Analysis of genetic diversity and population structure of Chinese yak breeds （Bos grunniens） using microsatellite markers

Nine Chinese yak breeds (Maiwa,Tianzhu White,Qinghai Plateau,Sibu,Zhongdian,Pall,Tibetan High Mountain,Jiulong,and Xin-jiang) and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations,genetic relationship between populations,and population structure for each breed.A total of 206 microsatellite alleles were observed.Mean F-statistics (0.056) for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds.The Neighbor-Joining phylogenetic free was constructed based on Nei's standard genetic dis-tances and two clusters were obtained.The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together.The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one clus-ter includes yaks from Tibet Autonomous Region and Qinghai Province,one cluster combines Zhongdian,Maiwa,and Tianzhu White,and Jiulong and Xinjiang come into the third cluster.Pali was mainly in the first cluster (90%),Jiulong was mainly in the second cluster (87.1%),Zhongdian was primarily in the third cluster (83%),and the other yak breeds were distributed in two to three clusters.The Gayal was positively left in the fourth cluster (99.3%).     

Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer)

The applicability of bovine autosomal microsatellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per marker was 5.0 (SE = 0.2) and the mean heterozygosity per marker was 0.61 (SE = 0.03). Considering the overall high level of polymorphism, it was concluded that most bovine microsatellite markers are applicable in African buffalo.     

牦牛分子遗传多样性研究进展

遗传多样性研究可有效地揭示牦牛的遗传变异, 是牦牛群体遗传学研究的主要内容之一。自20世纪70年代以来, 人们已对牦牛的体形外貌特征、染色体核型(带型)、生理生化特性和DNA序列变异等进行了较为深入地研究。随着分子遗传学和DNA测序技术的迅猛发展, 近年来的研究主要集中在牦牛的分子遗传多样性。文章对近15年来牦牛mtDNA和核基因组分子标记及侯选基因多样性的研究现状进行了综述, 对前景进行展望, 以期为牦牛群体基因组学等研究提供依据。     

Genetic relationships in the peregrine falcon (Falco peregrinus) analysed by microsatellite DNA markers

Microsatellite DNA markers were developed from a peregrine falcon (Falco peregrinus) and genetic relationships among peregrine falcons in southern Norway were analysed using the markers. The genomic DNA library was screened for the presence of dinucleotide microsatellite repeats. Twelve loci revealed polymorphism through the initial analysis of 24 unrelated peregrine falcons, and Mendelian inheritance was confirmed in two peregrine falcon families bred in captivity. The estimated mean probability of identical genotypes in two unrelated individuals was 3 x 10-8, and the combined exclusion probability for parentage testing was 0.99 and 0.94 for one or both parents unknown, respectively. The markers were used to investigate the parentage of peregrine broods from the same nest site from different breeding seasons, and subsequently the nest-site fidelity of the breeding peregrines. High nest-site fidelity was found by studying pairwise comparisons of relatedness (rxy) estimates among chicks at six nest sites from three different breeding seasons. Cross-species amplifications showed that most loci also appeared to amplify polymorphic products in the gyrfalcon (F. rusticolus), merlin (F. columbarius), hobby (F. subbuteo) and kestrel (F. tinnunculus), demonstrating that the loci will provide powerful genetic markers in these falcons too.     

The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by （δμ）^2 and DA distances, and the divergence times between populations were estimated by （δμ）^2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles （10）, whereas Bohai black and Buffalo had the smallest number of private alleles （2）. Chinese Holstein showed the highest genetic variability. Its observed number of alleles （Na）, mean effective number of alleles （MNA）, and mean heterozygosity （He） were 7.7500, 4.9722, and 0.7719, respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first, followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations. Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago （MYA）, however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600 MYA, respectively.     

野牦牛（Bos grunniens mutus）mtDNA D\|Loop区的遗传多样性

为从分子水平上评价野牦牛(Bos grunniens mutus)的遗传多样性,对6头野牦公牛线粒体DNA D-loop 区全序列进行了克隆和测定(GenBank登录号为:FJ548840～FJ548845),结合GenBank中已刊登的2条野牦牛的相应序列,使用BioEdit 7 0 9、DnaSP 4.10.1、Arlequin 3.11等生物信息学软件,对全部8条序列开展了比对分析,确定了多态位点与单倍型数目,计算了核苷酸多样度和单倍型多样度.结果表明8条野牦牛线粒体DNA D-loop 区全序列长度在891～894 bp之间,其中A、T、G和C 4种核苷酸的平均含量分别为32.68%、28.65%、13.46%和25.21%,A+T的平均含量为61.33%.排除4处核苷酸的插入或缺失后,共检测到39处转换和颠换位点,占分析序列总长度的4.38%,其中包括4处单一多态位点和35处简约信息位点.依据序列间核苷酸变异共确定了7种单倍型,单倍型多样度(h)为0.9643,核苷酸多样度(π)为0.02144,提示野牦牛群体具有丰富的遗传多样性.     

