利用微卫星DNA分子标记分析中华绒螯蟹养殖群体遗传分化

养殖河蟹苗种来自各繁育场,经过繁育场多年封闭或半封闭繁育后河蟹多样性是否降低?本研究以长江水系天然群体为对照,利用微卫星分子标记分析中华绒螯蟹(Eriocheir sinensis)江苏兴化、安徽宣城、辽宁盘锦养殖群体遗传分化。结果表明,4个群体平均有效等位基因数(Ne)分别为9.03、8.77和6.94、8.71;平均观测杂合度(Ho)为0.70～0.75;平均期望杂合度(He)为0.87～0.90;微卫星位点平均多态信息含量(PIC)介于0.84～0.87之间,呈现高度多态性;长江水系天然群体遗传多样性水平高于养殖群体。遗传分化系数F-统计量(FST)介于0.0123～0.0207(FST<0.05);分子方差分析(AMOVA)显示,大部分遗传变异(为98.64%)存在于个体间,少部分变异(为1.36%)存在于群体间。群体间FST和AMOVA分析说明,4个群体处于低等遗传分化水平,除安徽宣城群体与辽宁盘锦养殖群体间遗传分化不显著(P>0.05),其他群体间遗传分化极显著(P<0.01)。基于DA遗传距离构建NJ聚类发现安徽宣城养殖群体与辽宁盘锦养殖群体聚为一支,江苏兴化养殖群体与长江水系天然群体聚为另一支。结构分析107份参试中华绒螯蟹样本被分为二个种群,江苏兴化养殖群体与长江水系天然群体属同一种群,安徽宣城养殖群体与辽宁盘锦养殖群体为另一种群。研究显示,中华绒螯蟹养殖群体具有较高的遗传多样性水平,遗传分化水平低,具有新品种选育的利用价值。     

鳜原种群体和养殖群体遗传多样性的微卫星分析

本研究利用20对微卫星引物对鳜（Sinipelrca chuatsi）原种群体和养殖群体进行遗传多样性分析。结果表明,在鳜原种群体中检测到多态性位点14个,养殖群体11个。在两个群体中共检测到等位基因数96个,其中原种群体检测到等位基因数53个,每个位点的等位基因数在1～7之间,平均有效等位基因数为2．7390;养殖群体检测到等位基因数43个,每个位点的等位基因数在1-6之间,平均有效等位基因数为2．1284。原种群体的平均观察杂合度0．5708,Nei氏期望杂合度0．5295,平均多态信息含量PIC0．5353;养殖群体的平均观察杂合度0．3839,Nei氏期望杂合度0．4011,平均多态信息含量PIC0．5043。因此,与养殖群体相比,鳜原种群体仍有丰富的遗传多样性。本研究可为鳜种质资源的保护、监测和遗传育种提供分子水平上的数据。     

利用微卫星标记分析马氏珠母贝4个养殖群体遗传结构

2007年4月,从马氏珠母贝基础群体选取2、4、32和158个亲本分别繁殖4个子代群体,分别命名为P1、P2、P3和P4。2009年7月,从这4个子代群体随机取样30个个体,利用7对微卫星引物分析其遗传结构。结果表明,7对微卫星引物共检测到22个等位基因,每个座位的等位基因数目为2~4个,平均等位基因数为3个,平均有效等位基因数为2.3193。P1、P2、P3和P4群体平均观测杂合度分别为0.4737、0.5489、0.6767和0.7143;P1、P2、P3和P4群体平均期望杂合度分别为0.4737、0.5489、0.6767和0.7143;P1、P2、P3和P4群体的多态信息含量分别为0.4472、0.4224、0.4726和0.4930。本结果表明4个养殖群体均具有较高的遗传多样性,而且有效亲本数目对子代遗传结构有较大的影响,这为马氏珠母贝的遗传育种提供依据。     

