Fifteen novel polymorphic microsatellites in rock carp, Procypris rabaudi (Tchang), an endemic fish species in the upper reaches of the Yangtze River drainage

Fifteen new microsatellite markers were isolated in rock carp, Procypris rabaudi (Tchang), from an AC-enriched genomic library. The allele number of these loci ranged from three to 13 (average 6.87 per locus) in the tested 24 individuals. Polymorphism information content (PIC) ranged from 0.453 to 0.821 with an average of 0.719. Average observed and expected heterozygosities were 0.712 (range 0.565–0.917) and 0.772 (range 0.542–0.855), respectively. These microsatellite markers could be useful in the population genetic study of rock carp.     

Isolation and characterization of nine polymorphic microsatellite loci in the rock carp, Procypris rabaudi (Tchang)

Nine highly polymorphic microsatellite loci were isolated from AC- and GATA-repeat microsatellite enrichment DNA libraries in the rock carp, Procypris rabaudi (Tchang). The number of alleles for these loci ranged from eight to 18 in tested individuals. Polymorphism information content ranged from 0.712 to 0.908 with an average of 0.837. Average observed and expected heterozygosities were 0.719 and 0.870, respectively. These molecular markers will be useful for the assessment of genetic diversity and analysis of population structure in wild rock carp.     

Development of microsatellite DNA markers of grass carp (Ctenopharyngodon idella) and their cross-species application in black carp (Mylopharyngodon piceus)

Thirty-four microsatellite DNA loci were developed for grass carp (Ctenopharyngodon idella) and used to determine the diversity of 42 individuals of grass carp and 16 individuals of black carp collected from Jingzhou fragment (the middle reach) of Yangtze River. All the 34 loci were polymorphic in grass carp. The number of alleles found in grass carp at these loci ranged from 2 to 24. The observed and expected heterozygosities varied from 0.238 to 1.000 and from 0.162 to 0.945, respectively. Thirty of the 34 loci cross-amplified the DNA of black carp (Mylopharyngodon piceus), and 21 of them revealed polymorphism (more than one allele each locus).     

Polymorphic microsatellites from silver crucian carp (Carassius auratus gibelio Bloch) and cross‐amplification in common carp (Cyprinus carpio L.)

Fifteen polymorphic microsatellites were isolated from the genome of silver crucian carp (Carassius auratus gibelio Bloch). Allele numbers ranged from two to four with an average of 2.7/locus, and the proportion of tri‐ and diallelic heterozygotes was 99.3%. The individuals tested seem to have originated from two different clonal lines: 14 of 16 showed the same genotype at all loci tested, whereas the remaining two were also identical, but different from the former ones. Eleven out of 15 primer pairs cross‐amplified products from the genome of common carp, whereas only five from that of zebrafish.     

Polymorphic microsatellite markers for the Iberian rock lizard species,Iberolacerta cyreni,and cross‐species priming in other Iberolacerta species

Eight polymorphic microsatellite loci are described for the Iberian rock lizard species, Iberolacerta cyreni. Loci were isolated from a partial genomic library that had been enriched for AAAG repeat sequence. Number of alleles per locus ranged from two to 13 in a sample of 24 individuals from the Sierra de Guadarrama (central Spain). Observed heterozygosity ranged from 0.13 to 0.96. At least three loci were amplified and polymorphic in four other Iberian rock lizard species: Iberolacerta monticola, Iberolacerta bonnali, Iberolacerta aranica and Iberolacerta aurelioi. These markers will be used to study mating strategies and reproductive success in I. cyreni.     

Polymorphism of microsatellite markers in Russian common carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis> L.) breeds