Genetic diversity in Swiss goat breeds based on microsatellite analysis

Genetic diversity in eight Swiss goat breeds was estimated using PCR amplification of 20 bovine microsatellites on 20-40 unrelated animals per breed. In addition, the Creole breed from the Caribbean and samples of Ibex and Bezoar goat were included. A total of 352 animals were tested. The bovine microsatellites chosen amplified well in goat. The average heterozygosity within population was higher in domestic goat (0.51-0.58) than in Ibex (0.17) and Bezoar goat (0.19). Twenty-seven per cent of the genetic diversity in the total population could be attributed to differences between the populations. However, with the exclusion of Ibex from the total population, this proportion dropped to 17%. Principal component analysis showed that all Swiss goat breeds are closely related, whereas the Creole breed, Ibex and Bezoar goat are clearly distinct from all eight Swiss breeds.     

Polymorphism in mitochondrial DNA (mtDNA) of yak (Bos grunniens)

Mitochondrial DNAs (mtDNA) from 21 yaks (Bos grunniens) were assayed for restriction fragment length polymorphisms by using 20 restriction endonucleases, six of which (AvaI, AvaII, BglII, EcoRI, HindIII, and HpaI) detected polymorphism. Four different mtDNA haplotypes were identified. Combining this with previous reports about the mtDNA RFLPs of B. indicus and B. taurus, there are obvious differences in mtDNA polymorphism between the yak and other Bos species. We estimated that the divergence times between the ancestor of B. grunniens and the ancestor of B. taurus or B. indicus were about 1.2–2.2 and 1.01–2.02 million years ago, respectively.     

Efficiency of semi-automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations

Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.     

Five new microsatellite markers for Northern pike (Esox lucius)

Five new microsatellite markers were isolated from Northern pike (Esox lucius), a freshwater fish widely distributed in both Northern Europe and Northern America. Characterization in 30 individuals from a population from France revealed four to seven alleles and an expected heterozygosity of 0.243–0.642. No departure from Hardy–Weinberg equilibrium nor linkage disequilibrium were found. The level of polymorphism was higher than previously reported in the literature for pike populations from Northern America and Northern Europe, but with different microsatellite loci.     

Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.     

湖羊6号染色体微卫星标记多样性与产羔数的关系

选择位于绵羊6号染色体上FecB基因紧密连锁的6个微卫星标记, 即LSCV043、BMS2508、GC101、300U、Bulge5和471U, 分析其在湖羊中的遗传多样性以及和产羔数的关系。结果表明, 6个微卫星位点均属多态性位点, 共检测到34个等位基因、53种基因型。LSCV043、BMS2508和300U属高度多态位点, 其多态信息含量分别为0.6674、0.6035和0.5615。对不同基因型群体的产羔率进行统计分析, LSCV043基因型为107 bp/123 bp所对应的总体产羔数明显高于110 bp/123 bp基因型群体所对应的产羔数(P<0.05); BMS2508基因型为154 bp/154 bp、154 bp/170 bp和154 bp/200 bp所对应的群体第一胎产羔数明显高于170 bp/170 bp所对应的产羔数(P<0.05), 基因型170 bp/170 bp的群体总体产羔数均低于该位点的其他基因型(P<0.05); 其他位点各基因型之间产羔数均无显著差异。     

Development and characterization of polymorphic microsatellite markers in Rhododendron simsii (Ericaceae)

A set of 14 polymorphic microsatellite markers has been developed and characterized using FIASCO (fast isolation by AFLP of sequences containing repeats) methods for the garden plant, Rhododendron simsii Planch. Forty‐one R. simsii individuals showing large morphological differences were used to identify these markers. The total number of alleles for each locus ranged from 2 to 6, with an average value of 3.643. The expected heterozygosities and observed heterozygosities ranged from 0.137 to 0.778 and 0.000 to 0.769, respectively. Eight loci exhibited significant deviations from Hardy‐Weinberg equilibrium. Among these microsatellites, seven could successfully be transferred to four related species (R. pulchrum, R. hybrida, R. alutaceum and R. molle (Blume) G. Don). These novel microsatellite markers could be further used for assessment of genetic diversity and population structure, phylogeographic analysis and marker‐assisted selection for R. simsii and other Rhododendron species.     

