Isolation and characterization of eighteen polymorphic microsatellite loci in Schizopygopsis younghusbandi Regan and cross-amplification in three other schizothoracinae species

Eighteen polymorphic microsatellite loci were isolated from Schizopygopsis younghusbandi Regan and the characterization of these loci was assessed in 46 individuals collected from the Yarlung Tsangpo River in Tibet, China. The number of alleles per locus ranged from 2 to 14. The expected heterozygosity and Shannon-Wiener diversity index ranged from 0.022 to 0.879 and from 0.059 to 2.313, respectively. The cross-species amplification and applicability of these loci were tested in three other Schizothoracinae species belonging to Schizothorax and Oxygymnocypris. These loci will be useful for the evaluation of genetic diversity and population genetic structure in S. younghusbandi and other related species.     

甘肃地区回族人群18个STR基因座的遗传多态性

研究了D5S818、D8S1179、D7S820、CSF1PO、D2S1338、D3S1358、v WA、D21S11、D16S539、Penta E、TPOX、TH01、D19S433、D18S51、FGA、D6S1043、D13S317、D12S391等18个短串联重复序列(short tandem repeats,STR)基因座在甘肃地区回族人群的遗传多态性。采用荧光标记复合扩增及毛细管电泳技术对1 038名甘肃地区回族无关个体18个STR基因座进行分析。研究结果显示,1 038名甘肃地区回族个体在18个STR基因座上,共检出223种等位基因,982种基因型,其分布均符合Hardy-Weinberg平衡(P0.05),18个基因座的杂合度(H)介于0.601~0.929之间,匹配概率(Pm)介于0.012~0.213之间,个体识别概率(DP)介于0.787~0.988之间,多态信息含量(PIC)介于0.550~0.920之间,非父排除概率(PE)值介于0.292~0.854之间。本文研究结果对甘肃地区回族人群群体遗传学及法医学后续研究应用具有参考价值。     

Development of twenty-one polymorphic tetranucleotide microsatellite loci for Schizothorax o'connori and their conservation application

Schizothorax o'connori, of the subfamily Schizothoracinae, is an endemic fish in the Yarlung Tsangpo River in Tibet, China. To evaluate the population genetic diversity as a means of devising conservation strategies, a total of 21 polymorphic tetranucleotide microsatellite loci were isolated from S. o'connori using the fast isolation by AFLP of sequences containing repeats (FIASCO) protocol. The characterization of these loci was assessed against a panel of 42 individuals. The number of alleles per locus ranged from 4 to 29 with an average of 17.76. Expected locus-specific heterozygosity and the multilocus Shannon–Wiener diversity index ranged from 0.114 to 0.951 and from 0.280 to 3.131, with an average of 0.851 and 2.338, respectively. The cross-species amplification and applicability of these loci were tested against the two other Schizothorax species from the same river. These microsatellite loci will be valuable for further studies of population genetic diversity and genetic structure, and assessments of the artificial propagation release effect of S. o'connori and other related species.     

Characterization of polymorphic microsatellite markers in the Dalmatian wall lizard Podarcis melisellensis (Squamata: Lacertidae)

We describe polymerase chain reaction primers and amplification conditions for 13 highly polymorphic microsatellite DNA loci isolated from the Dalmatian wall lizard, Podarcis melisellensis. The number of alleles per locus ranged from 12 to 41, with levels of observed heterozygosity between 0.62 and 0.94. Most of these loci were successfully cross-amplified in the closely related species P. sicula, but levels of polymorphism were always lower.     

Microsatellite markers for Spergularia media (L.) C. Presl. (Caryophyllaceae) and their cross-species transferability

We developed 11 polymorphic microsatellite markers for Spergularia media (Caryophyllaceae), a perennial halophyte of coastal salt meadows and continental areas of western Eurasia. The number of alleles per locus observed in a single population of 20 individuals from the German North Sea coast ranged from 3 to 20. Observed and expected heterozygosities ranged from 0.200 to 0.850 and from 0.278 to 0.936 respectively. Observed heterozygosities were lower than expected heterozygosities at all loci, presumably as a consequence of inbreeding. All markers cross-amplified in the closely related S. salina. Of these, nine were polymorphic in the heterologous species. Only two primer pairs generated PCR products in S. diandra.     

