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1.
We characterized five polymorphic DNA microsatellite loci for the neotropical ponerine ant Pachycondyla inversa. The variability was initially tested in 19 workers from nine colonies from a Brazilian population. We found five to 12 alleles per locus, with observed heterozygosities between 0.72 and 0.95. The allele size ranged from 73 to 197 bp. The primers also successfully amplified DNA at all five loci in the closely related species P. villosa. 相似文献
2.
Selvaraju Kanagarajan Saraladevi Muthusamy Emily Chin-Fun Chen Hsin-Sheng Tsay 《Conservation Genetics》2009,10(5):1487-1490
We developed and characterized 8 polymorphic microsatellite loci or simple sequence repeats from the expressed sequence tags
database of the medicinal fungus, Antrodia cinnamomea. Variability was assessed in a panel of 23 strains collected from various regions of Taiwan. The number of alleles per polymorphic
locus ranged from two to seven loci with an average of 4.375 alleles per locus. The observed and expected heterozygosity values
ranged from 0.130 to 0.783 and from 0.122 to 0.809, respectively. No significant Hardy–Weinberg equilibrium was detected (P < 0.01) at all loci. The EST-SSR markers developed in the present study can be used for strain identification and population
genetic studies in A. cinnamomea. 相似文献
3.
Carol K. L. Yeung Yu-Cheng Hsu Cheng-Te Yao Shou-Hsien Li 《Conservation Genetics》2009,10(4):1081-1084
We isolated 23 polymorphic microsatellite loci of tetranucleotide, dinucleotide or compound repeat motif in the black-faced
spoonbill (Platalea minor). In a panel of up to 20 individuals, number of alleles per locus ranged from two to 19 (mean = 8) and heterozygosity from
0.278 to 0.950 (mean = 0.606). Allele frequencies of five loci deviated from that expected under Hardy–Weinberg Equilibrium,
and one of them was likely Z-linked. Excluding these loci, the remaining 18 loci should provide a sufficient set of molecular
markers for use in ecological and conservation genetic investigation of this globally endangered wader species, and cross-species
amplification test suggests that they are potentially useful in other Ciconiiformes waterbirds. 相似文献
4.
Tzen-Yuh Chiang Hung-Du Lin Tin-Yam Chan Cheng-Yu Hung Feng-Jiau Lin 《Conservation Genetics》2008,9(6):1653-1655
Populations of mudshrimp, Austinogebia edulis, in the intertidal mud flat of western Taiwan have severely declined due to habitat destruction and overfishing in the past
decades. Nine polymorphic microsatellite loci were isolated for this ecologically threatened species by using a polymerase
chain reaction-based procedure. The number of alleles per locus ranged from five to 14 in 20 specimens from Central West Taiwan.
Observed and expected heterozygosities ranged from 0 to 0.2500 (averaged at 0.0944) and 0.7333 to 0.9385 (averaged at 0.8524),
respectively. There were significant departures from Hardy–Weinberg expectations. Significant LD was discovered in most loci.
These primers may provide a tool for understanding population structure in A. edulis.
Tzen-Yuh Chiang and Hung-Du Lin contributed to the study equally. 相似文献
5.
Karine Monceau Maria Gaillard Estelle Harrang Diego Santiago-Alarcon Patricia. G. Parker Frank Cezilly Rémi A. Wattier 《Conservation Genetics》2009,10(5):1577-1581
Twenty-three polymorphic microsatellite loci, six dinucleotidic loci and 17 tetranucleotidic loci, were developed for the
Zenaida dove (Zenaida aurita), a bird species endemic to the Caribbean Islands. From a set of 30 individuals captured at one single location in Barbados,
we obtained 20 loci that did not deviate from Hardy–Weinberg Equilibrium. Number of alleles per locus ranged between 2 and
11 (average 7.05) and the expected heterozygosity per locus, He ranged between 0.321 and 0.881 (average 0.712). This gives an exclusionary power for parental analysis of 0.9999 and 1.0000,
knowing the genotype of one social parent, or both, respectively. Such results indicate that these 20 loci will be useful
for both studying population genetics and mate choice patterns in Z. aurita. All 20 loci amplified in four other Zenaida species, the Galápagos dove, Z. galapagoensis, the eared dove, Z. auriculata, the mourning dove, Z. macroura, the Pacific dove, Z. meloda, with 30–96% being polymorphic. 相似文献
6.
