镜鲤繁殖群体的遗传结构及微卫星标记与经济性状的相关性分析

选用35个多态性微卫星分子标记对天津换新良种场镜鲤一个繁殖群体的有效等位基因数(Ae)、观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC) 等进行了检测, 以卡方检验估计群体Hardy-Weinberg平衡。结果表明：在35个基因座共检测到118个等位基因, 平均等位基因数为3.37个, 每个座位检测到的等位基因数2~7个不等, 平均有效等位基因数为2.16, 观测杂合度平均值0.431, 无偏期望杂合度的平均值为0.4736, 平均多态信息含量0.42, 说明这个群体属于中度多态, 遗传多样性水平不高。卡方检验的P值显示多于半数的位点都发生了偏离。并将35个基因座的不同基因型与个体的体重、体长值进行了连锁分析, 得到了4个与体重、体长连锁的基因型, 并将所得结果与鲤鱼体长性状QTL定位结果进行对比, 其中HLJ319标记与QTL定位结果基本一致。分析了几个严重偏离平衡的基因型, 并讨论出现这种现象的可能原因。     

长江野鲤(Cyprinus carpio)及两种养殖鲤群体遗传多样性评估

为了给鲤鱼遗传资源保护及利用提供较为准确的基础数据,利用10对微卫星标记分析了黄河鲤(Huanghe Cyprinus carpio,人工养殖群体)、长江野鲤(Changjiang wild Cyprinus carpio,安徽段)、安徽养殖鲤(Anhui cultured Cyprinus carpio,宿州市)群体遗传多样性。遗传多样性分析实验表明:3个群体均具有较高的遗传水平,且长江野鲤群体遗传多样性高于黄河鲤、安徽养殖鲤;卡方检验表明:3个群体在较大程度上受到人类活动及生态环境变化的影响,30个位点中76.67%的位点显著偏离Hardy-Weinberg平衡。遗传距离、遗传相似度、非加权组平均法(unweighted pair-group method with arithmetic means,UPGMA)聚类树及贝叶斯聚类分析均显示,长江野鲤与安徽养殖鲤亲缘关系较近,研究情况与实际生产中养殖户从长江里获得鲤鱼亲本用于繁殖苗种的现象相符。突变-漂移平衡分析显示,在TPM模式下,Wilcoxon符号秩次检验中黄河鲤群体显著偏离突变-漂移平衡,需进一步扩大选育群体。总体来说,黄河鲤、长江野鲤、安徽养殖鲤群体遗传多样性均较高,具有进一步的选育空间。     

元江鲤种群遗传多样性

选择12对微卫星标记检测了于2011年采集自元江(红河上游中国江段)5个样点192尾鲤的群体遗传多样性.共检测到201个等位基因,每个位点等位基因2-27个.各群体各位点平均等位基因(NA)12.25-14.67个,平均有效等位基因(NE)8.28-9.73个,平均观察杂合度(Ho)o.7765-0.8037,平均期望杂合度(HE)0.7761-0.8080,平均多态信息含量(PIC)0.7534-0.7843.元江鲤种群192个个体各位点NA、NE、Ho、HE、PIC分别为16.50、11.26、0.7927、0.8049、0.7966,种群遗传多样性水平高.元江鲤群体之间遗传分化小,可作为一个种群管理单元进行管理.增殖放流要防止遗传多样性丧失.     