华南鲤选育品种与地方品种的遗传多样性比较分析

华南鲤(Cyprinus carpio rubrofuscus)作为优质的地方鲤鱼品种禾花鲤在广东省粤北地区有着悠久的稻田养殖历史。为了解人工养殖和选育对华南鲤群体的遗传多样性和遗传结构的影响,为华南鲤的种质资源保存和育种利用等提供依据,本研究采用16对微卫星引物对华南鲤第5代选育群体(F5)和2个地方品种(乳源群体,乐昌群体)的遗传多样性进行了比较分析。结果显示,在3个群体中,16对微卫星引物均表现为多态性,共扩增得到119个等位基因,每个微卫星座位检测到的等位基因数为3~10个,平均每对引物7.44个。3个群体的平均期望杂合度(He)分别为0.636 0、0.698 9和0.775 1,Shannon多样性指数(I)分别为1.206 3、1.402 0和1.612 2,平均多态信息含量(PIC)分别为0.570 1、0.645 8和0.720 7,表明3个群体都具有较高的遗传多态性(PIC0.5000),但地方品种的遗传多样性水平高于选育品种。3个群体各个微卫星位点上的遗传分化指数(Fst)值介于0.044 0~0.246 8,平均值为0.102 8,表明群体间的遗传变异水平中等。群体间遗传分化指数(Fst)配对比较结果显示,选育群体F5与乐昌群体的遗传分化指数值最大(0.182),乳源群体和乐昌群体2个地方群体间则最小(0.058)。实验结果表明,人工选育加快了华南鲤选育品种与地方品种的遗传分化,也导致了选育品种遗传多样性下降,但选育品种遗传多样性水平依然较高,还具有进一步选育的潜力。本研究结果为下一步制定华南鲤新品种选育计划提供基础遗传数据。     

5种笛鲷属鱼类的遗传多样性及分子标记

运用RAPD及SSR技术对笛鲷属的画眉笛鲷(Lutjanus vitta)、金带笛鲷 (L. fulvus)、金焰笛鲷 (L. fulviflamma)、千年笛鲷(L. sebae)和星点笛鲷(L. stellatus)等5种鱼的遗传多样性及其分子标记进行了研究。RAPD研究结果表明, 5种鱼的平均多态性位点比率(P)依次为89.30%、86.70%、92.11%、86.47%和86.00%; 种内两个体间平均遗传距离(D)分别为0.3431，0.2130，0.3121, 0.1825和0.1775；平均遗传多样性指数(Hi)分别为0.1634、0.1095、0.1353、 0.1022和0.1024。引物OPA8和OPP10的扩增产物中得到9个RAPD标记，分别为OPA8-413bp、OPA8-140bp、OPP10-418bp、OPA8-697bp、OPP10-526bp、OPA8-361bp、OPP10-449bp、OPA8-311bp和OPP10-599b，可鉴别5种鱼。SSR研究结果显示, 5种鱼的有效等位基因数依次为1.9610、3.3793、3.2957、1.7893和3.6591；群体的杂合度(H)分别为0.332、0.462、0.593、0.367和0.676；多态信息含量(PIC)分别为0.302、0.438、0.554、0.332和0.641。 在11个微卫星位点上得到6个微卫星标记，分别为13 Prs229-115 bp、4 Lca43-212 bp、4 Lca43-240 bp、13 Prs229-288 bp、19 Prs275-156bp和7Lca91-118 bp可用于鉴别5种鱼。     

江西野生毛花猕猴桃群体SSR遗传多样性研究

为分析江西野生毛花猕猴桃群体遗传多样性,以江西省境内的5个野生毛花猕猴桃雄性群体(72个个体)为试验材料,采用SSR分子标记技术,选取15对多态性引物,利用聚丙烯酰胺电泳对PCR产物进行检测。结果表明,15对SSR引物共检测到86个位点,多态性位点百分率为100.0%;观察到的平均等位基因数为5.733,有效等位基因数为3.002,Shannon信息指数为1.046。表观杂合度介于0.111~0.819之间,预期杂合度介于0.041~0.876之间,遗传分化系数为2.01,野生毛花猕猴桃雄性群体间存在较大的遗传分化。5个毛花猕猴桃雄性群体遗传距离范围为0.102~0.409,遗传相似度范围为0.665~0.903,群体间遗传距离与地理距离无相关性。群体的遗传多样性丰富度依次为庐山>井冈山>南源山>武功山>麻姑山,江西地区供试的野生毛花猕猴桃雄性群体在分子水平上具有丰富的多态性。本研究结果为毛花猕猴桃雄性品种选育、种质创新与利用提供了一定的理论基础。     