Marta Vila Neus Marí-Mena Shen-Horn Yen Carlos Lopez-Vaamonde 《Conservation Genetics》2010,11(3):1151-1154
Ten polymorphic microsatellite loci were developed for Graellsia isabelae. Polymorphism was assessed for 20 individuals from a Spanish population (Els-Ports-de-Beseit, Catalonia) and 39 more individuals
from one population in the French Alps and six other Spanish localities. Overall, the number of alleles per locus ranged from
5 to 24. Els-Ports-de-Beseit showed an average number of alleles per locus of 9.80 (SD = 4.32), observed heterozygosity was
0.71 (SD = 0.226), and expected heterozygosity was 0.788 (SD = 0.146). Genotypic frequencies conformed to Hardy–Weinberg equilibrium
at the Catalonian population, and no evidence for linkage disequilibrium was observed. Multilocus genotypes resulting from
this set of markers will be useful to determine genetic diversity and differentiation within and among populations of this
highly protected moth. Several loci amplified and resulted polymorphic in two related species: two loci in Actias neidhoeferi, and three loci in A. luna. 相似文献
7.
Tzen-Yuh Chiang Teh-Wang Lee Feng-Jiau Lin Kuo-Hua Huang Hung-Du Lin 《Conservation Genetics》2008,9(5):1399-1401
Varicorhinus alticorpus (Cyprinidae) is an endangered freshwater fish with a scattered distribution in the southern and eastern regions of Taiwan.
We described the development of nine polymorphic microsatellite loci in V. alticorpus for genetic studies. These new markers were tested in 20 individuals of the rare species. The number of alleles ranged from
4 to 13. Expected (H
E) and observed (H
O) heterozygosities ranged from 0.692 to 0.892 (averaged at 0.821) and from 0.000 to 0.350 (averaged at 0.088), respectively.
All loci are significantly deviated from Hardy–Weinberg expectations due to the heterozygote deficiency. This suite of highly
polymorphic microsatellites provides the first chance to undertake a conservation program for this species in Taiwan. It is
essential to evaluate its genetic diversity and the fine-scale population structure.
Tzen-Yuh Chiang, Teh-Wang Lee, and Feng-Jiau Lin contributed equally to this work. 相似文献
8.
The mud crab Scylla paramamosain plays a significant role in fishery resources in China. In this study, we developed 18 polymorphic microsatellite markers
in this important crab by 5′ anchored PCR technique. A total of 125 alleles were detected in a single population of 32 individuals
of S. paramamosain. The number of alleles per locus ranged from five to nine, with the allele size ranging from 166 to 316 bp. The polymorphism
information content (PIC), observed and expected heterozygosity ranged from 0.39 to 0.88, from 0.33 to 0.92 and from 0.42
to 0.86, respectively. Three loci (Scypa13, Scypa14 and Scypa15) deviated significantly from Hardy–Weinberg equilibrium (HWE)
after Bonferroni correction (P < 0.0028), and no linkage disequilibrium was found between loci pairs. These polymorphic microsatellite markers will be useful
for the study of population genetic structure, construction of genetic linkage maps and mapping of economically quantitative
trait loci (QTL) in S. paramamosain. 相似文献
9.
Emily R. A. Cramer L. Stenzler A. L. Talaba C. A. Makarewich S. L. Vehrencamp I. J. Lovette 《Conservation Genetics》2008,9(6):1657-1660
Single nucleotide polymorphisms (SNPs) are becoming more commonly used as molecular markers in conservation studies. However,
relatively few studies have employed SNPs for species with little or no existing sequence data, partly due to the practical
challenge of locating appropriate SNP loci in these species. Here we describe an application of SNP discovery via shotgun
cloning that requires no pre-existing sequence data and is readily applied to all taxa. Using this method, we isolated, cloned
and screened for SNP variation at 90 anonymous sequence loci (51 kb total) from the banded wren (Thryothorus pleurostictus), a Central American species with minimal pre-existing sequence data and a documented paucity of microsatellite allelic variation.
We identified 168 SNPs (a mean of one SNP/305 bp, with SNPs unevenly distributed across loci). Further characterization of
variation at 41 of these SNP loci among 256 individuals including 37 parent–offspring families suggests that they provide
substantial information for defining the genetic mating system of this species, and that SNPs may be generally useful for
this purpose when other markers are problematic. 相似文献
10.