三个鲤品种微卫星丰度与遗传多样性分析

{{@ convertAbstractHtml(article.abstractinfoCn, "cn")}}       

微卫星DNA标记探讨镜鲤的种群结构与遗传变异

采用30个微卫星分子标记, 对5个镜鲤群体的观测杂合度(^H_o)、期望杂合度(^H_e)、多态信息含量(PIC)和有效等位基因数(^A_e)等进行了遗传检测, 根据基因频率计算遗传相似系数和Nei氏标准遗传距离, 以c2检验估计Hardy-Weinberg平衡, 以近交系数(FST)和基因流(Nm)分析群体的遗传分化。同时, 使用PHYLIP3.63软件绘制基于Nei氏标准遗传距离的UPGMA聚类图, 并进行bootstrap自举检验验证进化树的可靠性。在德国镜鲤选育系(Scattered Cyprinus carpio L.)和来自4个不同养殖场(松浦、东岗、奉城和辽中)的德国镜鲤群体中共检测到7 083个扩增片段, 长度在102 ~ 446 bp之间, 在群体内扩增出等位基因1~16个不等, 共计356个等位基因。结果表明: (1)5个群体检测的有效等位基因数在1.07~12.30个不等, 平均多态信息含量为0.74、0.74、0.69、0.75和0.75, 无偏期望杂合度的平均值为0.74、0.78、0.70、0.76和0.78, 说明这几个群体属于高度多态, 遗传多样性水平较高。(2)群体间相似系数在0.52以上, 相似性较高。聚类分析显示, 东岗、奉城和辽中3个养殖场的德国镜鲤群体聚类成一个分支, 而德国镜鲤选育系与松浦群体聚类成另一分支。聚类的先后与它们在地理分布上距离远近有一定的相关性。(3)在与功能基因相关的多个微卫星基因座位上, 扩增产物呈现不同程度的缺失现象, 这些无效等位基因的产生可能与结构基因在育种中受到人工选择的影响较大有关。     

微卫星分子标记与松浦镜鲤3个表型性状的相关分析

本文利用SPSS 13.0分析软件对194尾松浦镜鲤的体重、体长和尾长值进行相关分析,并选用扩增效果好的30个微卫星标记,检测新品种松浦镜鲤繁殖群体的有效等位基因数(Ne)、观测杂合度(Ho)、期望杂合度(He)和多态信息含量(PIC)等遗传参数,以卡方检验估计群体Hardy-Weinberg平衡,最后还将30个基因座的不同基因型与个体的体重、体长和尾长进行了相关分析.结果显示,体重与体长高度线性相关,差异极显著;尾长与体重、体长分别呈显著相关,差异显著.多样性指数结果表明共检测到172个等位基因,片段长度在115～432 bp之间,有效等位基因数为1.14～5.32;观测杂合度为0.07～0.92,期望杂合度为0.13～0.91;多态信息含量为0.12～0.79,其中高度多态(PIC≥0.5) 21个,中度多态(0.25≤PIC≤0.5) 7个,表明这个群体的多样性较高,信息含量比较丰富.我们还发现有4个遗传位点:HLJ328、HLJ693、MFW29和MFW48与体长性状显著相关(P<0.05),其中,位点HLJ328、HLJ693和MFW48还与体重性状显著相关(P<0.05),未发现与尾长性状相关的位点.本文获得的这些标记具有生长特性优势,可作为松浦镜鲤分子辅助育种的参考标记.     

应用微卫星多态分析青海湖裸鲤（Gymnocypris przewalski (Kessler)）六个野生群体的遗传多样性

青海湖裸鲤是青海湖唯一的经济鱼类,由于湖区生态环境的恶化,使得该鱼种群数量越来越稀少.2004年中国环境发展国际合作委员会在<中国物种红色名录>中,将其列为濒危物种.研究利用生物素-磁珠富集法获得10个具有多态的微卫星分子标记,检测6个野生裸鲤群体:布哈河群体、沙柳河群体、哈尔盖河群体、泉吉河群体、黑马河群体、淡水系群体的遗传多样性.结果表明:每个座位上的等位基因数为2～8个, 大小在161～486bp之间.有效等位基因数在1.00～5.45个, 平均多态信息含量分别为0.3642、0.4044、0.3830、0.4047、0.3869和0.3940, 无偏观测杂合度的平均值在0.4145～0.5105之间, 说明这几个群体属于中度多态, 遗传多样性水平较高.根据群体间的遗传距离和遗传相似系数发现,布哈河群体与淡水系群体之间的遗传距离最大(DA=0.1607),哈尔盖河群体与泉吉河群体之间的遗传距离最小(DA=0.0125).由UPGMA聚类图可知:哈尔盖河和泉吉河两个群体聚为一个分支,布哈河、沙流河、黑马河和淡水系4个群体聚为另一个分支.     

