Preliminary studies on the genetic variability of six Hungarian common carp strains using microsatellite DNA markers

Genetic variation in six Hungarian common carp (Cyprinus carpio L.) strains was evaluated using 12 microsatellite loci. The domesticated (Tatai, Biharugrai and Szarvasi) strains were derived from fish farms. Two of wild strains (Tiszai and Dunai) were sampled from brood stocks maintained at fish farms for breeding, and Kis-Balatoni wild carp were sampled from the Small Balaton Lake. Pairwise Fst-values (0.013–0.161) were highly significant (p0.0001), demonstrating differentiation among strains. The mean number of alleles ranged between 3.9 and 8.2. Overall mean observed heterozygosity was lower (0.557) than the mean expected heterozygosity (0.700). By strain, the only exception to this trend was the Dunai (Danubian), which showed higher mean observed heterozygosity (0.764) than expected (0.602). For five loci the Dunai strain showed extremely high levels of heterozygosity (1.00). Two wild strains exhibited a number of loci (Tiszai, 4; Dunai, 6) that were not in Hardy–Weinberg equilibrium. A relatively high number of private alleles overall (n=26), as well as differences in allele frequencies supported our ability to assign most individual fish (over 90%) to each strain.     

Development of silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) genetic maps using microsatellite and AFLP markers and a pseudo-testcross strategy

Silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) are two of the four most important pond-cultured fish species inhabiting the major river basins of China. In the present study, genetic maps of silver carp and bighead carp were constructed using microsatellite and AFLP markers and a two-way pseudo-testcross strategy. To create the maps, 60 individuals were obtained from a cross of a single bighead carp (female) and a single silver carp (male). The silver carp map consisted of 271 markers (48 microsatellites and 223 AFLPs) that were assembled into 27 linkage groups, of which 22 contained at least four markers. The total length of the silver carp map was 952.2 cM, covering 82.8% of the estimated genome size. The bighead carp map consisted of 153 markers (27 microsatellites and 126 AFLPs) which were organized into 30 linkage groups, of which 19 contained at least four markers. The total length of the bighead carp map was 852.0 cM, covering 70.5% of the estimated genome size. Eighteen microsatellite markers were common to both maps. These maps will contribute to discovery of genes and genetic regions controlling traits in the two species of carp.     

A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers

Common carp (Cyprinus carpio) is an important fish for aquaculture, but genomics of this species is still in its infancy. In this study, a linkage map of common carp based on Amplified Fragment Length Polymorphism (AFLP) and microsatellite (SSR) markers has been generated using gynogenetic haploids. Of 926 markers genotyped, 151 (149 AFLPs, two SSRs) were distorted and eliminated from the linkage analyses. A total of 699 AFLP and 20 microsatellite (SSR) markers were assigned to the map, which comprised 64 linkage groups and covered 5506.9 cM Kosambi, with an average interval distance of 7.66 cM Kosambi. The normality tests on interval map distances showed a non‐normal marker distribution. Visual inspection of the map distance distribution histogram showed a cluster of interval map distances on the left side of the chart, which suggested the occurrence of AFLP marker clusters. On the other hand, the lack of an obvious cluster on the right side showed that there were a few big gaps which need more markers to bridge. The correlation analysis showed a highly significant relatedness between the length of linkage group and the number of markers, indicating that the AFLP markers in this map were randomly distributed among different linkage groups. This study is helpful for research into the common carp genome and for further studies of genetics and marker‐assisted breeding in this species.     

利用30个微卫星标记分析长江中下游鲢群体的遗传多样性

摘要: 利用30对微卫星分子标记对长江中下游5个鲢群体进行了遗传多样性分析。结果表明: 在30个基因座中, 共检测到144个等位基因, 每个座位检测到的等位基因数为1～10个, 其中有25个座位具有多态性, 多态位点百分率为83.33,5个群体的平均等位基因数A为4.0/4.1, 平均有效等位基因数Ne为2.4445～2.6332, 平均观察杂合度Ho为0.3233～0.3511, 平均期望杂合度He为0.4421～0.4704, 平均多态信息含量PIC为0.4068～0.4286。对数据进行F-检验, Fst值表明群体间的遗传分化程度中等, 并对基因型进行了基于Hardy-Weinberg平衡的卡方检验, 所得P值说明5个群体均一定程度上偏离了平衡。5个群体间的遗传相似系数为0.8466～0.9146,遗传距离为0.0893～0.1665, 并根据Nei氏标准遗传距离用UPGMA方法对5个鲢群体进行亲缘关系聚类。     

Development of microsatellite DNA markers of silver carp (Hypophthalmichthys molitrix) and their cross‐species application in bighead carp (Aristichthys nobilis)

Forty‐four microsatellite DNA markers were developed for silver carp, and used to investigate polymorphisms of 41 wild silver carps and seven wild bighead carps collected from Jingzhou fragment of Yangtze River. In silver carp, 40 markers were polymorphic. A total of 297 alleles were detected at 40 polymorphic loci. The number of alleles per locus varied from two to 16 with an average of 7.4 and the expected heterozygosities of each locus ranged from 0.07 to 0.91 with an average of 0.69. All markers amplified both silver carp and bighead carp DNAs.     