Hye Suck An Jung Youn Park Mi-Jung Kim Eun Young Lee Kyung Kil Kim 《Conservation Genetics》2009,10(6):1969-1972
Here we report development and characterization of 14 polymorphic microsatellite loci from Sebastes schlegel. Polymorphism at these loci revealed from 3 to 23 alleles. The observed heterozygosity ranged from 0.34 to 1.00, and the
expected heterozygosity ranged from 0.31 to 0.95. No linkage disequibrium was found. Two loci were significantly deviated
from HWE (P < 0.01). The 14 loci were also surveyed in four other Sebastes species and 12 loci successfully amplified, where allelic diversity ranged from highly polymorphic to monomorphic. These
results demonstrate these microsatellite markers can be used for the study of intra- and inter-specific genetic diversity. 相似文献
11.
CHRIS D. LOWE STEPHEN J. KEMP IAN F. HARVEY DAVID J. THOMPSON PHILLIP C. WATTS 《Molecular ecology resources》2007,7(5):880-882
We isolated and characterized 10 polymorphic microsatellite loci from the azure damselfly Coenagrion puella (Zygoptera; Coenagrionidae) as part of a study assessing reproductive success and genetic structure in an isolated population of this species. Levels of genetic diversity were assessed in 50 individuals collected from Queen Elizabeth Country Park, Hampshire, UK. The number of alleles per microsatellite loci ranged from three to 22 and the observed and expected heterozygosities varied between 0.26 and 0.84 and between 0.23 and 0.91, respectively. Two loci showed significant (P < 0.05) heterozygote deficits, likely because of null (non‐amplifying) alleles; one pair of loci was in linkage disequilibrium. 相似文献
12.
Guidong Miao Changwei Shao Hongyu Ma Xiaolin Liao Songlin Chen 《Conservation Genetics》2009,10(3):631-633
Starry flounder (Platichthys stellatus) is a rare fish species in China. Here, we reported 12 polymorphic microsatellite loci isolated from a dinucleotide-enriched
genomic library of starry flounder (P. stellatus). The number of alleles, observed and expected heterozygosity per locus in 30 individuals ranged from two to six, from 0.2500
to 1.0000 and from 0.4512 to 0.7667, respectively. One locus significantly deviated from Hardy–Weinberg equilibrium after
Bonferroni correction and no significant linkage disequilibrium between pairs of loci was found. Cross-species amplification
of these microsatellite loci in additional three fish species was performed. These polymorphic microsatellite loci would be
useful for investigating genetic population structure and construction of genetic linkage map in P. stellatus.
Guidong Miao and Changwei Shao have contributed equally. 相似文献
13.
The Yangtze sturgeon (Acipenser dabryanus) is an endemic species in China. Using 454 sequencing, eight polymorphic tri‐, tetra‐, penta‐, and hexanucleotide microsatellite loci were isolated in this study. The raw sequence data from a one‐eighth run of 454 sequencings were 38.0 Mbp containing 94 222 reads/sequences. Of 80 microsatellite loci, only eight loci were polymorphic in a population of 30 individuals. The number of alleles per locus ranged from 4 to 14 (mean 7.62), and the observed heterozygosities varied between 0.46 and 0.88 (mean 0.74). Cross amplification was tested in congeneric species Acipenser sturio and Acipenser sinensis. These new microsatellite markers will be useful for further studies on genetic variation, parentage analysis, and conservation management for this critically endangered species. 相似文献
14.
A. Geraldes S. P. DiFazio G. T. Slavov P. Ranjan W. Muchero J. Hannemann L. E. Gunter A. M. Wymore C. J. Grassa N. Farzaneh I. Porth A. D. McKown O. Skyba E. Li M. Fujita J. Klápště J. Martin W. Schackwitz C. Pennacchio D. Rokhsar M. C. Friedmann G. O. Wasteneys R. D. Guy Y. A. El‐Kassaby S. D. Mansfield Q. C. B. Cronk J. Ehlting C. J. Douglas G. A. Tuskan 《Molecular ecology resources》2013,13(2):306-323
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost‐effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre‐ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids. 相似文献
15.
MEI‐TING WANG YU‐CHENG HSU CHENG‐TE YAO SHOU‐HSIEN LI 《Molecular ecology resources》2005,5(2):439-442
From a partial genomic library enriched for GATA short tandem repeats, we developed 12 polymorphic microsatellite loci from the green‐backed tit (Parus monticolus). We characterized these loci by genotyping 30 adult individuals with unknown relationship. The number of alleles ranged from four to 17 per locus (mean = 9.3 alleles) and the observed heterozygosity for each locus ranged from 0.633 to 0.933 (mean = 0.789). All loci conformed to Hardy–Weinberg expectations. Four of 66 possible pairwise comparisons between loci showed significant gametic disequilibrium. 相似文献
16.