厚颌鲂两个野生群体遗传多样性分析

{{@ convertAbstractHtml(article.abstractinfoCn, "cn")}}       

梅花鹿3个种群遗传多样性的微卫星标记分析

利用16个微卫星标记对黑龙江省部分地区(兴凯湖农场、大庆市银浪牧场、五大连池大庆农场鹿苑)的3个梅花鹿(Cervus nippon)群体进行了遗传多样性检测.统计了3个鹿群的等位基因组成、平均有效等位基因数(Ne)、平均遗传杂合度(h)和多态信息含量(PIC).结果表明,除5个位点外,其余11个微卫星位点均表现出不同的多态信息含量,其中高度多态位点5个,中度多态位点4个.这说明本研究所选用的微卫星位点可较准确地评估3个梅花鹿群体的遗传多样性,并为今后相关研究筛选出了有价值的引物.3个梅花鹿群体的平均h在0.454～0.636之间变动,其中兴凯湖梅花鹿群体最高,为0.636,具有较大的遗传潜力.     

虾夷扇贝遗传结构及微卫星标记与经济性状相关分析

选用30个多态性微卫星分子标记对大连大长山(96个)、大连獐子岛(96个)及日本青森县陆奥湾(96个)3个地区虾夷扇贝养殖群体(Patinopecten yessoensis)进行遗传多样性分析。结果显示,30个基因座共检测到198个等位基因(Na),平均等位基因数为6.63个,每个座位检测到的等位基因数为3-12,有效等位基因数(Ne)每个位点平均为4.70个,观测杂合度(Ho)平均值0.58,期望杂合度(He)的平均值为0.75,30个位点的平均多态信息含量为0.703,说明3个地区虾夷扇贝群体遗传多样性水平较高。运用统计软件SPSS11.5对30个微卫星标记与大长山群体生长性状相关性进行了分析。结果表明,位点DQ221714和FJ262378与壳长、壳高、壳宽和鲜重显著相关(P0.05)位点;位点FJ262372与壳宽、软体部重和闭壳肌重显著相关;位点FJ262369与软体部重及闭壳肌重显著相关。对差异显著的位点进行不同基因型间的多重比较,找到了与虾夷扇贝生长性状相关的基因型,进一步将所得显著性标记对大长山虾夷扇贝个体最大的17个和个体最小的13个基因组DNA进行检测,验证其准确性。结果表明,位点DQ221714在两组虾夷扇贝中存在特异性条带,可作为QTL定位候选标记。     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

镜鲤(Cyprinus carpio)肌间刺数量微卫星标记筛选与相关性分析

该文从200个微卫星标记中筛选出149个多态性标记,并对镜鲤(Cyprinus carpio)子代个体数最多的家系进行了肌间刺数量的相关性分析。结果表明有8个微卫星标记与肌间刺数量显著相关(P<0.05)。其中,HLJ3086、HLJ2642及HLJ3515与肌间刺数量极显著相关(P<0.01)。多重比较同一标记不同基因型,得到与肌间刺数量相关的基因型。将得到的与肌间刺数量显著相关微卫星标记在NCBI上进行BLAST比对,结果显示HLJ2891与斑马鱼编码蜘蛛毒素亲和蛋白-2(latrophilin-2-like)基因相似,一致度达92%,HLJ3515与斑马鱼编码丝氨酸/苏氨酸激酶32B(serine/threonine-protein kinase 32B-like)基因相似,一致度达81%。该结果为镜鲤肌间刺数量的分子标记辅助育种(molecular marker assisted breeding)提供了有效依据。     

Comparative analysis of genetic diversity and population genetic structure in Abies chensiensis and Abies fargesii inferred from microsatellite markers

