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1.
Microsatellite markers derived from bay scallop <Emphasis Type="Italic">Argopecten irradians</Emphasis> expressed sequence tags 总被引：5，自引：0，他引：5
ABSTRACT: When data mining was performed on the National Center for Biotechnology Information database, a total of 2038 sequences from five different expressed sequence tag libraries were registered. Eighty sequences (3.9%) were found to contain 91 microsatellites. Clustering analysis indicated that 23 sequences of these expressed sequence tags fell into five clusters and that the remaining 57 sequences were independent. The di- and tri-nucleotide repeat motifs accounted for approximately 62.1% of the total microsatellites. The most abundant dinucleotide microsatellite was TA, followed by GA and CA, and the trinucleotide microsatellites GAT and GGT showed a high abundance. Nineteen sequences representing di-, tri-, tetra- and penta-nucleotides motifs were chosen for the design of polymerase chain reaction (PCR) primers. Of primer pairs, 16 successfully amplified scorable PCR products and 11 revealed polymorphism, with the average polymorphic information content value of 0.5082 and 3.1 alleles per locus. A transferability analysis on three other related scallop species, Chlamys farreri, Chlamys nobilis and Patinopecten yessoenssis , showed that only 1 of 16 primer pairs could amplify PCR products with the expected size in Chlamys nobilis . 相似文献
2.
仿刺参的微卫星标记 总被引：12，自引：5，他引：12
为了评价种质资源及基础生物学研究的需要，本文开发了仿刺参的微卫星标记。NCBI数据库中共有20个含有仿刺参微卫星的序列，从中选取8个设计引物，发现6个微卫星位点有多态性。不同的引物获得的等位基因数为3～9个不等，6个位点共获得了31个等位基因，每个位点平均获得5．2个等位基因。6个位点的平均观测杂合度（Ho）为0．3611，平均期望杂合度（He）为0．6402。位点AJMS004提供的多态性信息含量值较低，为0．4862；其他5个位点均在0．5以上。另外，还尝试了红海参（Parastichopus californicus）微卫星标记在仿刺参的通用性。实验结果表明，在较高的退火温度下，5对引物均能扩增仿刺参的基因组DNA并具多态性。5个位点共获得了22个等位基因，每个位点平均获得4．4个等位基因。5个位点的平均观测杂合度（Ho）为0．1733，平均期望杂合度（He）为0．4201。其中位点Psc2的多态性信息含量值最高，为0．8500。 相似文献
3.
根据前人FIASCO方法构建的三疣梭子蟹微卫星富集文库,对含微卫星的DNA序列设计了71对引物并对其进行了多态性筛选,筛选出21对多态的微卫星引物,对三疣梭子蟹1个野生群体的30个个体进行遗传多样性检测,同时对引物进行评价。21个位点共获得了188个等位基因,平均每个位点扩增得到8.9个等位基因。不同引物获得的等位基因数差异较大,从3～13个不等,其中Pot8、Pot37、Pot48、Pot53、Pot54、Pot66六个位点分别获得了11、12、12、11、13、11个等位基因,而Pot46仅获得了3个等位基因。等位基因的大小分布在131～312bp,基本符合引物设计时理论产物长度。21个微卫星位点的期望杂合度的范围为0.659～0.889,PIC值均高于0.5,表明它们都有很高的杂合度,均可用于三疣梭子蟹种群遗传结构分析,为三疣梭子蟹品种选育、种系评估提供更多的微卫星DNA信息。 相似文献
4.
Microsatellites have become the preferred molecular markers for strain selection and genetic breeding in fish. In this study
a total of 105 microsatellites were isolated and identified in gibel carp (Carassius auratus gibelio) by microsatellite sequence searches in GenBank and other databases and by screening and sequencing of positive clones from
the genomic library enriched for AG and GATA repeats. Moreover, nineteen microsatellites were randomly selected to design
locus-specific primer pairs, and these were successfully used to identify and discriminate different cultured strains of gibel
carp including strains A, D, L, and F. Three different types of microsatellite pattern were distinguished by the number and
length of fragments amplified from the 19 primer pairs, and some microsatellite primer pairs were found to produce different
microsatellite patterns among strains and strain-specific fragments. In addition, some duplicated alleles were also detected
in two microsatellite patterns. Therefore, the current study provides direct molecular markers to discriminate among different
cultured strains for selective breeding and aquaculture practice of gibel carp. 相似文献
5.
