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1.
Sónia Rosenbom Vania Costa Beatrice Steck Patricia Moehlman Albano Beja-Pereira 《European Journal of Wildlife Research》2012,58(3):609-613
Once a diverse family, the Equidae family is now reduced to a single genus, Equus. From the seven extant species of the genus, the African wild ass (Equus africanus) is the most threatened with extinction (last survey indicated 600 individuals). In this work we tested 25 published microsatellite primer pairs isolated from the horse genome on 22 African wild ass (E. africanus) individuals from wildlife reserves and zoos. From the 25 loci tested, 15 amplified well and showed moderate allelic richness (5.06, mean number of alleles) and moderately high expected heterozigosity (0.59). Although all possible loci pairs showed no significant gametic disequilibrium (P?>?0.007), deviations from Hardy–Weinberg proportions were found in 2 out of the 15 analysed microsatellite loci (AHT5 and VHL20). Here, we propose these polymorphic markers to be used as a standard set in future studies on population and conservation genetics of the African wild ass. 相似文献
2.
E. Ohara T. Nishimura T. Sakamoto Y. Nagakura K. Mushiake N. Okamoto 《Molecular ecology resources》2003,3(3):390-391
We developed five microsatellite primer pairs for the yellowtail Seriola quinqueradiata. The loci were highly polymorphic, with eight to 14 alleles per locus, and can be used to study kinship and/or population structure. Many of these primer pairs amplified polymorphic loci in cross‐species amplification tests for two other Seriola species (S. lalandi and S. dumerili). 相似文献
3.
G. Pellegrino D. Cafasso A. Widmer M. Soliva A. Musacchio S. Cozzolino 《Molecular ecology resources》2001,1(4):279-280
In this paper we describe the isolation and characterization of six polymorphic microsatellite loci from the orchid Serapias vomeracea. This species is widely distributed in the Mediterranean region. Microsatellite loci were isolated from an enriched library and primer pairs were designed for 18 loci. Primer pairs for six loci amplified well and were tested on samples from southern Italy. Levels of genetic variability detected at these six loci are high, with numbers of alleles per locus ranging from 3 to 6, and observed heterozygosity (HO) ranging from 0.35 to 0.86. All primer pairs tested amplified DNA from four other Serapias species, indicating that the primers are useful for population genetic studies throughout the genus. 相似文献
4.
V. Mohindra R. K. Singh M. Palanichamy A. G. Ponniah K. K. Lal 《Zeitschrift fur angewandte Ichthyologie》2007,23(1):104-109
Genetic variability in three clariid species, Clarias batrachus, C. gariepinus and C. macrocephalus, were investigated by allozyme electrophoresis and mitochondrial DNA (ND 5/6) RFLP markers. The catfish species C. batrachus and C. macrocephalus are native to the Indian subcontinent and Southeast Asia, respectively, while the African catfish C. gariepinus was introduced to Asian countries for culture. Sixteen gene loci from 12 enzyme systems were analyzed. Fixed allelic differences were evident between pairs of species at least at four loci. In mtDNA RFLP analysis, eight composite haplotypes were observed and each species was characterized by a set of haplotypes. The UPGMA phylogenetic tree revealed three distinct clusters: C. batrachus; C. gariepinus (India and Thailand); and C. macrocephalus. 相似文献
5.
CHRISTINE OUINSAVI NESTOR SOKPON JEAN BOUSQUET CRAIG H. NEWTON DAMASE P. KHASA 《Molecular ecology resources》2006,6(2):480-483
Eleven microsatellite primer pairs were developed for the tropical African tree Milicia excelsa. Genomic DNA was enriched for dinucleotide (TCn and TGn) and tretranucleotide (GATAn), and 188 random clones were sequenced from both orientations. We designed and tested 44 oligonucleotide primer pairs, which were evaluated using genomic DNA from 30 M. excelsa mature trees collected from a natural population in Benin. Eleven of the 44 markers showed good amplification and were polymorphic. The number of putative alleles for polymorphic primer pairs varied from three to seven, with expected and observed heterozygosities ranging from 0.10 to 0.64 and from 0.10 to 0.80, respectively. All 11 loci amplified the related species Milicia regia, indicating that these primers will be useful for population and ecology genetic studies in other species of the genus Milicia. 相似文献
6.
From (CATC)n, (GATA)n, (AAAC)n, and (CA)n–enriched libraries for the lake sturgeon Acipenser fulvescens, 254 primer pairs were developed. These primer pairs resulted in the identification of 128 microsatellite loci in either A. fulvescens or A. medirostris. Polymorphic loci were identified in both sturgeon species for 48 of the primer pairs and 14 of the primer pairs amplified polymorphic loci only in A. medirostris. Most of the identified loci appear to be tetrasomic (79.1% in A. fulvescens and 64.5% in A. medirostris). These results offer estimates of the degree of diploidization in each of these species. 相似文献
7.
