Tetranucleotide Microsatellite DNA Markers Research Articles

Isolation and characterization of 16 highly polymorphic tetranucleotide microsatellite DNA markers in Paa spinosa

The giant spiny frog, Paa spinosa is a vulnerable species. By using a modified FIASCO (Fast Isolation by AFLP Sequences Containing repeats) method, we isolated and characterized 16 polymorphic tetranucleotide microsatellite loci for P. spinosa. These loci had high polymorphism when screened in 33 randomly caught individuals. The average number of alleles for 16 loci was 7.13 (range 2–14). Observed and expected heterozygosities were 0.152–0.818 and 0.144–0.918, respectively, and did not deviate from Hardy–Weinberg expectations. There was no evidence for scoring error due to stutter, null alleles, or large allele dropout. No significant association between pairs of loci was found after Bonferroni correction. These polymorphic loci will be effective for evaluating genetic diversity, population structure, gene flow and determining paternity in this frog, and also for conservation management.

Tri- and tetra-nucleotide microsatellite DNA markers for the rayed bean freshwater mussel (Villosa fabalis)

Freshwater mussels are one of North America’s most imperiled species, and genetic characterization of these species is essential for recovery planning. The rayed bean (Villosa fabalis) is a small freshwater mussel found in the eastern United States currently listed as endangered. Fifteen microsatellite loci were identified and characterized in sixteen V. fabalis individuals. The number of alleles per locus observed ranged from 3 to 14 and averaged 7.9 alleles per locus. Average observed heterozygosity was 72.8 %. These markers should be useful for V. fabalis population analyses and restoration or recovery programs.

Isolation and characterization of 14 tetranucleotide microsatellite DNA markers in the elongate loach Leptobotia elongata (Cypriniformes: Cobitidae) using 454 sequencing technology

Anthropogenic factors have contributed to a severe decline of Leptobotia elongata. Conservation information of L. elongata will be required. Here, 14 tetranucleotide microsatellite DNA markers were developed from L. elongata through high-throughput (454) sequencing data. Twenty-four individuals of the species were genotyped using these markers. All of the loci displayed a high level of polymorphism with the number of alleles per locus ranged from 7 to 23, polymorphism information content ranged from 0.650 to 0.943. Observed and expected heterozygosities ranged from 0.609 to 1.000 and from 0.699 to 0.967, respectively. These markers provide an excellent toolkit to study population genetic structure and would benefit the conservation of this species.

Isolation and characterization of twenty tetranucleotide microsatellite DNA makers in a schizothoracin fish, Schizothorax prenanti (Tchang)

Prenant’s schizothoracin, Schizothorax prenanti (Tchang) is an important polyploidy fish in upper reaches of the Yangtze River. Given the extreme anthropogenic environmental alteration in the region, S. prenanti represents an excellent model organism to study historical and contemporary environmental changes. We developed twenty tetranucleotide microsatellite DNA markers from a tetranucleotide microsatellite enriched library. These highly polymorphic markers (2–23 alleles) will facilitate the population genetic analyses of this species.

Tools for the management and conservation of genetic diversity in brook trout (Salvelinus fontinalis): tri- and tetranucleotide microsatellite markers for the assessment of genetic diversity, phylogeography, and historical demographics

We document isolation and characterization of 13 tri- and tetranucleotide microsatellite DNA markers in brook trout (Salvelinus fontinalis). These markers displayed moderate to high levels of allelic diversity (averaging 20.5 alleles/locus) and heterozygosity (averaging 53.5%) in a range-wide survey of more than 13,000 fish. A comparison of two geographically proximal populations located on opposite sides of the eastern continental divide in Maryland, USA, found no deviations from Hardy–Weinberg equilibrium and minimal linkage disequilibrium. Microsatellite markers developed for S. fontinalis yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate phylogeographic structure; and (3) provide unique demographic perspectives of population sizes and historical demographics. This suite of markers also provided considerable cross-species amplification utility among related salmonids.

Assessing genetic diversity, fine-scale population structure, and demographics in the narrow endemic chittenango ovate amber snail (Novisuccinea chittenangoensis)

We document isolation and characterization of 12 tetra-nucleotide microsatellite DNA markers in the hermaphroditic Chittenango ovate amber snail ( Novisuccinea chittenangoensis ) endemic to Chittenango Falls in central New York State, USA. The markers displayed a moderate level of allelic diversity (averaging 5.2 alleles/locus) and heterozygosity (averaging 58.6%) in the single extant population. Allelic diversity was sufficient to produce unique multilocus genotypes; no indication of selfing was observed among this cosexual species. Minimal deviations from Hardy–Weinberg equilibrium and no linkage disequilibrium were observed when three collections, representing different rock ledge heights, were analyzed separately. A series of analyses identified weak population differentiation among the ledge collections. Demographic analyses suggested each collection has achieved mutation-drift equilibrium. The microsatellite markers developed for N. chittenangoensis yielded sufficient genetic diversity to: (i) distinguish all individuals and assess the level of selfing; (ii) elucidate fine-scale population structuring; and (iii) provide unique demographic perspectives for recovery efforts.