秦巴山区黄牛群体的微卫星DNA遗传多样性

为分析秦巴山区西镇牛、赤崖牛、陨巴牛和宣汉牛4个黄牛(Bos taurus)品种的遗传多样性,本研究以蜀宣花牛和郏县红牛作对照,利用12对微卫星引物对6个黄牛品种的289头黄牛个体进行了遗传多样性检测,统计了各品种的等位基因及频率、有效等位基因数、遗传杂合度、多态信息含量及各群体间遗传距离,并对其进行聚类分析.结果表明,6个黄牛品种在12个微卫星位点共发现110个等位基因,等位基因频率为0.001 6～0.517 3,总群体各位点平均有效等位基因数为2.787 7～7.132 6;各位点多态信息含量为0.5192～0.895 3;平均杂合度为0.667 2～0.724 1.群体间发现特有等位基因11个,基因频率为0.008 1～0.381 6;优势等位基因(P＞0.4) 19个,基因频率为0.403 2～0.820 0;共有等位基因41个,占全部等位基因的37.27％,仅有13个共有等位基因为优势等位基因(P＞0.4),占37.71％.群体间Nei's遗传一致度为0.596 5～0.840 8,标准遗传距离(Ds)为0.173 5～0.524 7.聚类分析结果显示,6个黄牛品种聚为3类,陨巴牛与宣汉牛首先聚在一起,然后同西镇牛聚在一类;赤崖牛与郏县红牛聚为一类;蜀宣花牛自成一类.研究结果表明,12对微卫星标记可用于秦巴山区黄牛遗传多样性的分析,秦巴山区各黄牛品种遗传多样性丰富,选育程度不同,4个黄牛品种虽然地理分布格局相近,自然环境相似,但亲缘关系并非相近,应为来源不同的品种.因此,西镇牛、赤崖牛、陨巴牛和宣汉牛不宜合并为1个品种.本研究所揭示的秦巴山区黄牛品种的遗传分化特点及亲缘关系,为研究品种的遗传共适应特点,预测杂交优势,制定育种战略等提供了科学依据.     

RAPD分析野生和养殖太湖秀丽白虾的遗传多样性

摘要：用60个随机引物对野生和养殖的太湖秀丽白虾进行随机扩增多态DNA(RAPD)分析,筛选的23个随机引物共检测到105个位点（200～2000bp）。用PopGen1.32分析结果表明：野生种群多态位点比例为50.47%,养殖种群多态位点比例为43.33%;野生种群和养殖种群的种群内遗传相似系数分别为0.8635和0.8795;野生种群和养殖种群之间的遗传距离为0.0361;野生种群平均Shannon多样性指数h0为0.2830,略高于养殖种群的0.272。     

泰国产方斑东风螺养殖群体遗传多样性的RAPD分析

用随机扩增多态性DNA(RAPD)技术对泰国产方斑东风螺养殖群体的遗传多样性进行检测,从100个随机引物中筛选出21个引物对方斑东风螺的DNA进行扩增,结果表明:21个引物共检测到222条清晰且重复性好的条带,每个引物可扩增出4~16条带,分子量在200~2200bp之间,其中多态位点为156个,占70.27%;群体的Shannon多样性指数为0.2818,Nei基因多样性指数为0.2491;个体间最大遗传距离为0.291,最小遗传距离为0.066。通过与其他贝类遗传多样性的研究结果比较,可初步判断泰国产方斑东风螺养殖群体的遗传多样性比较丰富。     

