Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers

The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE.     

Genetic diversity in Egyptian and Italian goat breeds measured with microsatellite polymorphism.

Seven microsatellite markers were used to study genetic diversity of three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian (Maltese and Montefalcone) goat breeds. The microsatellites showed a high polymorphic information content (PIC) of more than 0.5 in most of the locus-breed combinations and indicated that the loci were useful in assessing within- and between-breed variability of domestic goat (Capra hircus). The expected heterozygosity of the breeds varied from 0.670 to 0.792. In the geographically wider distributed Egyptian Baladi breed there were indications for deviations from random breeding. Analysis of genetic distances and population structure grouped the three Egyptian goat breeds together, and separated them from the two Italian breeds. The studied Mediterranean breeds sampled from African and European populations seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations.     

我国6个绵(山)羊群体遗传分化的微卫星分析

为进一步了解我国绵(山)羊群体的品种特性及其遗传分化,本文利用微卫星标记对我国6个绵(山)羊群体遗传分化进行了分析。采用中心产区典型群随机抽样方法用聚丙烯酰胺凝胶电泳检测乌珠穆沁羊7个微卫星位点,并引用同实验室小尾寒羊、滩羊、湖羊、同羊、长江三角洲白山羊(参照群体)的相关资料进行群体遗传分化水平分析。研究表明:7个微卫星位点在乌珠穆沁羊、小尾寒羊、滩羊、湖羊、同羊、山羊这6个品种中均存在遗传多态性,各座位等位基因均较丰富。根据标准遗传距离、DA遗传距离以及模糊相容关系进行聚类分析,湖羊与同羊首先聚为一类,乌珠穆沁羊和小尾寒羊聚为一类,然后与滩羊聚为一类,5个绵羊品种最后与山羊相聚。     

微卫星DNA标记在三个山羊品种中的遗传多态性研究

利用四个微卫星标记对波尔山羊、太行山羊和河北奶山羊的等位基因频率、群体多态信息含量、有效等位基因数和杂合度进行了遗传检测。结果表明：四个微卫星位点在波尔山羊、太行山羊和河北奶山羊三个品种中存在多态性。可以用于山羊遗传多样性的评估；位点OarFCB11变异最大，位点MCM38变异最小，从不同品种来看，太行山羊的遗传变异程度最大，而波尔山羊的遗传变异程度相对较小。     

Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation

The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A–D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows.     

新批准的西南地区5个山羊遗传资源mtDNA D-loop遗传多样性与亲缘关系研究

为了研究新批准的西南地区5个山羊遗传资源的遗传多样性及其与其他羊种的亲缘关系,试验利用设计的引物对山羊的mtDNA D-loop序列进行了PCR扩增和测序,对序列数据进行了核苷酸多样性、单倍型和亲缘关系分析。结果表明:在西南地区新批准的5个山羊遗传资源中,大足黑山羊、黔北麻羊和酉州乌羊平均多态位点数比较接近,均高于渝东黑山羊和贵州黑山羊;大足黑山羊、黔北麻羊和酉州乌羊遗传多样性高于贵州黑山羊和渝东黑山羊;从亲缘关系来看,渝东黑山羊与板角山羊和南江黄羊亲缘关系较近,酉州乌羊与板角山羊亲缘关系最近,贵州3个羊种(贵州白山羊、贵州黑山羊和黔北麻羊)遗传距离近,大足黑山羊与乐至黑山羊遗传距离较近。说明渝东黑山羊和贵州黑山羊遗传多样性较低,需要加强遗传资源的保护和提纯;新批准的5个山羊遗传资源的遗传距离和亲缘关系与其所处的地理位置存在密切关系。     

不同产地麦冬遗传多样性的SRAP分析

本研究使用SRAP分子标记技术对48份不同产地的麦冬进行遗传多样性分析,筛选出11对有效引物组合。11对引物组合共扩增出621条清晰、可辨认条带,平均每对引物扩增出56.45条带纹,多态性条带为621条,多态性位点百分率为100%,遗传相似系数（GS）范围为 0.058 4～0.936 7,平均为0.497 5,说明供试材料具有丰富的遗传多样性。对所有材料聚类分析发现,在遗传距离0.81处可将材料分为六大类群,部分来自同一地理位置的材料可聚为一类     