Using five microsatellite loci, genotyping and genetic diversity estimates were obtained for nine samples representing seven common carp breeds most widespread in Russia. For comparison, the samples of Amur wild common carp (Cyprinus carpio haematopterus) and a sample of European Hungarian carp were used. In the samples examined (n = 148) a total of 78 alleles were revealed. The highest mean allele number per locus (7.3) was identified in Amur wild common carp, while the lowest number was found in Cherepets carps (4.0). In different breeds, the observed heterozygosities varied from 0.819 (Altai carp) to 0.651 (Cherepets scaly carp). Three out of five microsatellite loci (MFW-24, MFW-28, and MFW-19) revealed a high level of population differentiation. In the dendrogram of genetic differences, all breeds clustered into two groups. One of these groups was composed of the two strains of Ropsha carp, Stavropol carp, Amur wild common carp, and the two samples of Cherepets carp. The second cluster included Altai carp (Priobskii and Chumysh populations), two Angelinskii carp breeds (mirror and scaly), and Hungarian carp. The pairs of breeds/populations/strains, having common origin, were differentiated. Specifically, these were two populations of Altai carp, two strains of Ropsha carp, as well as the breeds of Angelinskii and Cherepets carps. The reasons for genetic differentiation of Russian common carp breeds, as well as the concordance of the evolutionary histories of these breeds, some of which originated from the European breeds, while the others contain substantial admixture of the Amur wild common carp, are discussed.     

Novel polymorphic microsatellites for the red‐legged partridge (Alectoris rufa) and cross‐species amplification in Alectoris graeca

The red‐legged partridge, Alectoris rufa, is an endemic species of the southwestern Mediterranean, and the most popular game bird in the Iberian Peninsula. A total of 27 microsatellite loci was isolated from an enriched genomic library of A. rufa. Six perfect GT microsatellites were characterized and optimized in 45 individuals of A. rufa. All loci revealed high levels of polymorphism with a number of alleles that ranged from three to 13. Observed heterozygosity ranged from 0.2 to 0.6. Cross‐species amplification showed that all loci were also polymorphic in rock partridge, Alectoris graeca. The new markers will be useful in determining hybridization between both species of Alectoris.     

Genetic diversity of common carp from two largest Chinese lakes and the Yangtze River revealed by microsatellite markers

Six polymorphic microsatellites (eight loci) were used to study the genetic diversity and population structure of common carp from Dongting Lake (DTC), Poyang Lake (PYC), and the Yangtze River (YZC) in China. The gene diversity was high among populations with values close to 1. The number of alleles per locus ranged from 2 to 11, and the average number of alleles among 3 populations ranged from 6.5 to 7.9. The mean observed (H _O) and expected (H _E) heterozygosity ranged from 0.4888 to 0.5162 and from 0.7679 to 0.7708, respectively. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at majority of the loci and in all three populations in which heterozygote deficits were apparent. The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations and within populations were 3.03 and 96.97, respectively. The Fst values between populations indicated that there were significant genetic differentiations for the common carp populations from the Yangtze River and two largest Chinese freshwater lakes. The factors that may result in genetic divergence and significant reduction of the observed heterozygosity were discussed.     

Isolation and characterization of polymorphic trinucleotide microsatellites of the polyploid crucian carp (Carassius auratus)

In this study, we isolated and characterized nine polymorphic trinucleotide microsatellites (CAG and CCT) from the crucian carp (Carassius auratus). The number of alleles per locus ranged from two to six. Five loci showed a significantly excess homozygosity, and a genetic linkage between CAL0102 and CAL0495 was strongly suggested. Our results confirmed the triploidy of Korean individuals, and the microsatellites were found to be useful for analysing the allelic state of the polyploid crucian carp.     

Development and characterization of microsatellite markers to study population genetic diversity of Przewalski's naked carp Gymnocypris przewalskii in China

Two populations of Przewalski's naked carp Gymnocypris przewalskii, 30 individuals per population, were screened for 10 microsatellite loci. Moderate allele variation was found in these loci with two to eight alleles per locus. The expected and observed heterozygosity ranged from 0·019 to 0·805 and from 0·160 to 0·575, respectively.     

Multiplex microsatellite PCR panels and their application in genetic analyses of bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix)

In this study, three multiplex PCR panels involving twelve microsatellite loci were developed for cross-species amplification in bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix). The panels were verified using population genetic analyses, and species and simulated hybrid discriminations based on the genotype data of all individuals from two populations for each species. The number of alleles (Na), the observed and expected heterozygosity (Ho and He), and the polymorphic information content (PIC) of twelve loci were ranged from 5 to 20, 0.189 to 0.956, 0.177 to 901, and 0.169 to 0.887, respectively. Overall, almost all the microsatellite loci were detected as highly polymorphic across the two species. The populations of same species showed close genetic distances and similar genetic structures. Significant genetic differentiations were only detected between populations from different species, with a higher variation between species (21.17%) compared with that between populations within species (0.18%). In the species and simulated hybrid discrimination analyses, the individuals from different species were separated distinctly, and the simulated hybrids could almost be separated with the true individuals. In brief, the results indicated the high efficiency of the microsatellite multiplex panels developed in this study, which provide a practicable tool for further genetic analyses of H. nobilis and H. molitrix.     