不同种群草鱼遗传结构的TRAP分析

应用TRAP(targetregionamplifiedpolymorphism)技术,对草鱼(Ctenopharyngodonidella)野生种群和两个人工养殖种群的遗传结构进行了比较。从15个引物组合中,筛选出7个扩增效果比较好的引物组合,在3个种群中共检测到103个扩增位点,其中野生种群、淡水中心种群和前洲种群的多态性位点分别为67、55和46,表明人工养殖草鱼种群的遗传多样性有所降低。与野生种群相比较发现,人工养殖种群仅33.98%位点的基因频率保持不变,表明人工养殖种群的遗传结构发生了改变。淡水中心种群、前洲种群与野生种群间的遗传距离分别为0.0421和0.0809。引物组合Ga5-800-E5扩增的结果发现,人工养殖种群中存在扩增位点明显减少的区域,这为寻找鉴定草鱼野生种群和养殖种群的遗传标记提供了依据。     

Using SSR markers to determine the population genetic structure of wild apricot (<Emphasis Type="Italic">Prunus armeniaca</Emphasis> L.) in the Ily Valley of West China

Genetic structure of three wild populations (Xinyuan, Gongliu and Daxigou) of apricot in the Ily Valley, Xinjiang Uygur Autonomous Region of China, was investigated with microsatellite (simple sequence repeat, SSR) markers. The higher polymorphism and greater transportability of these markers between Prunus species proved SSR markers were much efficient for conducting genetic diversity studies in wild apricot. Nei's gene diversity (He) and Shannon's index of diversity (I) were 0.287 and 0.458, respectively. This indicated that the wild apricot in the Ily Valley still maintained a relatively high level of diversity. The Gst of 0.137 and Fst of 0.164 revealed that genetic variation mainly resided among individuals within populations (83.6–86.3%). Population differentiation could also be found according to the distribution of SSR alleles between the populations. Mantel test showed the genetic distance between populations was significantly correlated to the geographical distance. The modest amount of gene flow (2.684) would reduce the disjunction between wild apricots. The long-distance dispersal of pollen by insects was probably the main way of gene flow between populations. Based on the study of population genetic structure, an effective conservation strategy of the species was discussed.     

Genetic diversity and population structure of Guinea yams and their wild relatives in South and South West Ethiopia as revealed by microsatellite markers

Genetic diversity and population structure of Guinea yams and their wild relatives collected from south and south west Ethiopia were assessed using microsatellite markers. The total number of alleles amplified for the 7 loci studied was found to be 60, with an average of 8.6 alleles per locus. The average expected heterozygosity for the entire population was found to be 64 % indicating that Guinea yams and their wild relatives in the study area display a high level of genetic diversity. Using allelic richness as a measure of genetic diversity the wild forms exhibited greater allelic diversity than the cultigens. Contrary to what is expected in vegetatively propagated crops, none of the seven loci studied showed a significant excess of heterozygotes. In all the comparisons made, a low mean F_ST (but significant) has been observed, indicating that the majority of microsatellite diversity in the populations under study was found within rather than between populations.     

江西青岚湖五种淡水蚌遗传多样性的微卫星DNA分析

利用北美Epioblasma capsaeformis（蚌科）和中欧Margaritifera margaritifera L.（珍珠蚌科）两种淡水双壳类的20对微卫星引物对江西青岚湖五种淡水蚌群体进行了PCR扩增，筛选出8对多态性较高的引物，并用这8个微卫星座位分别对三角帆蚌、褶纹冠蚌、洞穴丽蚌、射线裂脊蚌和中国尖嵴蚌五种蚌类群体进行了遗传多样性分析。结果表明：不同蚌类群体的平均等位基因数为2.8750～4.000，平均观测杂合度（HO）为0.4417～0.6333，平均期望杂合度（HE）为0.4430～0.5706，平均多态信息含量（PIC）为0.368～0.498，五个群体表现出较高的遗传多样性。有多个座位在不同蚌类群体中偏离哈代－温伯格平衡。五种蚌类群体间的遗传距离在0.6228与1.4724之间，三角帆蚌和褶纹冠蚌之间的遗传距离最大，射线裂脊蚌和洞穴丽蚌之间的遗传距离最小。     

Genetic relationship of diploid wheat (<Emphasis Type="Italic">Triticum</Emphasis> spp.) species assessed by SSR markers