Abies chensiensis Tieghem and Abies fargesii Franchet are two closely related tree species of Pinaceae endemic to China. A. chensiensis is usually found scattered in small forest fragments, whereas A. fargesii is a dominant member of coniferous forest. To evaluate the genetic effect of fragmentation on A. chensiensis, a total of 24 populations were sampled from the whole distribution of the two species. Seven nuclear microsatellite loci were employed to analyze comparatively the genetic diversity and population genetic differentiation. Both A. chensiensis and A. fargesii have high level within-population genetic diversity and low inter-population genetic differentiation. Low microsatellite differentiation (2.1%) between A. fargesii and A. chensiensis was observed. But microsatellite marker was able to discriminate most populations of these two species. Compared to A. fargesii, A. chensiensi has lower allelic diversity and higher genetic differentiation among populations. It suggested the existence of negative genetic impacts of habitat fragmentation on A. chensiensis.     

Analysis of genetic diversity in the endangered Hucho taimen from China

Hucho taimen are listed as endangered in China. The population size has declined recently, prompting an increase in the level of listing from grade three in 2002 to grade five in 2006. We analyzed the genetic diversity of wild populations using 17 microsatellite markers to establish a scientific basis for conservation of this species. We collected tissue samples from four populations in the Heilongjiang River basin: Huma River (HM), Hutou (HT), Haiqing (HQ), and Zhuaji (ZJ). A total of 21 loci were amplified, 18 of which were polymorphic. The number of alleles per locus ranged from 2 to 9 (mean: 4.1905). There were 13 highly polymorphic loci and 5 moderately polymorphic loci. Analysis of five genetic diversity parameters (Na, Ne, Ho, He, and PIC) suggested moderate levels of diversity within the populations. The populations were ranked HT > HQ > ZJ > HM, but the differences in diversity were not statistically significant (P > 0.05). A comparison of variation among all four populations suggested Hardy–Weinberg disequilibrium at 20% of the loci. Genetic differentiation (Fst) was 0.0644 and the gene flow among populations was estimated at 3.36 individuals per generation. The majority of diversity (93.88%) occurred among individuals within a population. In contrast, relatively little (6.12%) of the genetic diversity was distributed between the populations. An analysis of genetic differentiation and genetic distance between pairs of populations revealed that both parameters were higher in comparisons of the HM population to the HT, HQ, and ZJ populations than among the three latter populations. This suggests that the HM population has a distinct genetic structure. We hypothesize that habitat degradation and excessive fishing, not low genetic diversity, has caused the decline in H. taimen populations. However, this species should be protected from further declines in genetic diversity.     

Isolation and characterization of microsatellite loci for the analysis of genetic diversity in Whitmania pigra

The objective of this study was to isolate microsatellite loci to analyze the genetic diversity of Whitmania pigra. Four new microsatellite markers of W. pigra were developed from an enriched library and ten from a modified SAMPL assay. A total of 127 alleles were detected, with an average of 9.1 alleles per locus. The expected heterozygosity (He) of each microsatellite locus varied from 0.451 to 0.857, with an average of 0.688. The polymorphism information content (PIC) of each microsatellite locus ranged from 0.361 to 0.838, with an average of 0.640. Analysis of molecular variance showed that the main variation component existed within the populations (81.64%) rather than among the populations (18.36%). Phylogenetic tree for 15 populations of Hirudo using the NJ method by MEGA 5.1 software were divided into two major clusters. These microsatellite markers will contribute to research on the individual identification, genetic diversity, population structure, genome mapping and conservation biology of Hirudo.     

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.     