Identification of microsatellite DNA markers for population structure analysis in Indian major carp, Cirrhinus mrigala (Hamilton-Buchanan, 1882)

Forty‐four primer sequences available for four cyprinid fishes were tested to amplify microsatellite loci in Indian major carp, Cirrhinus mrigala. A total of 12 loci were successfully amplified with clear scorable patterns and five thereof were polymorphic. Suitability of the identified polymorphic loci in population structure analysis of C. mrigala was assessed. Genetic variation was examined in 76 specimens collected from five different rivers. The mean observed heterozygosity ranged from 0.247 to 0.333. Significant heterogeneity in allele frequencies was detected, indicating that the samples analysed did not belong to homogenous populations. The identified microsatellite markers are promising for the analysis of intraspecific divergence in C. mrigala across its distribution range.     

Isolation and characterization of twenty-one polymorphic microsatellite loci in the Tibetan macaque (<Emphasis Type="Italic">Macaca thibetana</Emphasis>)

Twenty-one microsatellite loci were isolated from AC-enriched library of Tibetan macaque (Macaca thibetana). The number of alleles at the 21 microsatellite loci ranged from 8 to 15, with an average of 12.2 per locus. Polymorphism information content (PIC) ranged from 0.805 to 0.910 with an average of 0.873. The observed and expected heterozygosities ranged from 0.208 to 0.792 and from 0.843 to 0.938, respectively. These microsatellite loci will be useful for future studies that relate to the genetic diversity and population structure of Tibetan macaque.     

Isolation and characterization of microsatellite markers from Fangzheng silver crucian carp,Carassius auratus gibelio (Bloch), and cross‐amplification in the closely related species crucian carp,Carassius auratus auratus (Linnaeus)

We report the development of 20 microsatellite markers for Fangzheng silver crucian carp, Carassius auratus gibelio (Bloch). Nineteen out of 20 showed polymorphism with alleles ranging from two to 14. These loci were screened to amplify the closely related species crucian carp, Carassius auratus auratus (Linnaeus) and all of them can amplify DNA with the size similar to the former. The origin of silver crucian carp is in issue and the population genetic structure is still unclear. Microsatellite markers isolated from the silver crucian carp and their utility in the crucian carp will be useful for these researches.     

Development of microsatellite DNA markers of silver carp (Hypophthalmichthys molitrix) and their cross‐species application in bighead carp (Aristichthys nobilis)

Forty‐four microsatellite DNA markers were developed for silver carp, and used to investigate polymorphisms of 41 wild silver carps and seven wild bighead carps collected from Jingzhou fragment of Yangtze River. In silver carp, 40 markers were polymorphic. A total of 297 alleles were detected at 40 polymorphic loci. The number of alleles per locus varied from two to 16 with an average of 7.4 and the expected heterozygosities of each locus ranged from 0.07 to 0.91 with an average of 0.69. All markers amplified both silver carp and bighead carp DNAs.     

Ten polymorphic microsatellite loci in Tibetan chicken, <Emphasis Type="Italic">Gallus gallus domesticus</Emphasis>

Through an improved enrichment protocol, a genomic library for (AC)₁₂ repeats was constructed and 34 microsatellite loci were isolated and characterized in an endangered animal, Tibetan chicken, Gallus gallus domesticus. In the 34 loci, ten loci showed a distinct allelic variation ranging from 4 to 14 alleles in 54 individuals tested. Polymorphism information content (PIC) ranged from 0.590 to 0.869 with an average of 0.713. Average observed and expected heterozygosities were 0.7988 (ranged from 0.310 to 1.000) and 0.7495 (ranged from 0.609 to 0.897), respectively. These ten microsatellites loci would be the valuable genetic markers for further investigation of Tibetan chicken.     

Isolation and characterization of microsatellite DNA markers for the flagfish <Emphasis Type="Italic">Jordanella </Emphasis><Emphasis Type="Italic">floridae</Emphasis>

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.