Genetic diversity of 139 accessions of diploid Triticum species including Triticum urartu, Triticum boeoticum and Triticum monococcum was studied using 11 SSR (simple sequence repeats) markers. A total of 111 alleles with an average of 10 alleles per locus were detected. The polymorphism information content (PIC) of each SSR marker ranged from 0.30 to 0.90 with an average value of 0.62. Among the three Triticum species T. urartu had the highest number of total alleles (Na?=?81), private alleles (Npa?=?15) and showed higher genetic diversity (Hex?=?0.58; PIC?=?0.54). The genotypes from Turkey exhibited the highest genetic diversity (PIC?=?0.6), while the least diversity was observed among 4 Georgian accessions (PIC?=?0.11). Cluster analysis was able to distinguish 139 wheat accessions at the species level. The highest genetic similarity (GS) was noted between T. boeticum and T. monococcum (GS?=?0.84), and the lowest between T. urartu and T. monococcum (GS?=?0.46). The grouping pattern of the PCoA analysis corresponded with cluster analysis. No significant differences were found in clustering of T. urartu and T. monococcum accessions with respect to their geographic regions, while within T. boeoticum species, accessions from Iran were somewhat associated with their geographical origin and clustered as a close and separate group. The results from our study demonstrated that SSR markers were good enough for further genetic diversity analysis in einkorn wheat species.     

Genetic diversity of Bolivian wild potato germplasm: changes during ex situ conservation management and comparisons with resampled in situ populations

Potato wild relatives are important sources of novel variation for the genetic improvement of the cultivated potato. Consequently, many natural populations have been sampled and were deposited as accessions in gene banks around the world. Here we investigate to what extent the genetic variation of Bolivian wild potato species is maintained under gene bank conditions and how this diversity relates to that of current in situ populations. For this purpose, materials from seven potato species were screened for microsatellite variation. Genetic changes between different generations of ex situ germplasm were not observed for Solanum leptophyes and S. megistacrolobum, but were detected for S. neocardenasii and S. okadae, while each of the species S. acaule, S. avilesii and S. berthaultii showed stability in some cases and genetic change in others. The observed changes were ascribed to genetic drift and contamination resulting from human error during regeneration. Re-collected populations of six of the studied species showed highly significant genetic differences with the ex situ accessions that, apart from changes during ex situ maintenance, are most likely to be attributed to sampling effects during collecting and in situ genetic changes over time. The implications of the results for ex situ and in situ conservation strategies of wild potato species are discussed.     

白孔雀微卫星DNA遗传多样性及其分类地位

利用14对蓝孔雀(Pavo cristatus)和绿孔雀(P.muticus)的微卫星标记对白孔雀基因组DNA进行扩增,发现都能扩增出特异性条带,每对引物扩增的平均等位基因数为1.71,有7对引物具有较丰富的多态性,其中MCW0080和MCW0098标记期望杂合度分别为0.7207和0.7571,多态信息含量分别为0.658和0.695,表现出丰富的遗传多样性和较高的选择潜力。白孔雀×蓝孔雀和绿孔雀群体的遗传多样性分析结果表明,白孔雀、绿孔雀和蓝孔雀3个群体的杂合度和遗传多样性水平都很低,期望杂合度分别为0.2579、0.2482和0.2744,群体间的遗传分化系数为9.7%,群体间分化极显著(P<0.001),白孔雀与蓝孔雀的亲缘关系最近,Reynolds'遗传距离和基因流分别为0.0295和8.6112,表明白孔雀不是蓝孔雀一个亚种。     

The domestication and dispersal of the cultivated ramie (Boehmeria nivea (L.) Gaud. in Freyc.) determined by nuclear SSR marker analysis

Ramie (Boehmeria nivea) was domesticated in China. However, the geographic region of domestication is not exactly known. Genetic diversity and population structure of ramie and their wild relatives were assessed using microsatellite markers. The 8 microsatellite primers revealed 96 alleles in 50 ramie populations, with an average of 10.25 alleles per locus. Cultivated ramie gene pool harbors approximately 82.9 % of the SSR diversity presented in wild B. nivea var. nivea. It is suggested that ramie has experienced a relatively moderate domestication bottleneck. The distribution of genetic diversity shows that genetic diversity is relatively high in populations along the Yangtze River compared to the peripheral ones. The scatter plots of principal coordinates analysis indicated that there are three well-supported varieties in B. nivea. The NJ tree and the distribution of genetic diversity showed that ramie has been domesticated in the middle and lower regions of the Yangtze valley, and populations in Sichuan province have been introduced from this region, forming naturalized populations.     