ANA M. IBARRA JESSICA L. PETERSEN THOMAS R. FAMULA BERNIE MAY 《Molecular ecology resources》2006,6(1):153-156
Four microsatellite‐enriched DNA libraries yielded 35 microsatellite loci from 100 primer pairs designed for Pacific lion‐paw scallop, Nodipecten subnodosus. The number of alleles ranged from four to 28. Three of the 35 loci were not in Hardy–Weinberg equilibrium and linkage disequilibrium was found for one pair of loci. These microsatellites will be used to analyse the population structure of the species in Mexico's Baja Peninsula to propose management strategies for scallop aquaculture development. Twenty‐six primer pairs cross‐amplified in Nodipecten nodosus, whereas none (Argopecten ventricosus) or few cross‐amplified in the Argopecten species. 相似文献
8.
ALBANO BEJA‐PEREIRA EVE ZEYL LAHOUSINE OURAGH HAMID NAGASH NUNO FERRAND PIERRE TABERLET GORDON LUIKART 《Molecular ecology resources》2004,4(3):452-455
During the last century, North African ungulate species have suffered from habitat loss and over‐hunting. Gazella dorcas (Antilopidae subfamily) and Ammotragus lervia (Caprinae subfamily) are among the ungulates that have suffered most. To help to protect these species, conservation programs and population genetics studies are being implemented. Here, we tested 30 published microsatellite primer‐pairs from Bovids (cattle, sheep and goat) on eight individuals from each species. From the 30 loci tested, 20 amplified well and showed moderate allelic richness (3.75 and 4.65 mean number of alleles per species, respectively, for G. dorcas and A. lervia), and moderatly high heterozygosity (0.53 and 0.63 per species, respectively). These 20 polymorphic markers will facilitate conservation and genetic studies in these two species, and promise to be widely useful across divergent ungulate taxa. 相似文献
9.
Wöhrmann T Weising K 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,123(4):635-647
A collection of 5,659 expressed sequence tags (ESTs) from pineapple [Ananas comosus (L.) Merr.] was screened for simple sequence repeats (EST-SSRs) with motif lengths between 1 and 6 bp. Lower thresholds of
15, 7 and 5 repeat units were used to define microsatellites of the mono-, di-, and tri- to hexanucleotide repeat type, respectively.
Based on these criteria, 696 SSRs were identified among 3,389 EST unigenes, together representing 2,840 kb. This corresponds
to an average density of one SSR every 4.1 kb of non-redundant EST sequences. Dinucleotide repeats were most abundant (38.4%
of all SSRs) followed by trinucleotide repeats (38.1%). Flanking primer pairs were designed for 537 EST-SSR loci, and 49 of
these were screened for their functionality in 12 accessions of A. comosus, 14 accessions of 5 additional Ananas species and 1 species of Pseudananas. Distinct PCR products of the expected size range were obtained with 36 primer pairs. Eighteen loci analyzed in more detail
were all polymorphic in pineapple, and primer pairs flanking these loci also generated PCR products from a wide range of genera
and species from six subfamilies of the Bromeliaceae. The potential to reveal polymorphism in a heterologous target species
was demonstrated in Deuterocohnia brevifolia (subfamily Pitcairnioideae). 相似文献
10.
Wei Xia Bo Zhang Dan Xing Ying Li Wenqiang Wu Yong Xiao Jinhua Sun Yajing Dou Wenqi Tang Jinlan Zhang Xiaolong Huang Yun Xu Jun Xie Jihua Wang Dongyi Huang 《Ecology and evolution》2019,9(18):10843-10853
The genus Dioscorea is widely distributed in tropical and subtropical regions, and is economically important in terms of food supply and pharmaceutical applications. However, DNA barcodes are relatively unsuccessful in discriminating between Dioscorea species, with the highest discrimination rate (23.26%) derived from matK sequences. In this study, we compared genic and intergenic regions of three Dioscorea chloroplast genomes and found that the density of SNPs and indels in intergenic sites was about twice and seven times higher than that of SNPs and indels in the genic regions, respectively. A total of 52 primer pairs covering highly variable regions were designed and seven pairs of primers had 80%–100% PCR success rate. PCR amplicons of 73 Dioscorea individuals and assembled sequences of 47 Dioscorea SRAs were used for estimating intraspecific and interspecific divergence for the seven loci: The rpoB‐trnC locus had the highest interspecific divergence. Automatic barcoding gap discovery (ABGD), Poisson tree processes (PTP), and generalized mixed Yule coalescence (GMYC) analysis were applied for species delimitation based on the seven loci and successfully identified the majority of species, except for species in the Enantiophyllum section. Phylogenetic analysis of 51 Dioscorea individuals (28 species) showed that most individuals belonging to the same species tended to cluster in the same group. Our results suggest that the variable loci derived from comparative analysis of plastid genome sequences could be good DNA barcode candidates for taxonomic analysis and species delimitation. 相似文献
11.
