德宏水牛微卫星标记分析的群体遗传变异

德宏水牛是云南省地方水牛的优良品种之一,为了进一步阐明其群体遗传变异和遗传结构,筛选了分别位于水牛14条染色体上的15对微卫星引物,对德宏水牛81个个体进行了检测分析.共检测到62个等位基因,每个座位等位基因数目从2到6个不等,平均等位基因数为4.13,该水牛群体期望杂合度和多态信息含量分别为0.6520±0.1526和0.5863±0.1789,各座位的遗传分化系数在0～0.0919之间,平均值为0.0202.每个座位的基因流较大,平均12.1502.研究结果表明德宏水牛群体遗传多样性较丰富,亚群间的遗传分化程度低,基因流较大,且很少发生近交.     

QTL Scanning for Rice Yield Using a Whole Genome SNP Array

High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line （RIL） population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.     

Excap: Maximization of Haplotypic Diversity of Linked Markers

Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choosing the right set of markers for forensic applications can be difficult and requires careful consideration. In particular, one wants to maximize the utility of the markers. Until now, this has mainly been done by hand.We propose an algorithm that finds the most informative subset of a set of markers. The algorithm uses a depth first search combined with a branch-and-bound approach. Since the worst case complexity is exponential, we also propose some data-reduction techniques and a heuristic.We implemented the algorithm and applied it to two forensic caseworks using mitochondrial DNA, which resulted in marker sets with significantly improved haplotypic diversity compared to previous suggestions. Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy.     

Characterization of the Soybean Genome Using EST-derived Microsatellite Markers

We generated a high-density genetic linkage map of soybean usingexpressed sequence tag (EST)-derived microsatellite markers.A total of 6920 primer pairs (10.9%) were designed to amplifysimple sequence repeats (SSRs) from 63 676 publicly availablenon-redundant soybean ESTs. The polymorphism of two parent plants,the Japanese cultivar ‘Misuzudaizu’ and the Chineseline ‘Moshidou Gong 503’, were examined using 10%polyacrylamide gel electrophoresis. Primer pairs showing polymorphismwere then used for genotyping 94 recombinant inbred lines (RILs)derived from a cross between the parents. In addition to previouslyreported markers, 680 EST-derived microsatellite markers wereselected and subjected to linkage analysis. As a result, 935marker loci were mapped successfully onto 20 linkage groups,which totaled 2700.3 cM in length; 693 loci were detected usingthe 668 EST-derived microsatellite markers developed in thisstudy, the other 242 loci were detected with 105 RFLP markers,136 genome-derived microsatellite markers, and one phenotypicmarker. We examined allelic variation among 23 soybean cultivars/linesand a wild soybean line using 668 mapped EST-derived microsatellitemarkers (corresponding to 686 marker loci), in order to determinethe transferability of the markers among soybean germplasms.A limited degree of macrosynteny was observed at the segmentallevel between the genomes of soybean and the model legume Lotusjaponicus, which suggests that considerable genome shufflingoccurred after separation of the species and during establishmentof the paleopolyploid soybean genome.     

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF) ranging from 0.24 to 0.27). The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.     

Novel SNP Discovery in African Buffalo,Syncerus caffer,Using High-Throughput Sequencing

The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43–54% of the Bowtie SNPs and 57–58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.     

基于全基因组重测序SNP标记的148份马铃薯种质遗传多样性分析

为了解148份国内外四倍体马铃薯普通栽培种的遗传背景和亲缘关系,该研究通过第三代高通量测序手段进行全基因组重测序,以SNP为分子标记、遗传相似系数为指标,结合系谱信息,利用群体结构与聚类分析相结合的方法,分析该群体遗传多样性。结果表明:(1)通过有效过滤筛选后获得1 209 969个高质量SNP位点,明确定位在染色体水平上的SNP位点为1 192 472个,占比98.55%;除11号染色体没有位点分布外,5号染色体分布位点最多,7号染色体最少。(2)各品种间遗传相似系数在0.784～0.958之间,平均为0.842,且主要集中于0.800～0.880(有10 604个),占97.5%。(3)群体结构分析显示,将148份材料分为6个群组,Q值0.6的品种有36个,占比24.3%,遗传背景较单一的品种中,华北区育成品种有16个占44.4%,国外品种有13个占36.1%,二者共占80.5%,说明华北区育成品种及国外品种的遗传组分相对单一而且比例高于其他区域品种。(4)聚类分析结果表明148份马铃薯品种被划分为3个类群,‘中薯系列’、‘陇薯系列’及‘冀张薯系列’品种聚在一起有着一定的地理区域性,其他不同地理来源的马铃薯品种相互交错分布,说明育成区域的差别与亲缘关系并无必然联系,同时也说明各育种单位相互引种频繁,新品种选育过程中存在基因交流情况。群体结构分析与聚类分析分群结果基本吻合,相互验证。研究认为,马铃薯绝大部分普通栽培种品种间遗传相似性很高,遗传背景不够丰富,在育种中亟待引入新型种质,拓宽遗传基础。     