Development and characterization of microsatellite markers to study population genetic diversity of Przewalski's naked carp Gymnocypris przewalskii in China

Two populations of Przewalski's naked carp Gymnocypris przewalskii, 30 individuals per population, were screened for 10 microsatellite loci. Moderate allele variation was found in these loci with two to eight alleles per locus. The expected and observed heterozygosity ranged from 0·019 to 0·805 and from 0·160 to 0·575, respectively.     

Biochemical genetic comparison of the Chinese and European races of the common carp

An electrophoretic survey of the common carp revealed 33 loci. Nine were found to be polymorphic including two phosphoglucose isomerase loci, a phosphoglucomutase locus, three esterase loci, a lactate dehydrogenase locus, a malate dehydrogenase locus, and transferrin. Five of these polymorphic loci are reported for the first time, the two phosphoglucose isomerase loci, a phosphoglucomutase locus and two of the three esterase loci. Differences in allele frequencies between the European and Chinese races were found at most loci.     

转大麻哈鱼生长激素基因鲤生态安全性检测与分析

评价了转大麻哈鱼（Oncorhynchus Suckley）生长激素基因鲤生态安全性问题及研究转基因鱼对天然野生鲤群体遗传污染程度。通过RAPD和SSLP方法,用265个RAPD标记和35对鲤的微卫星标记对受杂交鲤污染的哈尔滨江段黑龙江鲤群体、未受污染的抚远江段黑龙江鲤群体及模拟转基因鲤占普通鲤群体的1%和10%比例获得繁殖子代等实验群体的DNA样本进行全基因组扫描统计分析得出结论,即转基因鲤占普通鲤群体1%时对普通群体的基因污染程度是微乎其微的,远远低于杂交鲤对野生群体基因污染,转基因鲤占普通鲤群体10%时对普通鲤遗传背景的影响稍有升高,但仍然远远低于杂交鲤对野生群体基因污染程度。总之,在现有的检测技术条件及有效的监控条件下,与杂交鲤相比转基因鲤对鲤野生群体的遗传背景的影响是微弱的,而外来种和杂交种则对生态环境有严重威胁。     

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.     

Development of microsatellite markers and their utilization in genetic diversity analysis of cultivated and wild populations of the mud carp （ Cirrhina molitorella）

Microsatellite markers have been increasingly used in genetic studies on fishery species because of their high applicability in selective breeding programs.Here we reported the development of microsatellite markers and their utilization in mud carp(Cirrhina molitorella).An (CA)15 enriched library has been constructed for mud carp,using the magnetic beads enrichment procedure.Sequence analysis of 60randomly picked positive colonies indicate that 56 (93.3%) of the colonies contain microsatellites.Microsatellite polymorphism was as-sessed using 10 mud carp individuals,and 12 microsatellite loci turned out to be polymorphic.We utilized these loci to study the genetic diversity of a wild population (WM) and a cultured population (CM) of the mud carp.A total of 109 alleles were detected with an average of 9.08 alleles per locus.The mean value of the observed heterozygosity of WM and CM was 0.6361 and 0.6417,respectively,and sig-nificant decrease of genetic diversity in CM was not observed.The genetic distance between the two populations was 0.1546 and the value of Gsr was 0.0473.This showed that there existed a slight genetic differentiation between WM and CM.     

Evaluation of the genetic variability of 13 microsatellite markers in native Indian pigs

We analysed polymorphism of 13 microsatellites in two Indian domesticated pig types (North Indian and Northeast Indian). Heterozygosity, polymorphism information content, and probability of identity of two random individuals were calculated for all microsatellites in both types. The number of alleles observed at a locus varied between five and 12. The evaluated microsatellites exhibited a very high heterozygosity and polymorphism information content. The probability of identity of two random individuals from different populations taking into account all the 13 microsatellites was as low as 3.51 × 10^-19. On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying the genetic diversity and for identification of individuals in Indian pig types.     

Polymorphic microsatellite DNA markers in the penduline tit, Remiz pendulinus

To describe the exceptional mating system of the penduline tit, Remiz pendulinus, we aim to combine field observation records with DNA analysis based on polymorphic microsatellite DNA markers. Here we describe features of nine loci and their corresponding polymerase chain reaction primers. The observed number of alleles varied from four to seven and the observed heterozygosity ranged from 0.419 to 0.802. Neither of the loci is sex-linked and as linkage disequilibrium analysis showed they assort independently. Seven of the nine loci were polymorphic in the Cape penduline tit, Anthoscopus minutus.     