Global analysis of Coffea canephora Pierre ex Froehner (Rubiaceae) from the Guineo-Congolese region reveals impacts from climatic refuges and migration effects

As the second species used for commercial coffee, evaluation of Coffea canephora Pierre ex Froehner population genetics is a challenging task for coffee breeding. This study examined the pattern of genetic variability and genetic relationships of cultivated and wild populations of C. canephora sampled across the Guineo-Congolese region of Africa and some improved populations maintained in field genebanks. A total of 293 individuals, sampled from 17 populations, were genotyped with 39 nuclear microsatellite markers. Genetic diversity and structure were investigated with both a model-based and a graphical approach; isolation by distance was also tested. Relationships between the diversity clusters are discussed with regard to differentiation due to several glacial refuges during the Last Glacial Maximum (LGM). High genetic diversity within C. canephora is confirmed with a mean number of alleles of 11.85 per marker, a mean gene diversity of 0.72 and a mean observed heterozygosity of 0.36. An overall structure of two main groups (Guinean and Congolese) subdivided in six subgroups (2 for the Guinean and 4 for the Congolese) was found, including one described for the first time in the Guinean group. A fine structure within the Guinean group was also newly detected. Genetic structure of C. canephora appears to be consistent with its geographic repartition at the continent scale. Structure of diversity was found in accordance with localizations of refuge zones during LGM and migration from this period. Results from this genetic structure study raise our capabilities to better manage and use the collections of genetics resources for breeding purposes. Those results will be used in future association studies to optimize the number of genotypes to be phenotyped.     

Genetic differences between the two remaining wild populations of the endangered Indian rhinoceros (Rhinoceros unicornis)

The management of rare and endangered species in the wild and in captivity requires an understanding of the characterization of the genetic units within each species and their relationships to each other. The Indian rhinoceros (Rhinoceros unicornis) is an endangered species with a current population size of c. 2800 individuals. We analyzed 26 individuals of known origin kept in captivity and 21 wild ranging individuals of the two remnant large wild populations in Assam (India) and Nepal employing mitochondrial and microsatellite markers to determine whether the two geographically isolated populations show distinct patterns of genetic diversity, and whether the genetic diversity of the populations is influenced by past demographic bottlenecks. We identified 10 different mitochondrial D-loop haplotypes, of which 4 were specific to the Assam population (10 sequences examined) and 6 specific to the Nepal population (19 sequences). Similarly, the microsatellite analysis demonstrated a strong genetic differentiation between the Assam and Nepal populations and allowed to assign each individual to its origin with high confidence. Furthermore, our analyses revealed the occurrence of a bottleneck in the Assam population long before the reported bottleneck in 1908, and it revealed that the Nepal population is a recent (probably post-glacial) colonization. In summary, the extent of genetic divergence between the two remnant R. unicornis populations suggests separate conservation programs (even for captive individuals) as long as the persistence of the entire species is not severely threatened. The microsatellite markers can also be used to determine the origin of confiscated material such as horns.     

白孔雀微卫星DNA遗传多样性分析及其分类地位的探讨

利用14对蓝孔雀和绿孔雀的微卫星标记对白孔雀基因组DNA进行扩增,发现都能扩增出特异性条带,每对引物扩增的平均等位基因数为1.71,有7对引物具有较丰富的多态性,其中MCW0080和MCW0098最为理想。白孔雀与蓝孔雀和绿孔雀群体的遗传多样性分析结果表明,白孔雀、绿孔雀和蓝孔雀3个群体的杂合度和遗传多样性水平都很低,期望杂合度分别为0.2579、0.2482和0.2744,群体间的遗传分化系数为9.7%,群体间分化极显著(P<0.001),白孔雀与蓝孔雀的亲缘关系最近, Reynolds'遗传距离和基因流分别为0.0295和8.6112。本试验结果支持白孔雀不能成为蓝孔雀的一个亚种而只是一个品系的观点。