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1.
Barfin flounder (Verasper moseri) and spotted halibut (Verasper variegatus) are two economically important marine fish species for aquaculture in China, Korea and Japan. Construction of genetic linkage
maps is an interesting issue for molecular marker-assisted selection (MAS) and for better understanding the genome structure.
In the present study, we constructed genetic linkage maps for both fish species using AFLP and microsatellite markers based
on an interspecific F1 hybrid family (female V. moseri and male V. variegatus). The female genetic map comprised 98 markers (58 AFLP markers and 40 microsatellite markers), distributing in 27 linkage
groups, and spanning 637 cM with an average resolution of 8.9 cM. Whereas the male genetic map consisted of 86 markers (48
AFLP and 38 microsatellite markers) in 24 linkage groups, covering a length of 625 cM with an average marker spacing of 10 cM.
The expected genome length was 1,128 cM in female and 1,115 cM in male, and the estimated coverage of genome was 56% for both
genetic maps. Moreover, five microsatellite markers were observed to be common to both genetic maps. This is the first time
to report the genetic linkage maps of V. moseri and V. variegatus that could serve as the basis for genetic improvement and selective breeding, candidate genes cloning, and genome structure
research. 相似文献
2.
The construction of a genetic linkage map and evaluation of population genetic diversity both require large numbers of polymorphic
molecular markers. In the present study, we report 31 polymorphic microsatellite markers, of which 28 were isolated from two
repeat-enriched libraries constructed from genomic DNA, and three were detected in two genes (MCH-R1 and MCH-R2) of barfin
flounder (Verasper moseri). A total of 94 alleles were detected with an average of 3.0 alleles per locus. The number of alleles, observed and expected
heterozygosity per locus ranged from two to six, from 0.30 to 1.00 and from 0.33 to 0.78, respectively. Three loci significantly
deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0016) and no significant linkage disequilibrum between pairs of loci was found. Cross-species amplification of these markers
was evaluated using the closely related species spotted halibut (Verasper variegatus). This study will potentially be useful for stock management, constructing of a genetic linkage map, mapping economically
important quantitative trait loci (QTL), and studying the population genetic diversity of barfin flounder (Verasper moseri). 相似文献
3.
In the context of stock enhancement for aquatic animals, the risk of negative genetic impacts of releasing hatchery-produced
seedlings upon the genetic diversity of indigenous recipient populations becomes a growing concern. This issue is particularly
relevant to threatened or rare species such as a member of right-eye flounder, the spotted halibut Verasper variegatus. We present here 29 microsatellite markers for spotted halibut, expecting that these markers could serve as a molecular tool
of choice to address a wide range of conservation issues in this species. 相似文献
4.
Gui-Dong Miao Chang-Wei Shao Xiao-Lin Liao Hong-Yu Ma Yong-Sheng Tian Song-Lin Chen 《Conservation Genetics》2009,10(3):701-703
Barfin flounder (Verasper moseri) is a rare fish species in the world. Here, we reported 10 polymorphic microsatellite loci isolated from a dinucleotide-enriched
genomic library of barfin flounder (Verasper moseri). The number of alleles, observed, and expected heterozygosity per locus in a test population ranged from 2 to 6, from 0.3333
to 1.0000, and from 0.4866 to 0.7774, respectively. One locus significantly deviated from Hardy–Weinberg equilibrium after
Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. Cross-species amplification
of these microsatellite loci in additional five fish species was performed. These polymorphic microsatellite loci would be
useful for investigating genetic population structure and construction of genetic linkage map in Verasper moseri.
Gui-Dong Miao and Chang-Wei Shao Contributed equally to this work. 相似文献
5.
6.