微卫星DNA在分子遗传标记研究中的应用

随着种群遗传学的发展 ,分子遗传标记特别是微卫星标记已经成为研究种群遗传的有力工具。本文就微卫星遗传标记的研究背景、技术应用以及优势与不足等方面进行了综述。     

微卫星标记对12个中外牛品种群体遗传结构的研究

选用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)推荐的12对微卫星引物, 采用荧光标记–多重PCR技术, 检测了9个中国地方黄牛品种和3个外来牛品种的遗传多样性。利用等位基因频率计算出各群体的平均遗传杂合度(H)、多态信息含量(PIC)和群体间的DA及DS遗传距离。基于DA遗传距离, 用UPGMA法进行聚类分析, 结果12个中外牛品种被聚为4类: Ⅰ类属于南方黄牛品种, 包括恩施牛、黎平牛、昭通牛和川南山地牛; Ⅱ类属于中原黄牛品种, 包括郏县红牛、早胜牛和平陆山地牛; Ⅲ类属于北方黄牛, 包括延边牛和长白地方牛; Ⅳ类属于外来牛品种, 包括西门塔尔牛、夏洛来牛和德国黄牛。研究结果为中国地方牛品种的保护和利用提供了理论依据。     

Chromosomal localization of six bovine microsatellite markers

Six lambda genomic clones containing polymorphic microsatellite (MS) markers were assigned to bovine chromosomes 1, 3, 5, 7, 13 and 24 by fluorescence in situ hybridization (FISH). Linkage data for four MS markers were presented earlier and linkage data for the remaining two on chromosome 7 and 24 are presented here. All assignments either orient or confirm the orientation of linkage groups relative to the centromere. A comparison of physical assignments and linkage intervals was possible on chromosome 5 (three loci, 38 cM) and 13 (two loci, 6 cM).     

Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.     

Evaluation of the genetic variability of 23 bovine microsatellite markers in four Belgian cattle breeds

The polymorphism of 23 microsatellites in the four main cattle breeds in Belgium (Holstein Friesian, Belgian Blue, Belgian Red Pied and East Flemish) was analysed. Heterozygosity, polymorphism information content, the effective number of alleles, exclusion probability and the probability of genotypic identity for two random individuals were calculated for all microsatellites and all breeds. The Belgian Blue breed is generally a little less polymorphic in comparison with the other three breeds. Estimates of the genetic distances between these breeds confirmed the widely accepted proposition that the Belgian Blue is the most genetically distinct of these breeds. The three other breeds are likely to become one population, given current breeding strategies. Exclusion probabilities in parentage control cases are >0·9999 in all four breeds when all 23 microsatellites are used and >0·98 with only the two most polymorphic multiplexes.     

Characterization of 42 highly polymorphic bovine microsatellite markers

We have isolated 42 highly polymorphic microsatellite (GT/CA)_n markers from Japanese black cattle Wagyu ( Bos taurus ). Forty-one of the markers were assigned to bovine autosomes with lod scores > 6, through linkage analyses performed on the International Bovine Reference Family Panel (IBRP). The remaining marker showed X-linked inheritance. These markers exhibited an average heterozygosity value of 0.67 with between four and 17 alleles on the IBRP.     

Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers

Six local chicken breeds are registered in Hungary and are regarded as Hungarian national treasures: Hungarian White, Yellow and Speckled, and Transylvanian Naked Neck White, Black and Speckled. Three Hungarian academic institutes have maintained these genetic resources for more than 30 years. The Hungarian Yellow, the Hungarian Speckled and the Transylvanian Naked Neck Speckled breeds were kept as duplicates in two separate subpopulations since time of formation of conservation flocks at different institutes. In this study, we investigated genetic diversity of these nine Hungarian chicken populations using 29 microsatellite markers. We assessed degree of polymorphism and relationships within and between Hungarian breeds on the basis of molecular markers, and compared the Hungarian chicken populations with commercial lines and European local breeds. In total, 168 alleles were observed in the nine Hungarian populations. The F _ST estimate indicated that about 22% of the total variation originated from variation between the Hungarian breeds. Clustering using structure software showed clear separation between the Hungarian populations. The most frequent solutions were found at K  = 5 and K  = 6, respectively, classifying the Transylvanian Naked Neck breeds as a separate group of populations. To identify genetic resources unique to Hungary, marker estimated kinships were estimated and a safe set analysis was performed. We show that the contribution of all Hungarian breeds together to the total diversity of a given set of populations was lower when added to the commercial lines than when added to the European set of breeds.