Yong-Sheng Tian Gui-Dong Miao Chang-Wei Shao Xiao-Lin Liao Song-Lin Chen 《Conservation Genetics》2009,10(4):1041-1043
Stone flounder (Kareius bicoloratus) is a rare fish species in China. Here, we reported 11 polymorphic microsatellite loci isolated from a repeat-enriched genomic
library of stone flounder. The number of alleles, observed and expected heterozygosity per locus in 32 individuals ranged
from 3 to 6, from 0.1613 to 0.8667 and from 0.1549 to 0.7932, respectively. Two loci significantly deviated from Hardy–Weinberg
equilibrium after Bonferroni correction and no significant linkage disequilibrium between pairs of loci was found. Cross-species
amplification of these microsatellite loci in additional three fish species was performed. These polymorphic microsatellite
loci would be useful for investigating genetic population structure and construction of genetic linkage map in Kareius bicoloratus.
Yong-Sheng Tian and Gui-Dong Miao are contributed equally. 相似文献
17.
Alessandra M. Tomasulo‐Seccomandi Nancy A. Schable A. Lawrence Bryan I. Lehr Brisbin Silvia N. Del Lama Travis C. Glenn 《Molecular ecology resources》2003,3(4):563-566
We isolated 11 polymorphic microsatellite loci for wood stork (Mycteria americana). Polymerase chain reaction (PCR) primers and conditions are described for the amplification of five dinucleotide, one trinucleotide and five tetranucleotide microsatellite loci. The PCR primers were tested on two wood stork populations, Fazenda Ipiranga, Mato Grosso, Brazil (n = 11) and Tamiami West, Everglades, Florida, USA (n = 20). The primers yielded two to four alleles per locus, an observed heterozygosity of 0.0–0.727 and a polymorphic information content of 0.048–0.604. The low level of polymorphism for these markers is consistent with previous studies of this species. 相似文献
18.
Peter Wimberger Jenni Burr Andy Gray Andres Lopez Paul Bentzen 《Marine biotechnology (New York, N.Y.)》1999,1(3):311-315
We describe the first microsatellites for rockfishes in the diverse genus Sebastes. Clones containing microsatellites were isolated from the genomic library of a quillback rockfish, Sebastes maliger. Twelve microsatellites are characterized; six of these are polymorphic in quillback rockfish, and eight are polymorphic in
at least one rockfish species on which they were tested. The number of alleles per variable locus ranged from 4 to 15 and
averaged 6.8. The expected heterozygosities ranged from 0.38 to 0.79 and averaged 0.60 in these loci. These loci should prove
valuable in studies examining species identification, population genetics, hybridization, paternity, kinship, and microsatellite
evolution.
Received September 8, 1998; accepted November 23, 1998. 相似文献
19.
Panyu Hua Tingting Guo Wenchao Liu Shuyi Zhang Stephen J. Rossiter 《Conservation Genetics》2009,10(3):597-600
We used the enriched genomic library method to isolate and characterize dinucleotide microsatellite loci in the least horseshoe
bat, Rhinolophus pusillus. Seventeen loci were obtained and tested on 31 individuals sampled from Guangxi Province in southern China. Thirteen of these
markers were polymorphic with expected heterozygosity ranging from 0.821 to 0.909. A total of 164 alleles were detected and
the number of alleles per locus ranged from 9 to 16 (mean 12.6). These polymorphic markers will be used to assess population
structure in R. pusillus. In addition, successful cross-amplification in five congeneric bat species suggests most of these markers will also be useful
for studying related species. 相似文献
20.
We have isolated and characterized 17 tetranucleotide microsatellite loci for Blanchard's cricket frog (Acris crepitans blanchardi), an anuran common in the central USA. Sixteen loci were organized into four multiplex amplification reactions. These loci were highly polymorphic when screened in 55 individuals from two distant populations, with 11–48 alleles per locus (average = 24.8). Observed and expected heterozygosities ranged from 0.18 to 0.97 and from 0.17 to 0.96, respectively. Nine loci were also polymorphic in Acris crepitans crepitans, with seven polymorphic in Acris gryllus. Five loci amplified in all three taxa. These loci will be useful for population‐ and species‐level investigations of this widespread group. 相似文献