Isolation and characterization of microsatellite loci in Ainsliaea faurieana (Asteraceae), an endemic plant species on Yakushima Island, Japan, and cross-species amplification in closely related taxa

Fourteen microsatellite loci were isolated and characterized for Ainsliaea faurieana, an endemic perennial plant species on Yakushima Island. In an analysis of 37 individuals from Yakushima Island, the observed number of alleles ranged from two to six. The expected and observed heterozygosities were 0.109-0.811 and 0.000-0.27, respectively. The inbreeding coefficient was 0.489-1.000. The interspecific applicability of these microsatellites was evaluated by analysing three closely related taxa from the Ryukyu Islands. All primer pairs for the 14 loci tested successfully amplified in all taxa.     

Microsatellite DNA markers for population-genetic studies of blue mackerel (Scomber australasicus) and cross-specific amplification in S. japonicus

Blue mackerel (Scomber australasicus) is targeted by large-scale purse-seiners in the western North Pacific, and its stock structure is still contentious. Herein, we described 10 polymorphic microsatellite loci for blue mackerel. The number of alleles among 32 individuals surveyed ranged from five to 27 (average of 16.2 alleles per locus). Departures from Hardy-Weinberg expectation were observed at two loci. Cross-specific amplification in the congener, S. japonicus, was successful, except for one locus, revealed to be diagnostic for these congeners. These microsatellite loci will be useful tools to address queries in population genetic structure, fishery management unit and taxonomic species status in the genus Scomber.     

Characterization and cross-amplification of 13 microsatellite loci in the northern pine processionary moth, Thaumetopoea pinivora (Lepidoptera: Notodontidae)

Thirteen polymorphic microsatellite loci were developed for the northern pine processionary moth (Thaumetopoea pinivora) and tested for cross-amplification in seven other species within the Thaumetopoea family. Number of alleles ranged from two to 10 when at least 28 individuals from one population were screened and one locus, Thapin06, appears to be sex linked. Expected heterozygosity ranged from 0.094 to 0.856 and observed heterozygosity ranged from 0.097 to 0.806. Amplification success varied between sister species, with two up to seven loci being successfully amplified. The described loci will be valuable for studying the population genetic structure and dispersal behaviour of this forest pest.     

Cytological studies on the Sino-Himalayan endemic Solms-laubachia (Brassicaceae) and two related genera

The karyotypes of six species of Solms-laubachia and one each of Parrya and Desideria (Brassicaceae) from the Himalayan-Hengduan Mountains (Tibet, Sichuan and Yunnan provinces) were investigated. Chromosome counts of S. xerophyta , S. lanata, S. platycarpa and D. baiogoinensis are reported for the first time and found to be diploid with 2 n  = 14. Diploid counts were also made of S. retropilosa , a species previously known to be a tetraploid. The karyotype formulae of D. baiogoinensis , S. eurycarpa , S. pulcherrima , S. retropilosa , S. xerophyta and S. platycarpa are 2 n  = 14 = 6 m + 6sm + 2st, whereas those of S. lanata and P. nudicaulis are 2 n  = 14 = 6 m + 2sm + 6st and 2 n  = 14 = 8 m + 4sm + 2st, respectively. Karyotypes and counts of S. eurycarpa and S. pulcherrima are in agreement with prior studies. The relationships within Solms-laubachia and among the three genera are discussed. Speciation within Solms-laubachia may have been the result of primarily intrachromosomal variation at the diploid level, and the genus probably evolved within the Himalayan-Hengduan Mountains instead of migrating from other regions.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 77−86.     