42份紫花苜蓿种质资源遗传多样性的SSR分析

为了补充现有苜蓿(Medicago sativa)种质资源的遗传多样性信息,采用SSR分子标记技术对1份野生紫花苜蓿种质和41份栽培紫花苜蓿品种的遗传多样性进行了研究。15对引物在供试苜蓿材料中共获得231条扩增带,其中163条具有多态性。引物的多态位点百分率、Nei’s基因多样性指数和Shannon信息指数的平均值分别为71.55%、0.210 0和0.326 3。供试材料间的相似系数介于0.641~0.913,平均为0.791,栽培品种间的平均相似系数相对较大,野生种质资源与栽培品种间的平均相似系数相对较小。聚类分析表明,供试材料在相似系数0.778处可聚为五大类,单独聚为类的陇东野生紫花苜蓿、CW 200和CW 787都表现出了与其他材料间较远的亲缘关系。基于主成分分析图,可把供试材料分为四大类,其中第Ⅰ、Ⅱ类与第Ⅲ、Ⅳ类材料间的亲缘关系较远。综上,供试苜蓿种质资源具有较丰富的遗传多样性,部分种质资源表现出了相对独立的遗传特性。     

十个歪头菜居群遗传多样性分析

采用ISSR分子标记对10个歪头菜自然居群的104个样本进行遗传多样性分析,筛选的10条ISSR引物共扩增出115个位点,其中多态性位点110个。在物种水平上多态性比率(PPB)为95.65%,在居群内多态位点比率为24.35%~49.70%。POPGENE分析结果显示,物种水平上Nei’s 基因多样性(H)为0.2632,Shannon’s遗传多样性信息指数(I)为0.4046,基因流(Nm)为0.4553,基因分化度(Gst)为0.5283,AMOVA分析居群间遗传分化程度为50.51%。研究表明,10个采样点的歪头菜在物种水平上具有较高的遗传多样性,但在居群之间已经出现了一定程度的遗传分化,且居群间的遗传分化程度高于居群内的分化程度。同时,证明了环境压力大小对于遗传多样性的高低具有选择作用,环境压力小的烟台和环境压力大的合作地区具有较高的遗传多样性,但环境压力介于二者之间的地区遗传多样性水平相对较低。本研究结果不仅对于了解歪头菜遗传进化和其生长地的环境的关系具有重要的参考价值,对合理利用歪头菜遗传资源及育种还具有非常重要的作用。     

利用微卫星标记对六个羊群体性的研究

采用中心产区典型群随机抽样方法采集了67只洼地绵羊样品,并用PCR-PAGE电泳技术检测了其7个微卫星位点(oarFCB11,oarFCB128,oarFCB48,oarFCB304,MAF33,MAF70和oarAE101)的遗传多态性,同时引用了小尾寒羊、滩羊、湖羊、同羊及长江三角洲白山羊(参照群体)相同资料进行群体遗传关系分析。研究结果表明:7个微卫星标记在洼地绵羊、小尾寒羊、滩羊、湖羊、同羊及长江三角洲白山羊6个品种中均存在多态性,可以用于绵羊群体遗传多样性的评估;7个微卫星标记在6个群体中的多态信息含量、平均有效等位基因数和平均杂合度分别为0.9182、13.9839、0.9511、0.9250、14.5013、0.9579、0.9157、12.9416、0.9446、0.9249、15.1723、0.9639、0.8835、10.0377、0.9333、0.8880、12.5156、0.9550、0.9078、12.1543、0.9389,其中oarFCB304遗传变异最大,oarAE101最小;6个绵(山)羊群体中小尾寒羊和洼地羊的遗传变异较大,对照群体(山羊)最小。通过计算DA距离和DS标准遗传距离,采用非加权配对算术平均法(UPGMA)绘制聚类图,得出洼地羊先和小尾寒羊聚为一类,然后和滩羊合并为一类;同时湖羊和同羊聚为一类;绵羊五个品种为一类后与山羊合并为一类。     

