Isolation and characterization of polymorphic microsatellite loci in the lance‐tailed manakin (Chiroxiphia lanceolata)

Eight microsatellite loci were isolated from the lance‐tailed manakin (Chiroxiphia lanceolata), a polygynous lek‐breeding bird from Central America. Five of these loci were polymorphic (two to seven alleles per locus), with observed levels of heterozygosity ranging from 0.100 to 0.860 (n = 50 individuals). These variable loci provide a valuable tool for assessing patterns of parentage and relatedness within lance‐tailed manakin social groups.     

Twenty-three polymorphic microsatellite markers for the Caribbean endemic Zenaida dove, Zenaida aurita, and its conservation in related Zenaida species

Twenty-three polymorphic microsatellite loci, six dinucleotidic loci and 17 tetranucleotidic loci, were developed for the Zenaida dove (Zenaida aurita), a bird species endemic to the Caribbean Islands. From a set of 30 individuals captured at one single location in Barbados, we obtained 20 loci that did not deviate from Hardy–Weinberg Equilibrium. Number of alleles per locus ranged between 2 and 11 (average 7.05) and the expected heterozygosity per locus, He ranged between 0.321 and 0.881 (average 0.712). This gives an exclusionary power for parental analysis of 0.9999 and 1.0000, knowing the genotype of one social parent, or both, respectively. Such results indicate that these 20 loci will be useful for both studying population genetics and mate choice patterns in Z. aurita. All 20 loci amplified in four other Zenaida species, the Galápagos dove, Z. galapagoensis, the eared dove, Z. auriculata, the mourning dove, Z. macroura, the Pacific dove, Z. meloda, with 30–96% being polymorphic.     

Genetic differences between wild and hatchery‐bred brown trout (Salmo trutta L.) in single nucleotide polymorphisms linked to selective traits

To study effects from natural selection acting on brown trout in a natural stream habitat compared with a hatchery environment, 3,781 single nucleotide polymorphism (SNP) markers were analyzed in three closely related groups of brown trout (Salmo trutta L.). Autumn (W/0+, n = 48) and consecutive spring (W/1+, n = 47) samples of brown trout individuals belonging to the same cohort and stream were retrieved using electrofishing. A third group (H/1+, n = 48) comprised hatchery‐reared individuals, bred from a mixture of wild parents of the strain of the two former groups and from a neighboring stream. Pairwise analysis of F_ST outliers and analysis under a hierarchical model by means of ARLEQUIN software detected 421 (10.8%) candidates of selection, before multitest correction. BAYESCAN software detected 10 candidate loci, all of which were included among the ARLEQUIN candidate loci. Body length was significantly different across genotypes at 10 candidate loci in the W/0+, at 34 candidate loci in the W/1+ and at 21 candidate loci in the H/1+ group. The W/1+ sample was tested for genotype‐specific body length at all loci, and significant differences were found in 10.6% of all loci, and of these, 14.2% had higher frequency of the largest genotype in the W/1+ sample than in W/0+. The corresponding proportion among the candidate loci of W/1+ was 22.7% with genotype‐specific body length, and 88.2% of these had increased frequency of the largest genotype from W/0+ to W/1+, indicating a linkage between these loci and traits affecting growth and survival under this stream's environmental conditions. Bayesian structuring of all loci, and of the noncandidate loci suggested two (K = 2), alternatively four clusters (K = 4). This differed from the candidate SNPs, which suggested only two clusters. In both cases, the hatchery fish dominated one cluster, and body length of W/1+ fish was positively correlated with membership of one cluster both from the K = 2 and the K = 4 structure. Our analysis demonstrates profound genetic differentiation that can be linked to differential selection on a fitness‐related trait (individual growth) in brown trout living under natural vs. hatchery conditions. Candidate SNP loci linked to genes affecting individual growth were identified and provide important inputs into future mapping of the genetic basis of brown trout body size selection.     

Microsatellite markers for <Emphasis Type="Italic">Pseudopanax</Emphasis> trees and their cross-species amplification in the Araliaceae

In order to study hybridisation, taxonomic boundaries and phylogeography in the genus Pseudopanax (Araliaceae), we developed seven novel microsatellite loci from enriched genomic libraries of P. lessonii and P. crassifolius. These loci were characterised in 16 individuals from a single population of P. crassifolius, and displayed 2–11 alleles per locus. Observed heterozygosities ranged from 0.063 to 0.688. Most loci were polymorphic in the closely related Pseudopanax species, and several loci amplified widely across the Araliaceae.     

Development of EST-SSRs in scallop (Patinopecten yessoensis) from sequence database

Patinopecten yessoensis is a kind of cold water shellfish, and is an important economic species in China. In our study, we developed and evaluated simple sequence repeat (SSR) markers of P. yessoensis. Characteristics of 11 EST-SSR loci were investigated using 40 P. yessoensis individuals. The number of alleles per locus ranged from two to five. The observed heterozygosity ranged from 0.1026 to 0.9487, while the expected heterozygosity ranged from 0.1865 to 0.7433. All loci except P4 departed from Hardy–Weinberg equilibrium (P < 0.05) significantly. There was no LD observed between all pairs of EST-SSRs loci. These loci and markers will be useful for population genetics and systemic evolution of scallop.     

Characterization of eight polymorphic microsatellite markers in the tarnished plant bug,Lygus lineolaris (Palisot de Beauvois)

A partial genomic library of the tarnished plant bug, Lygus lineolaris, enriched for microsatellite sequences was screened to identify marker loci. Eight polymorphic loci suitable for population genetic studies were identified by screening 192 field‐collected insects. The observed number of alleles ranged from four to 21 with an average of 12.25 (SE ± 1.94) while the effective number of alleles ranged from 1.23 to 11.05 with an average of 4.49 (SE ± 1.15). No linkage disequilibria or significant deviations from Hardy–Weinberg expectations were detected at any of the loci. Seven of the eight L. lineolaris microsatellite loci were transferable to Lygus hesperus.     

