower in humans than in the fruitfly, Drosophila melanogaster. Despite this difference, apparently as a result of a lower population size, patterns of genomic diversity are strikingly similar in being correlated with local rates of recombination, and influenced by similar interactions between positive natural selection and recombination. Both species also show lower levels of variation on average in non-African compared to African populations, reflecting a similar evolutionary history and perhaps both natural selection and founder effects in new environments.     

Phylogeography of Haplotypes of Five Microsatellites Located in a Low-recombination Region of the X Chromosome: Studies Worldwide and in Brazilian Populations

We studied five microsatellites (DXS995, DXS8076, DXS8114, DXS1002 and DXS1050) located in a region of very low recombination rate in the long arm of the human X chromosome (Xq13.3–Xq21.3). No recombination was seen in 291 meioses in CEPH families. To test whether haplotypes composed of the five microsatellites could differentiate among distinct human continental populations, we studied an international panel containing 72 males from Africa, Europe, Asia and the America. Haplotypic diversity was very high within these groups and no haplotypes were shared among them. This led to the hope that we might be able to identify continent-specific lineages. However, in a median joining network there was no clear discrimination of the different continental groups. We then tested whether we could identify X chromosomal lineages from different continental origins in Brazilians. We typed 180 white Brazilians from four different geographical regions and examined their proportions of haplotype sharing with Africans, Asians, Europeans and Amerindians. No phylogeographical patterns emerged from the data. Moreover, there were several instances of the same haplotype being shared by many (and in one instance all) groups, suggesting that recombination might be occurring. We thus studied pairwise the level of linkage disequilibrium (LD) between the microsatellites. No detectable linkage disequilibrium between the most external loci DXS995 and DXS1050 was observed. Thus, even though recombination may be absent on short time spans, as seen in the CEPH pedigrees, on a long term basis it occurs often enough to dissipate all linkage disequilibrium. On the other hand, we observed very strong linkage disequilibrium between the pairs DXS995/DXS8076 and DXS1002/DXS8114, raising the possibility of resequencing the segment between them to identify single nucleotide polymorphisms (SNPs) in their intervals. The combination of X-linked microsatellites and SNPs in strong linkage disequilibrium might provide a powerful new tool to investigate human demographic history.     

Linkage disequilibrium and association studies in higher plants: Present status and future prospects

During the last two decades, DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant systems. Therefore, alternative approaches have been suggested, and one of these approaches makes use of linkage disequilibrium (LD)-based association analysis. Although this approach of association analysis has already been used for studies on genetics of complex traits (including different diseases) in humans, its use in plants has just started. In the present review, we first define and distinguish between LD and association mapping, and then briefly describe various measures of LD and the two methods of its depiction. We then give a list of different factors that affect LD without discussing them, and also discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in plant genomics research and summarize the present status of LD research in different plant genomes. In the end, we discuss briefly the future prospects of LD research in plants, and give a list of softwares that are useful in LD research, which is available as electronic supplementary material (ESM) Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Identification of Single Nucleotide Polymorphisms and Analysis of Linkage Disequilibrium in Different Bamboo Species Using the Candidate Gene Approach

Bamboos are one of the most beautiful and useful plants on Earth. The genetic background and population structure of bamboos are well known, which helps accelerate the process of artificial domestication of bamboo. Partial sequences of six genes involved in nitrogen use efficiency in 32 different bamboo species were analyzed for occurrence of single nucleotide polymorphisms (SNPs). The nucleotide diversity θw and total nucleotide polymorphisms π_T of the sequenced DNA regions was 0.05137 and 0.03332, respectively. Both πnonsyn /πsyn and Ka/Ks values were <1. The nucleotide sequences of these six genes were inferred to be relatively conserved, and the haplotype diversity was relatively high. The results of evolutionary neutrality tests showed that the six genes were in line with neutral evolution, and that the NRT2.1 and AMT2.1 gene sequences may have experienced negative selection. An inter-SNP recombination event at the NRT2.1 gene in the all pooled sample, of all 32 bamboo species was the lowest at 0.0645, whereas the AMT gene recombination events were all >0.1. Estimation and analysis of linkage disequilibrium of five genes revealed that with the increase in nucleotide sequence length, the degree of SNP linkage disequilibrium decreased rapidly. We inferred the population genetic structure of 32 bamboo species based on the SNP loci of six genes with frequencies >18%. 32 bamboo species were divided into five categories, which indicated that the combined population of all bamboo species had obvious multivariate characteristics and was heterogeneous; red (Group 1) and green (Group 2) were the main groups.     

A genome‐wide scan for signatures of recent selection in Holstein cattle

The data from the newly available 50 K SNP chip was used for tagging the genome‐wide footprints of positive selection in Holstein–Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome‐wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P‐values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome‐wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.