Hongyu Ma Songlin Chen Jingfeng Yang Xiangshan Ji Siqing Chen Yongsheng Tian Jinzhen Bi 《Environmental Biology of Fishes》2010,88(1):9-14
Spotted Halibut (Verasper variegatus) is a commercially important marine fish species. In the present study, to isolate sex-specific markers in Spotted Halibut,
we screened the genomes of Spotted Halibut by AFLP technique with 64 different primer combinations. Two primer combinations,
MseI-CAG/EcoRI-ACC and MseI-CAT/EcoRI-AGG, produced a female-specific fragment in all females (n = 88) and in no males (n = 60, except 3 individuals), respectively. Both fragments were excised from the gel, cloned and characterized. The first
fragment (named VevaF533) was 533 bp long, while the length of the second one (named VevaF218) was 218 bp. The two sequences
showed no similarity to each other, and to the known sequences existing in the GenBank database using BLASTn. Cross-species
amplification showed that the marker VevaF218 is a species-specific marker which is present in Spotted Halibut females but
absent in Barfin Flounder (Verasper moseri). So this marker could be used for discriminating unambiguously between Spotted Halibut females and Barfin Flounder. Examination
of the patterns of inheritance of VevaF218 in an interspecific hybrid family (V. variegatus ♂×V. moseri ♀) showed a female-specific pattern of inheritance from mother to daughter, implying that the marker VevaF218
is located on the female sex chromosome. This study provides a reliable AFLP-based genetic sexing of Spotted Halibut that
could be useful for genetic mapping of the sex chromosomes and identification of sex-linked genes. 相似文献
7.
Isolation and characterization of microsatellite markers for the endangered <Emphasis Type="Italic">Taxus yunnanensis</Emphasis> 总被引:1,自引:0,他引:1
Ying-Chun Miao Jian-Rong Su Zhi-Jun Zhang Hui Li Jing Luo Ya-Ping Zhang 《Conservation Genetics》2008,9(6):1683-1685
Eleven polymorphic microsatellite loci were characterized for the endangered conifer Taxus yunnanensis. Eight loci were isolated through SSR-anchored PCR, one locus was developed by cross-species amplification tests, while the
last two loci were obtained from cross-species microsatellite sequences available in GenBank. Variability of these markers
was tested in 48 individuals collected from its main distribution range in Southwest China. The number of alleles per locus
ranged from 2 to 9, and the observed and expected heterozygosity varied from 0.000 to 0.625 and from 0.062 to 0.853, respectively.
Ten of these eleven loci were significantly deviated from Hardy–Weinberg expectation, except TS07 which showed a distinct
heterozygote excess. The availability of these new polymorphic microsatellite markers will provide an ideal marker system
for detailed population genetics studies in T. yunnanensis and potentially also for closely related species. 相似文献
8.
Fuli Liu Xiuliang Wang Jianting Yao Wandong Fu Delin Duan 《Journal of applied phycology》2010,22(1):109-111
Expressed sequence tag-derived microsatellite markers (EST-SSR) were generated and characterized in Laminaria japonica using data mining from updated public EST databases and polymorphism testing. Fifty-eight of 578 ESTs (10.0%) containing
various repeat motifs were used to design polymerase chain reaction (PCR) amplification primers. A total of 12 pairs of primer
were generated and used in the PCR amplification. Alleles per locus ranged from two to ten (average of 5.7). The observed
heterozygosities and expected heterozygosities were from 0.045 to 0.543 and from 0.056 to 0.814, respectively. All loci were
in Hardy–Weinberg equilibrium and no linkage disequilibrium was detected. These robust, informative, and potentially transferable
polymorphic markers appear suitable for population, genetic, parentage, and mapping studies of L. japonica. 相似文献
9.
The flagfish (Jordanella floridae) is commonly used in studies of wetlands ecology. Here we describe the isolation of ten microsatellite loci, six of which
were polymorphic. The observed number of alleles ranged from 4 to 24 and observed heterozygosities ranged from 0.59 to 0.81
for the polymorphic loci. The isolation of these markers will enable estimations of genetic diversity in natural populations. 相似文献
10.