微卫星标记在坛紫菜丝状体品系DNA指纹构建中的应用 总被引：3，自引：0，他引：3
用从条斑紫菜EST数据库中筛选合成的微卫星引物对8个坛紫菜丝状体品系进行微卫星DNA指纹扩增。5个微卫星引物共扩增出32条带,其中3对引物所扩增出的5个条带(AU192094—127、AU187410—335、AU187410—190、AU194267—203和AU194267—328)被用来构建8个坛紫菜丝状体品系的DNA指纹。在这个图谱中,每个丝状体品系都有独一的指纹模式,彼此很容易被区分开。所获得的DNA指纹图谱,可用来进行孟德尔分离研究,及为坛紫菜纯系鉴定提供分子基础。 相似文献
6.
通过分析栉孔扇贝BAC末端序列,发现大量微卫星DNA;随机选择14个多态性BES-SSR标记,在我国栉孔扇贝大连群体(DL)和青岛群体(QD)中验证标记的可用性,同时对这两个群体的遗传结构及其分化进行研究。结果表明,从17447条BESs中得到微卫星3374个,以四核苷酸重复为主(26.6%),五核苷酸重复次之(17.7%),六核苷酸重复最少(12.0%)。BES-SSR引物的扩增效率为77.3%(99/128),在作图亲本中的多态比例为33.6%(43/128),14个基因座在两群体中的平均等位基因数Na分别为18.9286和26.2143,平均有效等位基因数Ne为11.7505和17.0891,平均观察杂合度Ho为0.5100和0.4204,平均期望杂合度He为0.9156和0.9450,多态信息含量PIC分别为0.8940和0.9302,群体遗传多样性水平较高。两群体间的无偏遗传相似性系数为0.4879,遗传距离为0.7177,平均基因分化指数FST为0.0243,基因流Nm为10.0179,显示群体间遗传分化程度较弱,遗传变异主要来自于群体内个体之间,经Hardy-Weinberg平衡检验,两群体普遍存在杂合子缺失现象。研究表明,所开发的BES-SSR是高度多态位点,用于群体遗传多样性分析效果很好,显示BES是微卫星标记开发和应用的重要资源。 相似文献
7.
以1个人工授精获得的中国明对虾(Fenneropenaeus chinensis)F2家系为材料,对其中80尾中国明对虾进行正态分布检验,选择19个稳定扩增的微卫星位点对每一个体进行扩增和基因分型,分析家系遗传信息.利用最小二乘法对微卫星位点与中国明对虾体长、全长、体质量性状进行关联性分析.采用SPSS 11.5软件作微卫星分子标记与经济性状的方差分析,考察各微卫星位点对体长、全长、体质量3个经济性状的影响程度.结果表明,中国明对虾体长、全长、体质量3个性状均呈正态分布(P＞0.05);相关分析得到,19个微卫星位点中RS0683和FC019两个微卫星位点与体长、全长、体质量呈显著相关(P＜0.05);同时对差异显著的位点进行不同基因型间经济性状的多重比较,RS0683标记座位AA基因型在体长、全长、体质量的表型效应上极显著高于AB、BB基因型(P＜0.01),表明该标记位点基因型AA与3种经济性状正相关;FC019标记座位的AA基因型体长、全长、体质量显著低于AB、BC基因型(P＜0.05),表明该标记位点基因型AA与3种经济性状呈负相关. 相似文献
8.
Camilla A Santos Bruno C Rossini Carla G Marques Pedro M Galetti Jr Patrícia D Freitas 《Aquaculture Research》2012,43(10):1567-1570
In the present work, EST‐SSR (expressed sequence tag‐simple sequence repeat) loci were obtained by screening 45 000 ESTs from the Pacific white shrimp Litopenaeus vannamei, which was available in a database of the ShEST (Shrimp EST Genome Project) consortium. Fifty‐two of 600 EST‐SSR loci were selected. From this total, 21 EST‐SSRs were polymorphic among 40 individuals and had their gene products ascribed. Two to 20 alleles per locus were detected and the observed heterozygosity ranged from 0.15 to 0.86. Eight loci presented a significant heterozygote deficit after the Bonferroni correction, which was attributed to null alleles. Seven loci were able to have their protein products, molecular functions and biological processes determined. Our results are promising for future studies that relate the levels of these gene polymorphisms with different biological responses to stress in aquaculture. 相似文献
9.