Identification of a new Indian camel germplasm by microsatellite markers based genetic diversity and population structure of three camel populations

Camel invokes fascinating chapter of Indian desert history and is integral component of its ecosystem. Camel population has reached a crisis point after three decades of decline (75%) causing major concern to the policy makers. >28% of Indian camel is not yet characterized. It is imperative to describe country’s camel germplasm and its existing diversity for designing conservation plan. One such population is Sindhi, distributed along border with Pakistan. Twenty five microsatellite markers being valuable tool for estimating genetic diversity were selected to elucidate genetic variability and relationship of Sindhi with two registered camel breeds of India- Marwari and Kharai. The standard metrics of genomic diversity detected moderate variability in all the three populations. A total of 303 alleles with a mean of 8.116 ± 0.587 alleles per locus were found in total of 143 animals. Sindhi population had intermediate allelic diversity with 8.522 ± 1.063 alleles per locus. Corresponding values in Marwari and Kharai were 8.783 ± 0.962 and 7.043 ± 1.030, respectively. Genetic variability within the breeds was moderate as evidenced by the mean observed heterozygosity of 0.556 ± 0.025. Sindhi camel population harbors higher genetic variability (Ho = 0.594) as compared to the two registered camel breeds (Marwari, 0.543 and Kharai, 0.531). Mean expected heterozygosity under Hardy-Weinberg equilibrium was higher than the observed values across the three camel groups, indicating deviations from assumptions of this model. In fact, average positive F value of 0.084 to 0.206 reflected heterozygote deficiency in these populations. These Indian camel populations have not experienced serious demographic bottlenecks in the recent past. Differences among populations were medium and accounted for 7.3% of total genetic variability. Distinctness of three camel populations was supported by all the approaches utilized to study genetic relationships such as genetic distances, phylogenetic relationship, correspondence analysis, clustering method based on Bayesian approach and individual assignment. Sindhi camel population was clearly separated from two registered breeds of Indian camel. Results conclude Sindhi to be a separate genepool. Moderate genetic diversity provides an optimistic viewpoint for the survival of severely declining indigenous camel populations with appropriate planning strategies for conserving the existing genetic variation and to avoid any escalation of inbreeding.     

Evaluation of the genetic diversity of Laiwu pigs using twenty-seven microsatellite markers

The Laiwu pig, an indigenous pig breed known for extremely high intramuscular fat content, is a well-preserved ancient breed due to long-term natural and artificial selections. In this study, using 27 microsatellite markers jointly recommended by the International Society of Animal Genetics (ISAG) and the Food and Agriculture Organization (FAO), we investigated the genetic diversity of the Laiwu pig breed. The genetic diversity of Laiwu pigs is dramatically low, with the observed heterozygosity ranging from 0.067 to 0.767. Among the 27 microsatellite markers, 10 were high polymorphic loci, 10 were moderate polymorphic loci, six were low polymorphic loci, and no polymorphism was detected at one locus (IGFI). Further analyses with the 10 high polymorphic loci and five moderate polymorphic loci revealed that the Laiwu pig breed was inbred and heterozygous deficient to some extent, but not severely, and that the Laiwu pigs were relatively pure, with almost no hybridization with other breeds. Two subgroups of the current 13 Laiwu pig pedigrees were identified. These results suggest that the Laiwu pig breed has a low diversity and a conservation program must be developed to preserve the “Laiwu pig” gene pool.     

Microsatellite markers based genetic diversity and bottleneck studies in Zanskari pony

Genetic diversity in Zanskari pony breed was evaluated at 48 microsatellite loci using fifty adult, healthy and unrelated animals. Allele frequency data was used to detect genetic diversity and bottleneck. The estimated average number of alleles (±s.e.) was 8.5208±2.5010 with a total of 409 alleles. A high level of genetic diversity within this breed was observed in terms of number of alleles, observed heterozygosity (0.6763±0.1704), expected Leven's heterozygosity (0.7724±0.795), expected Nei's heterozygosity (0.7644±0.0787) and polymorphism information content (>0.5). In-breeding coefficient (F(is)) was 0.115±0.0209, suggesting moderately high in-breeding in Zanskari breed. Although analysis of bottleneck revealed no bottleneck in recent past but population of Zanskari ponies has decreased drastically and only a few thousand pure-bred animals are left. The information is useful for proposing effective population management strategies for future.