KATHRYN A. HODGINS IVANA STEHLIK PAULINE WANG SPENCER C. H. BARRETT 《Molecular ecology resources》2007,7(3):510-512
We report microsatellite primer pairs for the wild tristylous daffodil, Narcissus triandrus (Amaryllidaceae). From enriched libraries, we identified 58 unique microsatellite loci. We designed primer pairs for 27 of these loci and screened genomic DNA from 38 to 40 adults from a single population. For eight polymorphic loci, the number of alleles per locus ranged from five to 17. As six primers also amplified loci in three other Narcissus species, including two horticultural varieties, we expect that some of these markers will be transferable to other Narcissus species. 相似文献
12.
R. Kölliker E. S. Jones M. C. Drayton M. P. Dupal J. W. Forster 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(2-3):416-424
Highly informative molecular markers, such as simple sequence repeats (SSRs), can greatly accelerate breeding programs. The
aim of this study was to develop and characterise a comprehensive set of SSR markers for white clover (Trifolium repens L.), which can be used to tag genes and quantitative trait loci controlling traits of agronomic interest. Sequence analysis
of 1123 clones from genomic libraries enriched for (CA)
n
repeats yielded 793 clones containing SSR loci. The majority of SSRs consisted of perfect dinucleotide repeats, only 7% being
trinucleotide repeats. After exclusion of redundant sequences and SSR loci with less than 25 bp of flanking sequence, 397
potentially useful SSRs remained. Primer pairs were designed for 117 SSR loci and PCR products in the expected size range
were amplified from 101 loci. These markers were highly polymorphic, 88% detecting polymorphism across seven white clover
genotypes with an average allele number of 4.8. Four primer pairs were tested in an F2 population revealing Mendelian segregation. Successful cross-species amplification was achieved in at least one out of eight
legume species for 46 of 54 primer pairs. The rate of successful amplification was significantly higher for Trifolium species when compared to species of other genera. The markers developed in this study not only provide valuable tools for
molecular breeding of white clover but may also have applications in related taxa.
Received: 3 April 2000 / Accepted: 12 May 2000 相似文献
13.
Bon MC Jones W Hurard C Loiseau A Ris N Pickett C Estoup A Fauvergue X 《Molecular ecology resources》2008,8(4):930-932
We have developed 21 dinucleotide repeat microsatellite loci from African populations of Psyttalia lounsburyi (Silvestri) (Hymenoptera: Braconidae), a parasitoid wasp of the olive fruit fly, as part of a study assessing the role of introgression/hybridization in the success of a biological control introduction. We proposed suitable conditions for polymerase chain reaction multiplexing. All 21 loci were polymorphic with two to 21 alleles per locus within the Kenyan and South African populations tested. Most of them were successfully amplified in two other Psyttalia species. 相似文献
14.
J. A. COYER T. B. H. REUSCH W. T. STAM E. A. SERRO G. PEARSON G. PROCACCINI J. L. OLSEN 《Molecular ecology resources》2004,4(3):497-499
Zostera noltii is an important species of eelgrass occurring along European, north African, Mediterranean, Black Sea and Azov Sea coasts. Nine microsatellite loci were developed and no linkage disequilibrium was observed. Cross‐amplification was observed for all loci (polymorphic) in Z. japonica; only four loci amplified (monomorphic) in Z. marina. 相似文献
15.
M. E. Jones R. L. Stokoe M. J. Cross L. J. Scott T. L. Maguire M. Shepherd 《Molecular ecology resources》2001,1(4):276-278
Corymbia variegata (spotted gum) is an important commercial hardwood timber species in Australia. Fourteen polymorphic microsatellite loci were isolated from C. variegata, with 3–5 alleles amplified in three individuals examined. Cross‐species amplification in Corymbia was successful for all primer pairs, while 10 loci (71%) were successfully transferred to at least one species in the closely related genus Eucalyptus. 相似文献
16.
This study describes 12 microsatellite loci identified in the African grey parrot Psittacus erithacus. Eleven were polymorphic, with observed heterozygosities 42–94% (average 68) and exclusion powers of PE1 = 0.996 and PE2 = 0.999. Microsatellites have previously been developed for a number of other parrots but showed limited cross‐species polymorphism. Here high levels of cross‐species amplification were observed: 71% of 32 Psittacines (22 genera). At least seven loci, 58%, were polymorphic in other African parrots as well as Neotropical and Australasian parrots, which diverged from the African parrots c30.6 and over 41.4 million years ago, respectively. 相似文献
17.