基于全基因组SNP分子标记分析青海云杉遗传结构

以张掖龙渠青海云杉（Picea crassifolia）无性系种子园中的106个青海云杉亲本无性系为研究材料,采用改良CTAB法,提取的青海云杉基因组DNA,构建SLAF文库并进行高通量测序,之后分析SLAF测序数据和筛选SNP位点,基于邻接法分析得到样品的聚类情况。研究得出：将测序的水稻日本晴reads与其参考基因组进行比对,显示本试验双端比对效率为95.33%,说明SLAF建库成功。本研究中所测序列的Q30较高,碱基测 序错误率低,测序质量高;本研究共开发4 058 883个SLAF标签,标签的平均测序深度为21.21×。共开发 12 275 765个青海云杉SNP标记,各青海云杉样本的SNP数量为1 890 934~4 487 841。利用已开发的高质量青海云杉SNP标记,构建了106个青海云杉的系统发育树,发现来自不同种源的青海云杉在各组中分布比较均匀,不同种源的青海云杉多聚为一类。通过SNP标记和主成分分析,这些无性系来源于同一个祖先的可能性较大,表明无性系间亲缘关系相近。为今后遗传多样性的分析、遗传图谱的构建等提供了基础数据,也为青海云杉初级种子园去劣疏伐提供依据,为高世代种子园的营建奠定基础。     

High Density LD-Based Structural Variations Analysis in Cattle Genome

Genomic structural variations represent an important source of genetic variation in mammal genomes, thus, they are commonly related to phenotypic expressions. In this work, ∼770,000 single nucleotide polymorphism genotypes from 506 animals from 19 cattle breeds were analyzed. A simple LD-based structural variation was defined, and a genome-wide analysis was performed. After applying some quality control filters, for each breed and each chromosome we calculated the linkage disequilibrium (r ²) of short range (≤100 Kb). We sorted SNP pairs by distance and obtained a set of LD means (called the expected means) using bins of 5 Kb. We identified 15,246 segments of at least 1 Kb, among the 19 breeds, consisting of sets of at least 3 adjacent SNPs so that, for each SNP, r ² within its neighbors in a 100 Kb range, to the right side of that SNP, were all bigger than, or all smaller than, the corresponding expected mean, and their P-value were significant after a Benjamini-Hochberg multiple testing correction. In addition, to account just for homogeneously distributed regions we considered only SNPs having at least 15 SNP neighbors within 100 Kb. We defined such segments as structural variations. By grouping all variations across all animals in the sample we defined 9,146 regions, involving a total of 53,137 SNPs; representing the 6.40% (160.98 Mb) from the bovine genome. The identified structural variations covered 3,109 genes. Clustering analysis showed the relatedness of breeds given the geographic region in which they are evolving. In summary, we present an analysis of structural variations based on the deviation of the expected short range LD between SNPs in the bovine genome. With an intuitive and simple definition based only on SNPs data it was possible to discern closeness of breeds due to grouping by geographic region in which they are evolving.     

Water Buffalo Genome Science Comes of Age

The water buffalo is vital to the lives of small farmers and to the economy of many countries worldwide. Not only are they draught animals, but they are also a source of meat, horns, skin and particularly the rich and precious milk that may be converted to creams, butter, yogurt and many cheeses. Genome analysis of water buffalo has advanced significantly in recent years. This review focuses on currently available genome resources in water buffalo in terms of cytogenetic characterization, whole genome mapping and next generation sequencing. No doubt, these resources indicate that genome science comes of age in the species and will provide knowledge and technologies to help optimize production potential, reproduction efficiency, product quality, nutritional value and resistance to diseases. As water buffalo and domestic cattle, both members of the Bovidae family, are closely related, the vast amount of cattle genetic/genomic resources might serve as shortcuts for the buffalo community to further advance genome science and biotechnologies in the species.     

Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection

Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.     

SNP-为人类基因组描绘新的蓝图

几乎所有的慢性疾病都或多或少与遗传因素有关。在过去的二十年中,对人类遗传学的研究使人们认识到,理清各种疾病中遗传因素所起的作用将对诊断学、治疗学以及预防医学等各个领域带来革命。同时,了解遗传因素在疾病病因学中所占的地位也有利于人们对非遗传的环境因素对...     

Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets.     