Development of microsatellite markers for parentage analysis in the great tinamou (Tinamus major)

Eighteen microsatellite loci were isolated from great tinamous (Tinamus major), which are large terrestrial birds found in the Neotropics. These are the first primers developed for the Order Tinamiformes. Paternity analyses are possible because the levels of heterozygosity are sufficiently high (0.29-0.90).     

Isolation and characterization of nine microsatellite loci for the tropical understory tree Miconia affinis Wurdack (Melastomataceae)

We isolated nine microsatellite loci from the Neotropical understorey tree Miconia affinis (Melastomataceae) and optimized them for research on gene flow and genetic structure. Loci screened in 43 individuals from a 2.26-km(2) region were shown to be unlinked and polymorphic, with 5 to 14 alleles per locus and observed heterozygosity ranging from 0.394 to 0.810.     

中国龙虾微卫星标记的筛选及遗传多样性分析

文章以M13通用引物和重复序列(CT)₁₅、(AT)₁₅引物, 利用PCR法对中国龙虾(Panulirus stimpsoni Hoehuis)部分基因组DNA文库进行筛选。共获得78个微卫星序列, 分别分布于55个阳性重组克隆中, 其中完美型(perfect)共50个, 占64%; 非完美型(imperfect)3个, 占3.8%; 混合完美型(compound perfect)6个, 占7.7%; 混合非完美型(compound imperfect)19个, 占24.5%。根据微卫星序列, 设计并筛选出15对微卫星多态性引物, 对中国龙虾的群体进行了遗传多样性分析。获得3~12个等位基因, 等位基因大小在78~425 bp之间, 基本符合引物设计的理论长度。期望杂合度范围为0.48~0.87, 平均值为0.71, 表明中国龙虾基因组微卫星具有较高的杂合度与遗传多样性。15个微卫星位点的PIC值从0.44到0.84, 平均值为0.60, 说明这些微卫星位点在中国龙虾基因组中包含丰富的遗传信息, 合适用于中国龙虾的各种分子标记及遗传学分析和应用。     

种间转移扩增筛选仙湖苏铁微卫星位点及其遗传多样性研究

运用刺叶苏铁、葫芦苏铁、海南苏铁的SSR引物,在仙湖苏铁中进行种间转移扩增,筛选得到7对引物能扩增出清晰的特异带,其中3对引物的扩增产物具有多态性.为验证微卫星的真实性,扩增产物切胶回收后克隆测序.结果表明：重复单元的数目变化是扩增片段长度多态性的主要来源.运用筛选出的3对 SSR标记对4个仙湖苏铁野生种群进行遗传结构研究,等位基因数从2~5,杂合度从0．000~0．667,期望杂合度为0．000~0．610.种群两两遗传分化系数从0~0．382.总体上仙湖苏铁遗传多样性水平低,而种群间遗传分化显著.STRUCTURE分析结果表明,4个野生种群可被分配到3个假想的遗传簇.BOTTLENECK 分析结果表明种群近期没有遭遇瓶颈效应.     

Population genetic diversity and species relationships in the genus Rhinanthus L. based on microsatellite markers

The genus Rhinanthus L. is complex, containing many taxonomically unresolved taxa. In this paper we studied genetic variation and species relationships in 15 populations of six Rhinanthus species from three sections. For this purpose, we developed new microsatellite primers for R. osiliensis and used them to investigate genetic variation in two narrow endemics (R. osiliensis, R. javorkae) and in four widespread species (R. rumelicus R. wagneri, R. angustifolius and R. minor). Species‐specific private alleles were found in all species except R. osiliensis and R. angustifolius. The Bulgarian endemic R. javorkae showed the lowest genetic variation, followed by widespread R. minor and Estonian endemic R. osiliensis. Rhinanthus javorkae and R. minor were genetically most differentiated. Section Cleistolemus is weakly structured genetically, indicating close affinity between R. osiliensis, R. rumelicus, R. wagneri and R. angustifolius.