Development of nine new microsatellite loci for the American beaver, Castor canadensis (Rodentia: Castoridae), and cross-species amplification in the European beaver, Castor fiber

We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cross-species amplification in Castor fiber was successful only in four loci, we tested also nine recently published C. canadensis loci in the Eurasian species. Eight of the published loci amplified; however, three were monomorphic. The number of alleles was lower in C. fiber than in C. canadensis at all loci tested.     

Isolation and characterization of 12 tetranucleotide repeat microsatellite loci from the green‐backed tit (Parus monticolus)

From a partial genomic library enriched for GATA short tandem repeats, we developed 12 polymorphic microsatellite loci from the green‐backed tit (Parus monticolus). We characterized these loci by genotyping 30 adult individuals with unknown relationship. The number of alleles ranged from four to 17 per locus (mean = 9.3 alleles) and the observed heterozygosity for each locus ranged from 0.633 to 0.933 (mean = 0.789). All loci conformed to Hardy–Weinberg expectations. Four of 66 possible pairwise comparisons between loci showed significant gametic disequilibrium.     

Isolation and characterization of microsatellite markers for Pinellia ternata and cross-species amplification

In this study, we isolated and characterized 12 microsatellite loci for Pinellia ternata. Polymorphism of these 12 loci was assessed in 46 individuals collected from two wild populations. All the loci were polymorphic with four to 13 alleles per locus and the observed and expected heterozygosities ranged from 0.312 to 0.680 and from 0.506 to 0.734, respectively. None of the loci showed significant deviation from Hardy–Weinberg equilibrium (P < 0.05). No significant linkage disequilibrium was observed between pairs of studied loci. In addition, most markers amplified successfully in three closely related taxa that are Pinellia cordata, P. peltata and P. pedatisecta. These microsatellite markers could provide a useful tool for genetic structure studies of the Pinellia species.     

Isolation and characterization of polymorphic microsatellite loci in the field vole,Microtus agrestis,and their cross‐utility in the common vole,Microtus arvalis

We developed nine polymorphic microsatellite loci for the field vole, Microtus agrestis. The number of alleles ranged from five to 15 and observed heterozygosities ranged from 0.40 to 1.00. We also tested the microsatellite loci for amplification and polymorphism in the congeneric species Microtus arvalis. Five of the nine loci were successfully analysed in this species. The microsatellite markers will be employed in studies of reproductive success and fine‐scale spatial genetic structure.     

Isolation and characterization of 11 microsatellite loci from the black fly, Simulium negativum (Diptera: Simuliidae)

Eleven polymorphic microsatellite loci were isolated and developed from the black fly, Simulium negativum, a member of the Simulium arcticum sibling species complex. The observed heterozygosity of the 11 loci ranged from 0.03 to 0.83. The number of alleles per locus ranged from 8 to 19. Significant linkage disequilibria were encountered only for the primer pairs BF7-1 with BF7-5 and BF6-32 with BF7-16. Presumably, these microsatellite loci can be used to study genetic structure within the entire S. arcticum complex.     

Characterization of microsatellite loci in the Jamaican fruit‐eating bat Artibeus jamaicensis and cross‐species amplification

Artibeus jamaicensis is one of the most common bat species in the neotropics, with a well‐defined polygynous social structure in caves. In order to study behaviour and to examine patterns of paternity and relatedness between different harem groups, we developed 14 microsatellite loci from two different enriched genomic libraries. We screened 125 individuals from two different bat colonies and found that polymorphism ranged from five to 13 alleles. Heterozygosity ranged from 63 to 95%. The primers amplified across 14 bat species, indicating their potential utility for population‐level studies in several closely related bat species.     