Nguyen Van Dan Nirala Ramchiary Su Ryun Choi Tae Sik Uhm Tae-Jin Yang In-Ok Ahn Yong Pyo Lim 《Conservation Genetics》2010,11(3):1223-1225
Panax ginseng, commonly known as Korean ginseng, is a valued source of herbal medicine in Korea and China. We have developed and characterized
35 microsatellite markers in P. ginseng from available BAC end sequences. Characterization of these 35 SSR primer pairs in 14 cultivars of P. ginseng showed 12 primer pairs to be polymorphic and 19 primer pairs to be monomorphic, while the remaining four primer pairs did
not produce any product. The number of alleles amplified ranged from 4 to 8 per primer pair, with an average of six alleles
per locus. The expected and observed heterozygosities ranged from 0.7500 to 0.9678 and 0.5645 to 0.7109, respectively. None
of these loci deviated from Hardy–Weinberg equilibrium. All of the functional primer pairs of P. ginseng showed cross-species transferability with Panax quinquefolium. The cross-species transferable markers could be used for ginseng cultivar identification, for genomic studies, including
mapping of specific trait QTL/genes, and for measuring conservation of ginseng. 相似文献
11.
Transposable elements are important factors driving plant genome evolution. Upon their mobilization, novel insertion polymorphisms
are being created. We investigated differences in copy number and insertion polymorphism of a group of Mariner-like transposable
elements Vulmar and related VulMITE miniature inverted-repeat transposable elements (MITEs) in species representing subfamily Betoideae. Insertion sites of these elements were identified using a modified transposon display protocol, allowing amplification of longer fragments representing
regions flanking insertion sites. Subsequently, a subset of TD fragments was converted into insertion site-based polymorphism
(ISBP) markers. The investigated group of transposable elements was the most abundant in accessions representing the section
Beta, showing intraspecific insertion polymorphisms likely resulting from their recent activity. In contrast, no unique insertions
were observed for species of the genus Beta section Corollinae, while a set of section-specific insertions was observed in the genus Patellifolia, however, only two of them were polymorphic between P. procumbens and P. webbiana. We hypothesize that Vulmar and VulMITE elements were inactivated in the section Corollinae, while they remained active in the section Beta and the genus Patellifolia. The ISBP markers generally confirmed the insertion patterns observed with TD markers, including presence of distinct subsets
of TE insertions specific to Beta and Patellifolia. 相似文献
12.
Practically no studies on the population genetics of the spinner dolphin (Stenella longirostris) exist. Seventeen pairs of DNA primers, cloned from an Mbo I digestion of S. longirostris liver DNA, were selected from a total of 288 sequences. Eight polymorphic microsatellite DNA markers were selected from the
17 primer pairs following amplification of DNA from skin samples of 65 spinner dolphins. Characterization of the polymorphisms
revealed between three and nine alleles per loci. The observed heterozygosity ranged from 0 to 0.6032, while the expected
heterozygosity ranged from 0.5834 to 0.73. Seven of the eight designed primer pairs amplified DNA from three other delphinid
species. There was a marked low observed heterozygosity in the spinner dolphin suggesting a high level of inbreeding within
this species in the southern Atlantic. 相似文献
13.
Katherine P. Munkres Line K. Bay Dean R. Jerry Mark I. McCormick Lynne Van Herwerden 《Conservation Genetics》2007,8(4):987-990
Five new polymorphic microsatellite loci were developed for the coral reef damselfish Pomacentrus amboinensis. Twenty-four individuals from two Great Barrier Reef populations were genotyped at the five loci, with numbers of alleles
per locus ranging from 6–23 and observed heterozygosity between 0.42–0.92. In addition, the cross-species testing of six primers
developed for Stegastes partitus revealed one primer (SpGATA40) that was also polymorphic for P. amboinensis. Due to high levels of polymorphism (≥14 alleles) in at least four of the six loci and a high proportion of tetranucleotide
repeats, these microsatellite markers should be useful for parentage assignment as well as other investigations of individual
relatedness. 相似文献
14.