10.
本研究从NCBI的EST数据库中下载大叶藻EST序列共计10 659条,从中得到SSR位点共65个,SSR发生频率为1.7%,平均分布距离为21.7 kb。其中三核苷酸为优势重复类型,占49.2%,二核苷酸数量仅次于三核苷酸,占33.8%。基于65条含有SSR的EST序列,设计并合成了30对引物,其中26对引物的扩增产物单一,片段大小与预测的相近或较大。在由16个大叶藻个体组成的群体中,其中8对引物的扩增条带具有多态性。利用这8对引物对青岛汇泉湾大叶藻自然群体进行了遗传多样性分析,结果表明,8个SSR共检测出33个等位基因,平均每个SSR能检测出4.1个等位基因,多个遗传多样性参数表明,青岛汇泉湾大叶藻群体具有较高的遗传多样性（Ho=0.538 2;He=0.577 6;I=0.560 7）。本研究开发的EST-SSR标记,可进一步丰富大叶藻SSR标记信息,为大叶藻分子生态和群体遗传研究提供更多的标记选择。 相似文献
11.
Lingling Wang Linsheng Song Huan Zhang Qiang Gao & Ximing Guo 《Aquaculture Research》2007,38(4):409-419
The bay scallop (Argopecten irradians irradians Lamarck 1819) has become one of the most important aquaculture species in China. Genetic improvement of cultured bay scallop can benefit greatly from a better understanding of its genome. In this study, we developed amplified fragment length polymorphisms (AFLPs) and simple sequence repeat markers from expressed sequence tags (EST‐SSRs) for linkage analysis in bay scallop. Segregation of 390 AFLP and eight SSR markers was analysed in a mapping population of 97 progeny. Of the AFLP markers analysed, 326 segregated in the expected 1:1 Mendelian ratio, while the remaining 74 (or 19.0%) showed significant deviation, with 33 (44.6%) being deficient in heterozygotes (A/a). Among the eight polymorphic EST‐SSR loci, one marker (12.5%) was found skewing from its expected Mendelian ratios. Eighteen per cent of the markers segregating from female parent were distorted compared with 21% of the markers segregating from male parent. The female map included 147 markers in 17 linkage groups (LGs) and covered 1892.4 cM of the genome. In the male map, totally 146 AFLP and SSR markers were grouped in 18 LGs spanning 1937.1 cM. The average inter‐marker spacing in female and male map was 12.9 and 13.3 cM respectively. The AFLP and SSR markers were distributed evenly throughout the genome except for a few large gaps over 20 cM. Although preliminary, the genetic maps presented here provide a starting point for the mapping of the bay scallop genome. 相似文献
12.
云斑尖塘鳢微卫星标记在两种虾虎鱼亚目鱼类群体间的适用性研究 总被引：1，自引：1，他引：0
利用微卫星DNA-聚合酶链式反应(STR-PCR)技术对已开发的14对云斑尖塘鳢(Oxyeleotrismarmorata)微卫星标记在线纹尖塘鳢(Oxyeleotris lineolatus)和河川沙塘鳢(Odontobutis potamophila)群体间进行通用性分析。结果显示,14对云斑尖塘鳢微卫星标记在线纹尖塘鳢群体均能扩增出特异性条带,在河川沙塘鳢群体中也有10对引物可稳定扩增,其中9对在线纹尖塘鳢群体中具有高度多态性,6对在河川沙塘鳢群体中具有高度多态性。通过这10对通用微卫星标记检测3个种群的平均观测杂合度(Ho)为0.344 9,平均期望杂合度(He)为0.704 3,平均多态信息(PIC)含量为0.536 9。同时获得3个有着较高的通用性微卫星位点(H27、H142和H97),平均PIC值均大于0.5,具有高度多态性,在3种虾虎鱼亚目鱼类中具有较高的通用性,这3个位点在3种虾虎鱼亚目鱼类之间共检测得到6～22个不等的等位基因,并获得1个可以用于鉴别沙塘鳢科与塘鳢科特异基因型的等位基因位点(H97)。因此,通过已开发的云斑尖塘鳢微卫星标记来获得适用相近物种的微卫星标记是可行的。 相似文献
13.