Polymorphic Microsatellite Markers for Solen grandis and Their Cross-Species Amplification in Three Other Species

The grand jackknife clam Solen grandis is a commercially important mollusk species, but has been suffering from severe population decline due to over-exploitation and habitat destruction in China. To promote a conservation program for this species, it is necessary to evaluate its genetic diversity and population genetics. In this study, 10 novel polymorphic microsatellite makers were developed and characterized from the S. grandis through high throughput sequencing. The number of alleles at each locus ranged from 10 to 34 with an average of 20.8 alleles per locus. The observed and expected heterozygosities varied from 0.433 to 1.000 and from 0.696 to 0.976, with an average of 0.793 and 0.884, respectively. The polymorphism information content (PIC) value ranged from 0.633 (Sg43838) to 0.958 (Sg3754), with an average of 0.858. The cross-species amplification transferability of 10 loci to three closely related species ranged from 4.17 to 62.5%. These microsatellite loci will be useful for further investigation of population structure and conversation genetics of this species.     

Isolation and characterization of fifteen polymorphic microsatellite loci in the threatened freshwater mussel Solenaia oleivora (Bivalvia: Unionidae)

Freshwater mussels are among the most endangered fauna in the world, while little is known about their genetic diversity. We isolated 15 polymorphic microsatellite loci in a threatened freshwater mussel, Solenaia oleivora. The characteristics of these loci were tested with 46 individuals. The number of alleles per locus ranged from 2 to 15, and the PIC value ranged from 0.250 to 0.880. The observed and expected heterozygosity ranged from 0.167 to 0.929 and from 0.297 to 0.900, with an average of 0.562 and 0.647, respectively. Eight loci deviated significantly from Hardy–Weinberg equilibrium. These polymorphic microsatellites will be useful for the assessment of population genetic diversity and resource conservation of S. oleivora. Cross-species amplification demonstrated that six of 15 microsatellite loci amplified successfully in two other unionid species.     

Isolation and characterization of polymorphic microsatellite loci in the endangered Portuguese freshwater fish Squalius aradensis (Cyprinidae)

Here we describe the isolation and characterization of six polymorphic microsatellite loci for Squalius aradensis. The number of observed alleles per locus ranged from three to 16 and the observed heterozygosity from 0.22 to 0.95. These primers will be useful in determining the population structure of S. aradensis and for conservation genetics of this endangered and endemic species. Furthermore, successful cross‐species amplification in S. alburnoides and Chondrostoma lusitanicum suggests that a wider amplification of these markers is possible.     

Isolation and characterization of polymorphic microsatellite DNA markers in the Japanese eight‐barbel loach,Lefua echigonia

We isolated and characterized 17 polymorphic microsatellite loci for the Japanese eight‐barbel loach, Lefua echigonia, an endangered freshwater species in streams including agricultural canals in Japan. The number of observed alleles for each locus ranged from two to nine, and the values of observed and expected heterozygosities ranged from 0.125 to 0.844 and from 0.148 to 0.876, respectively. All loci conformed to Hardy–Weinberg equilibrium. Genetic linkage disequilibrium analysis between all pairs of the loci showed no significant departure from the null hypothesis between any of the loci.     

Rapid isolation and characterization of polymorphic microsatellite loci in the mud crab, Scylla paramamosain (Portunidae)

Scylla paramamosain is a widespread and commercially important species of coastal marine crab. We identified 13 polymorphic microsatellite loci from a genome library constructed with 5'-anchored PCR method. Thirty-two S. paramamosain from the East China Sea were used to analyze the characteristics of these loci. The number of alleles per locus ranged from 3 to 8, with a mean of 5.923. Observed and expected heterozygosities ranged from 0.500 to 0.875 and from 0.500 to 0.859, respectively. Eleven of the 13 loci were highly polymorphic (polymorphic information content >0.5). All of the 13 novel loci were in Hardy-Weinberg equilibrium after Bonferroni's correction (P < 0.0038). There was no null allele, stuttering errors or evidence of allelic dropout in any of the loci analyzed by MICRO-CHECKER. According to pairwise tests, no significant linkage disequilibrium was found among the 13 loci (P < 0.0038, adjusted value). These novel developed microsatellites will be useful for studies of genetic variation, population structure, conservation genetics, and molecular-assisted selective breeding of S. paramamosain.