The use of primers designed originally to amplify DNA for one species in a different one can save time and resources, particularly for microsatellite loci. Microsatellite amplification improvements across two kelp families are reported, where loci originally described in Laminaria digitata (Laminariaceae) were tested in Lessonia nigrescens) was observed in two localities affected by massive mortality events. Nei’s distances among five populations presented similar patterns to those of 30 multilocus dominant loci (RAPD) evaluated in the same localities. Although some success might be achieved in cross-species microsatellite amplifications, the strong mutations detected between these two Laminarian families suggests that better results of cross-amplifications should be expected at much lower taxonomic levels. Thus, although more expensive, construction of new gene libraries is strongly recommended. 相似文献
15.
Jerzy K. Kulski Atsuko Shigenari Takashi Shiina Kazuyoshi Hosomichi Makoto Yawata Hidetoshi Inoko 《Immunogenetics》2009,61(4):257-270
The study of the association of the Human Leukocyte Antigen (HLA) alleles and polymorphic retrotransposons such as Alu, HERV, and LTR at various loci within the Major Histocompatibility Complex allows for a better identification and stratification of disease associations and the origins of HLA haplotypes in different populations. This paper provides sequence and association data on two structurally polymorphic MER9-LTR retrotransposons that are located 54 kb apart and in close proximity to the multiallelic HLA-A gene involved in the regulation of the human immune system. Direct DNA sequencing and analysis of the PCR products identified DNA nucleotide variations between the MER9-LTR sequences at the two loci and their associations with HLA-A alleles as potential haplotype and evolutionary markers. All MER9-LTR sequences were haplotypic when associated with common HLA-A alleles. The number of SNP loci was 2.5 times greater for the solo LTR at the AK locus, which is located closer to the HLA-A gene than the solo or 3′ LTR at the HG locus. Our study shows that the nucleotide variations of the MER9-LTR DNA sequences are additional informative markers in fine mapping HLA-A genomic haplotypes for future population, evolutionary, and disease studies. 相似文献
16.
We developed 11 polymorphic microsatellite markers for an endangered shrub Ammopiptanthus mongolicus using the Fast Isolation by AFLP of Sequences Containing repeats protocol. Polymorphism of each locus was assessed in 24
individuals from five natural populations of A. mongolicus. The average allele number of these markers was 4.2, ranging from 2 to 7. The observed (H
O) and expected (H
E) heterozygosities were 0.044–0.956 and 0.044–0.827, respectively. Further assessment in the congeneric species A. nanus revealed that nine of eleven loci were successfully amplified, but only two loci showed polymorphism. These markers provide
powerful tools for the conservation genetics studies of A. mongolicus. 相似文献
17.
Fanna Kong Yunxiang Mao Hui Yang Haijun Qu Xinghong Yan Li Wang 《Plant Molecular Biology Reporter》2009,27(4):496-502
Microsatellites are repetitive genomic elements that show high levels of variation and therefore are useful tools for studying
genetic polymorphism and constructing genetic linkage maps of eukaryotic organisms. Porphyra yezoensis Ueda is an economically important seaweed that is being targeted for genetic improvement using marker-assisted breeding.
Hence, in an attempt to develop microsatellite markers for P. yezoensis, a microsatellite (or simple sequence repeat)-enriched library was constructed to identify (GA)n and (CA)n motifs. A total
of 71 perfect microsatellite clones were identified, of which 30 simple sequence repeat primer pairs were developed. Of these,
24 (80%) amplified polymerase chain reaction products of expected sizes. Twelve primer pairs amplified two to four bands,
whereas another 12 primer pairs produced monomorphic banding patterns. Data for 12 loci were analyzed using POPGENE software
version 1.32. A total of 29 alleles were produced at 12 loci, with an average of 2.42 alleles (Na) and 1.81 effective alleles (Ne) per locus. These markers were used to analyze the genetic diversity within 11 geographically different lines of P. yezoensis. Overall, these lines were clustered into two divisions with those from close geographic locations clustering together. Further
cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of motif repeats
in different alleles were major sources of polymorphisms. 相似文献
18.
