Development of Microsatellite Markers for Siamese Crocodile (Crocodylus siamensis)
5
Citation
13
Reference
20
Related Paper
Citation Trend
Abstract:
New microsatellite markers were developed for Siamese crocodile (Crocodylus siamensis) by constructing a library for microsatellite DNA. Construction and characterization of the library are described in the present study. Twenty microsatellite markers were developed from a (AC)15 enriched microsatellite DNA library. Among the twenty microsatellite loci, ten (50%) were polymorphic, where as the rest were monomorphic (with two to four alleles per locus). The microsatellite sequences obtained could be classified structurally into perfect repeats (80%) and imperfect repeats (20%). No incomplete repeat type was observed. These markers were tested in five individuals of the same species and these tests resulted in twenty new microsatellites markers for C. siamensis. Low number of alleles (1-4 alleles) with an average of 1.7 alleles per locus was observed. The average length of uninterrupted repeats from the selected clones was 12.3.Keywords:
Crocodylus
Cite
In the present study, ten novel microsatellite markers were developed from an enriched-(CA) 13 genomic library of Epinephelus akaara.The mean number of alleles per locus was 21.6, with a range of 12 to 33.Observed heterozygosity ranged from 0.767 to 0.967, and expected heterozygosity ranged from 0.831 to 0.975, with mean values of 0.877 and 0.923, respectively.Among the ten loci, three loci deviated from Hardy-Weinberg equilibrium after sequential Bonferroni's correction.These polymorphic microsatellite markers may be useful for studies on the population genetics of E. akaara.
Bonferroni correction
Cite
Citations (2)
Shorthorn
Bovine genome
Cite
Citations (3)
Cite
Citations (0)
Four polymorphic microsatellite markers were developed for the spotted babylon, Babylonia areolata, from a microsatellite enriched library. Those markers, characterized in 32 individuals from one wild population, were polymorphic with allele numbers ranging from 5 to 15 per locus, expected and observed heterozygosity ranging from 0.60 to 0.92 and from 0.36 to 0.88, respectively. One locus showed significant (p<0.05 after Bonferroni correction) deviation from Hardy–Weinberg equilibrium, probably due to the presence of null alleles. These microsatellite markers should be useful for population genetics studies in this species. In addition, nine primer pairs amplified duplicated microsatellites, with four multiple loci clearly linked in tandem, which provides a good opportunity to study the evolution of repetitive DNA sequences in the genome.
Link (geometry)
Cite
Citations (4)
An enrichment library of GATA-repeats from genomic DNA was constructed in this study to isolate and characterize microsatellite loci in Tsaiya duck (Anas platyrhynchos).Thirty-three microsatellite markers were developed and used to detect polymorphisms in 30 Tsaiya ducks.A total of 177 alleles were observed and all loci except APT022 were polymorphic.The number of alleles ranged from 2 to 9 with an average of 5.5 per microsatellite locus.The observed and expected heterozygosity of these polymorphic markers ranged from 0.07 to 0.93 with an average number of 0.60 and 0.10 to 0.86 with an average number of 0.61, respectively.Among the polymorphic markers, the observed heterozygosities of 23 loci were higher than 0.50 (69.70%).The polymorphism information content (PIC) in the 32 loci ranged from 0.09 to 0.83 with an average of 0.57.Seven of the 33 duck microsatellite loci had orthologs in the chicken genome, but only APT004 had a similar core repeat to chickens.These microsatellite markers will be useful in constructing a genetic linkage map for the duck and a comparative mapping with the chicken can also provide a valuable tool for studies related to biodiversity and population genetics in this duck species.
Isolation
Characterization
Cite
Citations (9)
We developed 20 polymorphic microsatellite loci by 5 0 -anchored PCR and constructing a microsatellite- enriched genomic library. The number of alleles per locus ranged from two to twelve, and observed and expected heterozygosities from 0.2357 to 1.0000 and from 0.4156 to 0.9169, respectively. Seven loci deviated from the HWE in the sampled population, null alleles were found in four loci, and gamete linkage disequilibrium between two loci was significant. These microsatellite markers will be useful for the study of population structure and genetic diversity of M. nipponense.
Linkage Disequilibrium
Null allele
Cite
Citations (0)
Multiplex
Cite
Citations (1)
Microsatellite markers specific to Cheirostylis yunnanensis Rolfe were developed using an enriched genomic DNA library technique. The library was constructed using (AG) 20 and (CAG) 20 oligonucleotide repeats. A total of 48 primer pairs were designed and tested with 48 C. yunnanensis Rolfe samples, resulting in 11 polymorphic loci. The number of alleles per locus ranged from 2 to 12, with an average of six alleles. The observed and expected heterozygosity ranged from 0.0426 to 0.8085 and 0.0421 to 0.9078, respectively. Of the 11 polymorphic loci, three showed a significant deviation from Hardy–Weinberg equilibrium and one exhibited linkage disequilibrium. Cross-species amplification was tested with five samples of Cheirostylis of unknown species resulting in eight loci that could be amplified, with the number of alleles ranging from one to two. The microsatellite markers developed in this study will be useful for the genetic analysis of C. yunnanensis in order to differentiate species as well as to establish a conservation plan for this species.
Linkage Disequilibrium
Cite
Citations (2)
Linkage Disequilibrium
Null allele
Cite
Citations (4)
Duck conservation strategy based on genetic characteristics has been undertaken to preserve indigenous breeds and produce high quality offspring. In addition, the genetic characteristic analysis provides further information for studying avian influenza viruses. The aim of this research was to study the genetic characterisation of indigenous Central Javanese duck in Indonesia using microsatellite markers. Microsatellite or simple sequence repeats (SSR) or short tandem repeats (STR) of various breeds of Central Javanese duck were analysed on 35 local ducks which consisted of seven variants of Javanese ducks in Central Java. Ten pairs of duck microsatellite primers were used to amplify the DNA from feathers. Nine out of 10 microsatellite loci (90%) demonstrated polymorphic patterns containing 50 alleles. The number of alelles varied from two to 10 alleles at various polymorphic microsatellite loci with an average of 5.56 alelles per locus. From the study, CAUD013 locus was determined as the highest heterozygosity with 0.882 score while CAUD030 locus was the lowest one with 0.034 score.Similarly, CAUD030 locus had the lowest PIC score (0.30) whereas the CAUD013 locus had the highest PIC value (0.869). Hence, it was showed that microsatellite markers were highly polymorphic in several loci for the Central Javanese duck and may be useful for genetic description of other native duck in terms of species conservation.
Cite
Citations (4)