Drift across the Atlantic: genetic differentiation and population structure in Brazilian and Portuguese native goat breeds

Brazilian goat breeds are believed to derive mainly from animals brought by Portuguese settlers since the 16th century. We used microsatellite markers in a sample of 436 animals to study genetic variability and differentiation of the six Portuguese (PT) and six Brazilian (BR) goat breeds currently recognized in the two countries. These breeds were also compared with an outgroup represented by a sample of Alpine (ALP) goats. The effective number of alleles and allelic richness were slightly higher in PT than in BR breeds. The global F(ST) was nearly 0.11 when PT and BR breeds were considered, with a mean pairwise F(ST) of about 0.03 among PT breeds, 0.07 among BR breeds and 0.15 between PT and BR breeds. The dendrogram illustrating relationships between populations and the correspondence analysis indicate the existence of two very distinct clusters, corresponding to the countries of origin of the breeds studied, which are nearly equidistant from the Alpine outgroup. The analysis with structure confirmed the separation between PT and BR breeds but suggests that some BR breeds, especially Graúna and Canindé, may share a common ancestry with PT breeds. The divergence observed between PT and BR breeds may result from founder effects and genetic drift but could also reflect the introduction in Brazil of goats originating from other regions, e.g., West Africa.     

四川7个地方山羊品种(类群)mtDNA遗传多样性研究

测定了四川7个地方山羊品种（类群）43个个体的mtDNA控制区全序列，结果表明：山羊mtDNA控制区全序列长度为1212bp或1213bp，A＋T含量（59．9％）明显高于G＋c含量（40．1％）。共检测到74个变异位点，序列均为中性突变，核苷酸多样度为1．686％，这些差异共定义了27种单倍型，单倍型多样度为0．966，遗传多样性较为丰富，品种（类群）间存在不同程度的遗传分化。7个地方山羊品种（类群）间的遗传距离变异范围为0．0017～0．0306。用MEGA软件的NJ法构建单倍型序列的系统发育无根树，结果表明四川地方山羊品种（类群）有两个母系来源，但是否就对应于角笋骨羊（Capra aegagrus）和捻角山羊（Capra falconeri）两个野生祖先，还有待于进一步研究。     

利用微卫星标记分析乌骨大骨鸡的遗传多样性

利用微卫星标记分析了乌骨大骨鸡的遗传多样性和遗传结构,筛选了鸡基因组7条染色体上的7个微卫星标记位点,随机选取24羽乌骨大骨鸡个体,进行多态性检测,共检测到23个等位基因,每个座位等位基因数目从2个到5个不等,平均等位基因数为3.3个。该群体平均多态信息含量和平均杂合度分别为0.660 3和0.717 6。结果表明乌骨大骨鸡属多态性较丰富的群体。     

Development of SNP markers for individual identification and parentage test in a Japanese Black cattle population

This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers. The allelic frequencies for each marker were estimated by using PCR‐RFLP in the Japanese Black population. Based on the frequency data, the estimated identity power of these markers was 2.73 × 10^?12. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.96929 and 0.99693, respectively. This panel of SNP markers is theoretically sufficient for individual identification, and would also be a powerful tool for a parentage test in Japanese Black cattle. The markers could contribute to the management of the beef industry in Japan.     

能源草芦竹遗传多样性的ISSR分析

采用ISSR分子标记技术,对我国6省11个芦竹种群共89个个体的遗传多样性水平和遗传结构进行了研究。从UBC801~900中筛选出7个有效引物,共扩增出40个位点,其中多态性位点为38个。PCR产物的分子量为100~2 000 bp。在物种水平上,Shannon多样性指数为0.494,Nei指数为0.329,遗传分化系数G_st为0.826,平均基因流N_m为0.097。种群内的平均遗传多样度H_s为0.040。表明芦竹在物种水平上具有较高的遗传多样性而种群内的分化极小。UPGMA法聚类结果表明, 芦竹11个种群分为3个类群:浙江和江苏的芦竹聚为一簇,湖南、贵州和广西的芦竹聚为一簇,云南种群单独为一支。不同种群芦竹亲缘关系的远近与它们的地理距离有一定的关系,但不完全一致。     