Cupressus chenggiana S. Y. Hu (Cupressaceae) is an endemic and endangered conifer species in southwest China. In order to study the population
genetics and design the effective conservation methods, we aimed to develop microsatellite primers for this species in the
present study. We developed eight new microsatellite loci for this species through biotin capture method. Polymorphism of
each locus was further assessed in 18 individuals from three geographically distant populations. The number of alleles per
locus ranged from 6 to 11 with an average of 8.13. The observed and expected heterozygosities ranged from 0.219 to 0.296 and
from 0.374 to 0.470, with averages of 0.254 and 0.417, respectively. We further found that three of nine microsatellite loci
developed previously for another congeneric species showed polymorphic banding patters. We performed primer-crossing tests
of these loci in the other two congeneric species which are closely related to C. chenggiana (C. gigantea and C. duclouxiana). These microsatellite markers would be effective for analyzing genetic diversity and population genetic structure of this
species and its morphological differentiation with the close relatives. 相似文献
19.
M. P. Fernández Y. Núñez F. Ponz S. Hernáiz F. J. Gallego J. Ibáñez 《Molecular breeding : new strategies in plant improvement》2008,22(3):455-465
Single nucleotide polymorphisms or SNPs are the most abundant form of genetic variation in the genome of plants and animals.
Microsatellites are hypervariable regions of genome, while their flanking regions are assumed to be as conserved as the average
of the genome. In the present study, flanking sequences of 10 microsatellite loci were compared in different cultivars of
Vitis to determine the existing polymorphism. For every microsatellite, about 8 homozygous cultivars (regarding the microsatellite
genotype) were chosen for sequencing. A total of 45 different varieties of Vitis and 91 sequences were analysed. Sequence polymorphisms were detected for all the microsatellite flanking regions studied,
including single nucleotide polymorphisms (SNPs), insertions and deletions. The number of identified changes varied considerably
among the loci with a frequency of one polymorphism every 41 nucleotides, being VVMD5 the most polymorphic one. A number of
SNPs were used to design SNP markers, which were scored by dideoxy single base primer extension and capillary electrophoresis
methodology. These SNP markers were employed to genotype 21 cultivars of Vitis vinifera and 4 varieties of other Vitis species. The utility of the markers developed as well as their utility for varietal identification and pedigree studies is
discussed, using a similar study carried out with the 10 microsatellites as a reference. 相似文献
20.
M. M. Belokon D. V. Politov E. A. Mudrik T. A. Polyakova A. V. Shatokhina Yu. S. Belokon N. V. Oreshkova Yu. A. Putintseva V. V. Sharov D. A. Kuzmin K. V. Krutovsky 《Russian Journal of Genetics》2016,52(12):1263-1271
Siberian stone pine, Pinus sibirica Du Tour is one of the most economically and environmentally important forest-forming species of conifers in Russia. To study these forests a large number of highly polymorphic molecular genetic markers, such as microsatellite loci, are required. Prior to the new high-throughput next generation sequencing (NGS) methods, discovery of microsatellite loci and development of micro-satellite markers were very time consuming and laborious. The recently developed draft assembly of the Siberian stone pine genome, sequenced using the NGS methods, allowed us to identify a large number of microsatellite loci in the Siberian stone pine genome and to develop species-specific PCR primers for amplification and genotyping of 70 microsatellite loci. The primers were designed using contigs containing short simple sequence tandem repeats from the Siberian stone pine whole genome draft assembly. Based on the testing of primers for 70 microsatellite loci with tri-, tetra- or pentanucleotide repeats, 18 most promising, reliable and polymorphic loci were selected that can be used further as molecular genetic markers in population genetic studies of Siberian stone pine. 相似文献