Tri- and tetra-nucleotide microsatellite DNA markers for assessing genetic diversity, population structure, and demographics in the Holmgren milk-vetch (Astragalus holmgreniorum)

We document the isolation and characterization of 17 tri- and tetra-nucleotide microsatellite DNA markers in the Holmgren milk-vetch (Astragalus holmgreniorum) surveyed among plants from three critical habitat units (CHUs) located in southern Utah and northern Arizona, USA. These markers displayed moderate to high levels of allelic diversity (averaging 19.5 alleles/locus) and heterozygosity (averaging 75.1%). No deviations from Hardy–Weinberg equilibrium and limited (1.8%) linkage disequilibrium were observed. A series of analyses identified significant population differentiation among the three CHUs. Demographic analyses suggested that each collection has achieved mutation-drift equilibrium. The microsatellite markers developed for A. holmgreniorum yielded sufficient genetic diversity to: (1) distinguish individuals and delineate kinship; (2) elucidate population structure; (3) define management units; and (4) provide unique demographic perspectives for recovery efforts.

Tools for assessing kinship, population structure, phylogeography, and interspecific hybridization in Asian carps invasive to the Mississippi River, USA: isolation and characterization of novel tetranucleotide microsatellite DNA loci in silver carp Hypophthalmichthys molitrix

We document the isolation and characterization of novel tetranucleotide microsatellite DNA markers for the invasive silver carp Hypophthalmichthys molitrix and provide the results of cross-species amplification for three additional invasive carp species: bighead (H. nobilis), grass (Ctenopharyngodon idella) and black (Mylopharyngodon piceus). In the target species these markers yielded levels of allelic diversity (average 4.4 alleles/locus) and heterozygosity (average 54.7%) sufficient to: (1) provide unique multilocus genotypes; (2) delineate kinship relationships; (3) differentiate populations/species; (4) estimate effective population sizes; and (5) provide unique demographic perspectives for control or eradication. Currently these markers are being utilized to determine the degree of introgressive hybridization between H. molitrix and H. nobilis, to quantify gene flow between different sub-basins established in the central United States, and to assess the demographic status of sub-basin groups. This information will be critically important in the management/control of these invasive species.

Novel tetra-nucleotide microsatellite DNA markers for assessing the evolutionary genetics and demographics of Northern Snakehead (Channa argus) invading North America

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy–Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness.

Ten novel tetranucleotide microsatellite DNA markers from Asiatic black bear, Ursus thibetanus

Ten polymorphic microsatellite markers were developed for the endangered Formosan black bear (Ursus thibetanus formosanus) from a partial genomic library enriched for GAAA repeat. Polymorphism of these loci was evaluated in 27 Formosan black bear specimens of unknown relationship. The number of alleles per locus ranged from 5 to 15 and the observed heterozygosity of each locus ranged from 0.556 to 0.889. These loci should provide useful molecular tools to study conservation genetics of the Formosan black bear and other Asiatic black bears.

Development of 10 tri‐ and tetranucleotide microsatellite loci for population studies in the common carp (Cyprinus carpio L.)

Ten tri- and tetranucleotide microsatellite DNA markers were isolated and characterized from common carp (Cyprinus carpio L.) to estimate genetic potential. These markers were tested in the samples from two closely related carp populations (Cyprinus carpio var. xingguonensis and Cyprinus carpio var. wananensis). The number of the alleles ranged from three to nine, and observed and expected hererozygosities varied from 0.207 to 1.000 and from 0.499 to 0.900 in each population, respectively. No evidence for linkage disequilibrium was found, indicating that these markers will be useful for population studies.

Microsatellite DNA markers for assessing phylogeographic and population structure in Preble's meadow jumping mice (Zapus hudsonius preblei) and cross‐amplification among neighbouring taxa

AbstractWe document the isolation and characterization of 14 tetranucleotide microsatellite DNA markers in Preble's meadow jumping mouse (Zapus hudsonius preblei). The identified markers displayed moderate levels of allelic diversity (averaging 4.9 alleles per locus) and heterozygosity (averaging 55.1%). Genotypic and allelic frequencies in a collection of 30 individuals conformed to Hardy–Weinberg equilibrium expectations and indicated no linkage disequilibrium. High levels of cross‐amplification (95% overall) among neighbouring subspecies and two congeners (Zapus princeps and Zapus trinotatus) were observed. Multilocus genotypes resulting from these markers appear to provide ample genetic diversity for studies assessing individual‐ and population–level ecological interactions within Z. h. preblei and evolutionary relationships among neighbouring subspecies (Z. h. campestris, Z. h. intermedius, Z. h. pallidus and Z. h. luteus).

Novel tetranucleotide microsatellite DNA markers for the wood frog, Rana sylvatica

AbstractFifteen tetranucleotide microsatellite loci were identified and characterized for wood frogs (Rana sylvatica) collected from three vernal pools in the southeastern US. These markers revealed a high degree of genetic diversity (nine to 34 alleles per locus), heterozygosity (30.6–92.3%) and allelic heterogeneity (69% of comparisons were statistically significant). Considerable differentiation among populations was observed as genetic distances (chord) ranged between 0.40 and 0.55 and all FST values (0.02–0.05) were statistically significant. Genotypic assignment tests correctly classified 103 of 113 individuals to their respective collection. These markers should prove useful for investigating fine‐scale population structure and metapopulation dynamics.

Isolation and characterization of novel tetranucleotide microsatellite DNA markers for the spotted salamander, Ambystoma maculatum

AbstractFifteen tetranucleotide microsatellite loci were identified and characterized for spotted salamanders (Ambystoma maculatum) collected from three vernal pools in the south‐eastern USA. These markers revealed a high degree of genetic diversity (7–32 alleles per locus), heterozygosity (31.6–86.3%) and allelic heterogeneity (91% of comparisons were statistically significant). Considerable differentiation among populations was observed as genetic distances (chord) ranged between 0.50 and 0.65, and all FST values (0.08–0.14) were statistically significant. Moreover, genotypic assignment tests correctly classified all individuals to their respective collection. These markers should prove useful for investigating fine‐scale population structure and mating system.