四川常羽乌骨鸡群体遗传多样性分析

利用选自家禽基因组的10个微卫星标记,对四川常羽乌骨鸡5个群体(四川山地乌骨鸡白羽系、黑羽系;黄忠山地乌骨鸡;黄忠山地乌骨鸡绿壳蛋系;草科乌骨鸡)的遗传多样性进行了检测,计算了各群体的群体杂合度、群体间遗传距离,并根据遗传距离进行了聚类分析。结果表明所选择的微卫星标记在各群体中表现出较高的多态性;四川5个乌骨鸡群体遗传多样性比较丰富,群体平均杂合度为0.5383到0.6659;各群体间的遗传距离有一定的差异;聚类分析将5个群体聚为三类。     

亚丁牦牛和拉日马牦牛遗传多样性及遗传结构分析

亚丁牦牛和拉日马牦牛均为肉乳兼用型优良地方牦牛资源,本研究旨在探究亚丁牦牛和拉日马牦牛的遗传多样性及各牦牛群体间的亲缘关系,对亚丁牦牛、拉日马牦牛以及其他7个地方牦牛群体(九龙牦牛、麦洼牦牛、金川牦牛、昌台牦牛、中甸牦牛、玉树牦牛、类乌齐牦牛)进行RAD简化基因组测序,基于检测到的SNP信息计算遗传统计量.结果表明,亚...     

新疆狗牙根种质遗传多样性的SSR分析

利用SSR分子标记技术,对采自中国新疆的51份野生狗牙根（Cynodon dactylon）及19份新疆农业大学选育的材料进行遗传多样性研究。结果表明,11对引物共得到多态性条带数55条,平均每对引物扩增出5条带,每对引物检测到36个等位基因,平均每对引物检测到5个等位基因。每个SSR位点的多态性信息量(PIC)在0.650.83,平均0.78;SSR标记揭示的新疆70份材料间的遗传相似系数变化范围为0.500.84,表明新疆狗牙根具有较丰富的遗传多样性。UPGMA聚类分析表明,SSR标记能够将新疆70份材料区分开;供试材料可聚为4类,其中Cd071单独聚成1类,野生材料聚为2类。表明这些材料遗传差异较大,各生态地理类群间的遗传分化与其所处的生态地理环境具有一定的相关性。     

基于微卫星标记的中国斑翅山鹑遗传多样性及遗传结构分析

斑翅山鹑(Perdix dauuricae)是具有很高经济价值的猎用禽.为了获得其群体遗传多样性及遗传变异信息,为我国斑翅山鹑进一步有效保护和合理利用提供科学依据,本研究共采用了8个微卫星标记位点对分布于我国北方的斑翅山鹑23个地理种群285个个体进行了群体遗传多样性及遗传结构分析.结果表明,我国斑翅山鹑为遗传多样性较丰富的群体,且每一群体均表现出较高的遗传多样性,其中柴达木盆地地区的种群拥有最高的遗传多样性.遗传分化分析显示组间及组内种群间均表现为遗传分化显著,遗传分化系数(FST)值表明大部分种群间表现出显著的遗传分化.系统树构建和贝叶斯聚类分析结果均显示斑翅山鹑23个地理种群被分化为明显的两个组群.另外,通过BOTTLENECK对各地理种群的分析显示斑翅山鹁种群曾经历过近期瓶颈效应.本研究结果表明,柴达木盆地地区种群、华北平原地区种群、静宁种群、张家川种群以及六盘山地区种群应予以相应关注,以保证有足够的种群大小来保持这些种群的遗传多样性.     

微卫星标记BM143在4个山羊品种中的遗传多样性分析

利用经筛选的微卫星引物BM143,对4个山羊品种的BM143基因座进行了多态性分析,研究结果表明,该基因座的等位基因大小在100～123bp范围内,分析检测了各山羊品种该位点的等位基因频率、杂合度、多态信息含量和有效等位基因数。结果表明,该微卫星标记BM143在4个山羊品种中的遗传多态性可以用于山羊遗传多态性的评估,为山羊品种的保存和利用提供了一定的科学理论依据。