不同鳊鲂鱼类群体微卫星DNA指纹图谱的构建和遗传结构分析 总被引：9，自引：2，他引：7
为对不同鳊鲂鱼类进行群体鉴定和遗传多样性分析,从60对微卫星标记中筛选出18对多态性高的引物,构建了6个鳊鲂鱼类群体的微卫星DNA指纹图谱。结果显示,东江三角鲂、钱塘江三角鲂、厚颌鲂、广东鲂、团头鲂和长春鳊6群体的平均等位基因数(N a)分别为5.17、6.11、3.50、6.56、5.22、5.22,平均期望杂合度(H e)分别为0.634 2、0.720 4、0.546 2、0.681 2、0.675 2、0.559 7,平均多态信息含量(PIC)分别为0.575 6、0.666 9、0.472 0、0.630 6、0.606 4、0.517 0,表明钱塘江三角鲂的遗传多样性最高,厚颌鲂的遗传多样性最低;聚类分析表明,钱塘江三角鲂和团头鲂首先聚为一支,遗传距离较近,为0.560 6;厚颌鲂与长春鳊的遗传距离最远,为1.759 2。引物Mam03和EST37产生的特异条带可将鲂属和鳊属鱼类区分,鉴定出鳊属鱼类长春鳊;引物TTF3、EST37、TTF2/TTF10、EST66依次组合可区分出鲂属东江三角鲂、厚颌鲂和广东鲂这3个群体。研究结果为我国鳊鲂鱼类种质资源保存、种群鉴定和良种选育奠定了基础。 相似文献
14.
本研究利用MISA软件挖掘长江刀鲚(Coilia ectenes)肌肉和肝脏转录组中的微卫星标记,为刀鲚选育群体的种质资源评估和分子标记辅助育种奠定基础。结果显示,从71869条Unigenes中共获得33896条重复单元长度为1~6碱基的微卫星序列;刀鲚转录组中不同类型微卫星的重复基序具有不同的分布特征,其中,单核苷酸重复、二核苷酸重复和三核苷酸重复为主要的微卫星重复类型,分别占总微卫星数目的34.94%、49.47%和13.34%;不同微卫星重复类型的优势重复基序亦有所不同,其中,A/T为单核苷酸重复基序的优势重复基序占86.25%,AC/GT为二核苷酸重复基序的为优势重复基序占75.25%,AGG/CCT为三核苷酸重复基序的优势重复基序占28.57%;不同微卫星重复基序核苷酸的数量和重复次数亦有所不同,重复次数伴随着重复单元中核苷酸数量的增加而呈现降低的趋势;从100对四核苷酸重复的SSR引物中筛选获得了16对多态性微卫星标记,并以此为基础,对长江刀鲚选育群体(F3)的遗传学特征进行了初步评估,结果显示,长江刀鲚选育群体F3的平均有效等位基因数(Ne)、平均观测杂合度(Ho)、平均期望杂合度(He)和Shannon多样性指数I分别为1.7580、0.3414、0.3977和0.6278。以上结果表明,基于刀鲚转录组数据批量开发微卫星是切实可行的,所开发的多态性微卫星标记能够应用于长江刀鲚选育群体的遗传背景评估和进一步的遗传育种研究。 相似文献
15.
ABSTRACT: In order to assess a daily change of genetic variability during spawning season, hatched larvae of red sea bream sampled on different dates were assayed by polymorphic markers such as microsatellite DNA (msDNA) and mitochondria DNA (mtDNA) control region. Based on the microsatellite loci, the average number of alleles per locus ranged between 13.7 and 18.3. The expected heterozygosities ranged between 0.843 and 0.919. A total of 23 mtDNA haplotypes were detected via digestion of mtDNA D-loop sequences with five endonucleases: Taq I, Alu I, Mbo I, Rsa I and Hinf I. Significant fluctuation of genetic variability during spawning season was detected by both types of DNA markers. It was suggested that the genetic variability was maintained by pooling the seed fish collected on different spawning dates in a hatchery. 相似文献
16.
We describe herein the discovery of 3905 putative single-nucleotide polymorphisms (SNPs) from the alignment of 4968 sequences
in a bay scallop Argopecten irradians irradians expressed sequenced tag (EST) database. The observed frequency of SNPs was estimated at one every 118.2 bp of contig sequences.