JESSICA STAPLEY CHRISTINE M. HAYES JONATHAN K. WEBB J. SCOTT KEOGH 《Molecular ecology resources》2005,5(1):54-56
A total of 15 microsatellite primers pairs were developed for the Australian small‐eyed snake Rhinoplocephalus nigrescens. Five primers were used to screen 93 individuals of R. nigrescens and were also tested against eight species of the closely related genus Suta. Allelic diversity in R. nigrescens was high in three loci (12–27) and there was high heterozygosity (0.58–0.82). Observed heterozygosity did not deviate from Hardy–Weinberg expectations for the five loci tested. These primers will be useful in studies of population genetics and mating systems of small‐eyed snakes and related species. 相似文献
18.
Microsatellites and microsynteny in the chloroplast genomes of Oryza and eight other Gramineae species 总被引:9,自引:0,他引:9
T. Ishii S. R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(8):1257-1266
Primer pairs flanking ten chloroplast microsatellite loci, originally identified in Oryza
sativa cv Nipponbare, were evaluated for amplification and allelic diversity using a panel of 13 diverse cultivars of rice (O. sativa), 19 accessions of wild rice (three O. officinalis, five O. latifolia, five O.
minuta, four O. australiensis, one O. brachyantha and one O. ridleyi) and eight other Gramineae species (maize, teosinte, wheat, oat, barley, pearl millet, sorghum and sugarcane). Amplified
products were obtained for all samples at nine out of ten loci. Among the rice cultivars, the number of alleles per locus
ranged from one to four, with monomorphic patterns observed at five loci. The average polymorphism information content (PIC)
value at the other five (polymorphic) loci was 0.54 among the 13 cultivars. When wild rice and the other Gramineae species
were compared based on the proportion of shared alleles, their phylogenetic relationships were in agreement with previous
studies using different types of markers; however, the magnitude of the differences based on chloroplast microsatellites underestimated
the genetic distance separating these divergent species and genera. A sequence-based comparison of homologous regions of the
rice and maize chloroplast genomes revealed that, while a high level of microsynteny is evident, the occurrence of actively
evolving microsatellite motifs in specific regions of the rice chloroplast genome appears to be mainly a species or genome-specific
phenomenon. Thus the chloroplast primer pairs used in this study bracketed mutationally active microsatellite motifs in rice
but degenerate, interrupted motifs or highly conserved, mutationally inert motifs in distantly related genera.
Received: 17 March 1999 / Accepted: 11 November 1999 相似文献
19.
Isolation and characterization of Ligustrum micranthum (Oleaceae) microsatellite loci using paired‐end Illumina reads
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Twenty‐six microsatellite loci were developed and characterized for Ligustrum micranthum, a species endemic to the Ogasawara Islands, Japan. The genetic structure of this species must be clarified in order to restore the island's ecosystem. A total of 8511 primer pairs were designed from de novo sequencing. Of the 48 primer pairs selected, amplification and polymorphisms were tested using one population each from the Chichijima and Hahajima Islands of the Ogasawara Islands. Twenty‐six microsatellite loci were successfully amplified and the number of alleles for these loci ranged from five to 31 per locus, and the mean expected heterozygosities were 0.858 and 0.849, respectively. No significant deviation from the Hardy–Weinberg equilibrium was observed in either population, and no significant linkage disequilibrium was detected between any locus pair. The microsatellite loci reported in this study can be used in future studies to evaluate the genetic structure and mating system of L. micranthum. 相似文献
20.
Enriched genomic libraries were used to isolate and characterize dinucleotide microsatellite loci in Erica coccinea, a South African Cape fynbos heath species with distinct resprouter and seeder populations. Microsatellites were required
to investigate the effect of the contrasting demographic pattern driven by these two post-fire responses in the population
genetic structure of seeder and resprouter forms within this species. Eight microsatellite loci were characterised and amplified
a total of 106 alleles in 2 samples each of 30 individuals from 1 resprouter and 1 seeder population. Mean allele numbers
were 7.88 and 11.0 for the resprouter and seeder population, respectively. Both populations showed similar average observed
and expected heterozygosity levels, H
O(resprouter) = 0.683, H
O(seeder) = 0.696; H
E(resprouter) = 0.726, H
E(seeder) = 0.756, and average positive inbreeding coefficients F
IS(resprouter) = 0.058, F
IS(seeder) = 0.080. This set of microsatellite loci will be used to conduct a population genetic survey of seeder and resprouter
populations throughout the range of the species. Cross-species transferability was also assayed in four other South African
and four European species of the genus Erica, supporting their potential use for population genetic analyses. 相似文献