利用SSR标记技术研究棉属A、D染色体组的进化

利用SSR分子标记技术,对棉属A、D染色体二倍体及四倍体代表棉种进行了遗传多样性分析。供试的10个二倍体代表棉种间遗传多态性丰富,分子聚类结果与Fryxell棉属分类结果相同。分子水平上进一步揭示出属于D染色体组的拟似棉与其他D染色体组棉种的相似系数最低,A,D染色体组间相似系数很高,该结果支持拟全民族似棉是D染色体组最原始棉种,棉属不同染色体组是共同起源,单元进化的理论,利用栽培的异源四倍体棉种不太适于研究棉属A、D染色体组的进化。     

Buffalo Herd Structure and its Repercussions for Condition of Individual African Buffalo Cows

The African buffalo Syncerus caffer was studied in Lake Manyara National Park, Tanzania. Emphasis was placed on the study of (individual) buffalo cows, which live in mixed herds. Buffalo herds are discrete social units and females were never observed in another herd than their own. The herd showed a structure with respect to the distribution of sex-age classes. Individual cows generally kept the same location within the herd. The location in the herd appeared to be coupled to food intake and was strongly related to physical condition. The best location (highest intake and best condition) was between the front and the centre of the herd, the worst location was the rear of the herd (when moving or grazing). Females with calves appeared to have the highest position in the hierarchy as determined from the rate of displacement over food; adult bulls did not interact with cows. Few births were observed during the late dry season and it appears that there is a calving peak at the end of the long rains. Conception rate increased when cows increased in condition and dropped when cows lost condition. Cows showed a strong seasonality in condition but bulls on average hardly changed in condition, except for a loss in condition during the inferred conception peak. Buffalo herds in Manyara showed a fusion-fission pattern independent of season but strongly influenced by the size of the herd: large herds split more often than smaller ones. In large herds, buffalo grazed closer together than in small herds and it appeared likely that competition was more severe in large herds. Animals in the rear of a large herd lost condition faster during the dry season than animals in the best location in the herd, and especially cows in the rear split off most frequently from the herd to graze in a smaller fragment. From the literature on cattle, it is inferred that the reproductive success of cows in the rear of the herd will be lower than of cows in the best location, and this differential is confirmed by the behaviour of adult bulls. It is as yet unclear what the advantage is for adult cows in the rear of a large herd to stay in that herd but the sharing of information with more successful individuals seems a good candidate.     

Sweet Cherry Cultivar Identification by High-Resolution-Melting (HRM) Analysis Using Gene-Based SNP Markers

Single nucleotide polymorphisms (SNPs) provide an important tool for cultivar identification in studies of genetic diversity, but until now, the time-consuming and costly nature of DNA sequencing has limited the identification of new markers. Herein, we describe the application of high-resolution melting (HRM), a recent enhancement to traditional DNA melting analysis, for the characterization of polymerase chain reaction products and the identification of nine gene-based SNPs for distinguishing the main Greek sweet cherry cultivars. The expected heterozygosity value of nine SNPs averaged at 0.518. The combined power of discrimination for the SNP markers was 0.999969. The ability of HRM to accurately discern nucleotide changes in a DNA sequence makes it a cost- and time-effective alternative to traditional sequencing for the detection of gene-based SNPs.     

雄性不交换条件下F2群体高密度分子区间标记QTL的精确作图

提出雄性不交换条件下F2群体间标记定位QTL的相关方法，研究高密度分子标记存在强烈交叉干涉时，QTL的精确定位方法。     

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

Background

The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay.

Methodology/Principal Findings

A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina''s Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274.

Conclusions/Significance

Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.     

居群遗传结构研究中显性标记数据方法初探

为对比显性标记应用于居群遗传结构研究时不同统计参数的适用性,利用RAPD技术对中国5个居群的100个疣粒野生稻个体进行了遗传结构分析。在衡量居群遗传多样性水平时,多态位点比率（PPB）会低估遗传变异的量,其价值不如Shannon多样性指数和Nei基因多样性指数,而采用Nei指数时不必进行Lynch-Milligan矫正。对个体间遗传关系进行分析时,17种遗传相似性指数矩阵两两之间的Mantel检测都表现出极显著的相关性（r＞0.95,t＞t     

Mixed Model Methods for Genomic Prediction and Variance Component Estimation of Additive and Dominance Effects Using SNP Markers

We established a genomic model of quantitative trait with genomic additive and dominance relationships that parallels the traditional quantitative genetics model, which partitions a genotypic value as breeding value plus dominance deviation and calculates additive and dominance relationships using pedigree information. Based on this genomic model, two sets of computationally complementary but mathematically identical mixed model methods were developed for genomic best linear unbiased prediction (GBLUP) and genomic restricted maximum likelihood estimation (GREML) of additive and dominance effects using SNP markers. These two sets are referred to as the CE and QM sets, where the CE set was designed for large numbers of markers and the QM set was designed for large numbers of individuals. GBLUP and associated accuracy formulations for individuals in training and validation data sets were derived for breeding values, dominance deviations and genotypic values. Simulation study showed that GREML and GBLUP generally were able to capture small additive and dominance effects that each accounted for 0.00005–0.0003 of the phenotypic variance and GREML was able to differentiate true additive and dominance heritability levels. GBLUP of the total genetic value as the summation of additive and dominance effects had higher prediction accuracy than either additive or dominance GBLUP, causal variants had the highest accuracy of GREML and GBLUP, and predicted accuracies were in agreement with observed accuracies. Genomic additive and dominance relationship matrices using SNP markers were consistent with theoretical expectations. The GREML and GBLUP methods can be an effective tool for assessing the type and magnitude of genetic effects affecting a phenotype and for predicting the total genetic value at the whole genome level.