Thirty of the SNPs were chosen for validation by tetra-primer amplification refractory mutation system-polymerase chain reaction
procedure, and 17 of them were polymorphic with minor allele frequency ranging from 0.016 to 0.484. BLASTX gave significant
hits for all but one of the 17 genotyped SNP-containing contigs, 11 of which were located in coding regions and all resulted
in a synonymous substitution. Parentage simulation demonstrated that SNP markers were more sensitive to the number of parents
compared with microsatellites, thus more SNPs were needed to counteract low polymorphism. A table of optimal codons was deduced
from the analysis of the A. i. irradians EST dataset to explain the frequency difference for a specific SNP. It seems that the selection of codon usage may be partly
responsible for the frequency difference between the two alleles of the coding SNPs. These are the first SNPs developed for
the bay scallop and will provide a useful complement to currently available genetic markers. 相似文献
17.
采用磁珠富集法,以生物素标记的(CA)10寡核苷酸为探针,构建了三角帆蚌(Hyriopsis cumingii)基因组微卫星富集文库。根据微卫星位点的侧翼序列设计引物,随机挑选扩增出与预期大小相符的32对引物,引物荧光标记后对24个三角帆蚌个体分别进行PCR扩增,共筛选出20对多态性较好的引物。结果表明,20个微卫星位点的等位基因数为5～20,有效等位基因数2.321 3～13.260 3。观察杂合度和期望杂合度分别为0.318 2～1.000 0和0.582 5～0.946 1;PIC值0.547 2～0.919 9;其中14个位点符合Hardy-Weinberg平衡(P>0.05)。本研究筛选的20个微卫星标记可作为三角帆蚌遗传多样性、种群遗传结构等研究的理想分子标记。 相似文献
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19.
采用FIASCO(Fast Isolation by AFLP Sequences Containing Repeats)方法构建了仿刺参基因组富集CA微卫星序列的基因组短片段文库,筛选得到118条微卫星DNA序列。根据重复单元的排列特点,完美型共83个,占70.4%;非完美型共30个;占25.4%;复合型标记5个,占4.2%。选取其中20条微卫星序列设计引物进行多态性检测,并利用这20对引物对采自中国、韩国(西海岸及东海岸)、俄罗斯和日本沿海的野生仿刺参以及美国沿海的具疣拟刺参进行遗传多样性水平和遗传结构分析。结果表明,所设计的20对引物的扩增产物均具有多态性,其中16个位点为高度多态(PIC>0.5)。遗传多样性分析结果显示,20个微卫星座位的平均观察杂合度(Ho)和平均期望杂合度(He)分别为0.39和0.69,共检测到231个等位基因(102个有效等位基因),在每个座位上获得3～20个等位基因,平均等位基因数为11.6个,20个位点在6个群体中不同程度偏离遗传平衡(P<0.05),所有群体在整体上均表现为杂合子缺失(Fis>0);5个仿刺参群体间的遗传相似系数在0.71以上,相似性较高,而仿刺参群体与具疣拟刺参的相似性则较低。聚类分析结果表明,中国群体与韩国西海岸群体聚类成一支,而俄罗斯群体、韩国东海岸群体和日本群体聚类成另外一支,聚类的先后与它们在地理分布上的海域位置有一定的相关性。 相似文献
20.
ABSTRACT: Genetic differentiation and relationships between Crassostrea plicatula and Crassostrea gigas populations from China were studied by means of the microsatellite technique. Seven loci were used to screen five populations each collected from C. plicatula and C. gigas . All loci showed high polymorphism for all populations, as observed in average number of alleles per locus (19.1–28.1), and average expected heterozygosity (0.891–0.954). Significant departures from Hardy–Weinberg equilibrium due to heterozygote deficiency were observed over most populations at each locus and were best explained by null alleles. F ST values showed significant genetic differentiation between C. plicatula and C. gigas populations. According to the neighbor-joining tree constructed on the basis of the genetic distance ( D A ), the ten populations fell into two distinct groups ( C. plicatula and C. gigas groups), and the results of principal coordinate analysis and assignment tests also supported the neighbor-joining clustering. The outcomes presented here suggested that the microsatellite markers have great potential for differentiating C. plicatula from C. gigas populations. The information obtained in this study has important implications for the suitable management and conservation of these genetic resources in China. 相似文献