Isolation of 22 new Haliaeetus microsatellite loci and their characterization in the critically endangered Madagascar fish‐eagle (Haliaeetus vociferoides) and three other Haliaeetus eagle species

We isolated a total of 22 microsatellite loci from two Haliaeetus species: the Madagascar fish‐eagle (Haliaeetus vociferoides) and the bald eagle (Haliaeetus leucocephalus). Five loci were monomorphic in both the Madagascar fish‐eagle (n = 24–43) and the bald eagle (n = 2–8) but were found to be polymorphic in other Haliaeetus species. Haliaeetus loci have proved useful for investigating gene flow in Haliaeetus and Aquila eagles. Ten loci were polymorphic in the critically endangered Madagascar fish‐eagle and will be used to investigate the genetic population structure and mating system in this species.     

Isolation and characterization of microsatellite DNA markers from mangrove crab,Scylla paramamosain

The first five variable microsatellite DNA loci for mangrove crab, Scylla paramanosain, were developed. Allelic variation and other characteristics at these loci were examined in this species captured at the Urado Bay, Japan. The number of alleles per locus ranged from 24 to 44. The expected heterozygosity across loci ranged from 0.900 to 0.999 and probability of identity (P_I) ranged from 2.8 × 10^?3 to 1.7 × 10^?2. Therefore, these microsatellite markers could be useful for estimating effect of stock enhancement release and population genetic structure of mangrove crab.     

Isolation and characterization of fourteen novel microsatellite loci in the Hong Kong oyster, Crassostrea hongkongensis

Fourteen polymorphic microsatellite markers were isolated from the Hong Kong oyster, Crassostrea hongkongensis, with a partial genomic library enriched for tandem repeat sequences of (CA)₁₂, (GA)₁₂, (ATG)₆ and (TAGA)₄. Polymorphism of these loci was assessed in a sample of 48 wild unrelated individuals. The average allelic number of these polymorphic loci was 6.36 per locus, with a range of 4–16. The observed and expected heterozygosity varied from 0.208 to 0.729 (averaging 0.502) and from 0.193 to 0.789 (averaging 0.615), respectively. After Bonferroni correction (P > 0.0036), 11 of the 14 loci accorded with Hardy–Weinberg equilibrium, and the rest three were detected significant departure from HWE. Additionally, two loci (Ch103 and Ch104) showed significant linkage disequilibrium (P < 0.01). This is the first set of microsatellite loci developed in this species and would be useful for studies of population genetics, stock management and other relevant research in C. hongkongensis.     

Isolation and characterization of microsatellite markers for the heavily exploited rockfish Sebastes schlegeli, and cross-species amplification in four related Sebastes spp.

Here we report development and characterization of 14 polymorphic microsatellite loci from Sebastes schlegel. Polymorphism at these loci revealed from 3 to 23 alleles. The observed heterozygosity ranged from 0.34 to 1.00, and the expected heterozygosity ranged from 0.31 to 0.95. No linkage disequibrium was found. Two loci were significantly deviated from HWE (P < 0.01). The 14 loci were also surveyed in four other Sebastes species and 12 loci successfully amplified, where allelic diversity ranged from highly polymorphic to monomorphic. These results demonstrate these microsatellite markers can be used for the study of intra- and inter-specific genetic diversity.     

Isolation of microsatellites from two species of scleractinian coral

Microsatellites were isolated from two broadcast‐spawning species of scleractinian coral (Platygyra daedalea and Goniastrea favulus) from Australia's Great Barrier Reef. We found 27 microsatellites across both species, although only five loci were polymorphic in each species. Microsatellite loci displayed a wide range of diversity levels with four to 11 alleles per locus (H_O = 0.26–0.91) in P. daedalea and two to seven alleles per locus (H_O = 0.16–0.96) in G. favulus. Most loci showed departures from Hardy–Weinberg equilibrium which may reflect nonrandom mating but may also be related to difficulties associated with coral DNA.     

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper,Lissotriton helveticus,and Triturus cristatus) and comparison with Illumina‐based approaches

The development of microsatellite loci has become more efficient using next‐generation sequencing (NGS) approaches, and many studies imply that the amount of applicable loci is large. However, few studies have sought to quantify the number of loci that are retained for use out of the thousands of sequence reads initially obtained. We analyzed the success rate of microsatellite loci development for three amphibian species using a 454 NGS approach on tetra‐nucleotide motif‐enriched species‐specific libraries. The number of sequence reads obtained differed strongly between species and ranged from 19,562 for Triturus cristatus to 55,626 for Lissotriton helveticus, with 52,075 reads obtained for Calotriton asper. PHOBOS was used to identify sequences with tetra‐nucleotide repeat motifs with a minimum repeat number of ten and high quality primer binding sites. Of 107 sequences for T. cristatus, 316 for C. asper and 319 for L. helveticus, we tested the amplification success, polymorphism, and degree of heterozygosity for 41 primer combinations each for C. asper and T. cristatus, and 22 for L. helveticus. We found 11 polymorphic loci for T. cristatus, 20 loci for C. asper, and 15 loci for L. helveticus. Extrapolated, the number of potentially amplifiable loci (PALs) resulted in estimated species‐specific success rates of 0.15% (T. cristatus), 0.30% (C. asper), and 0.39% (L. helveticus). Compared with representative Illumina NGS approaches, our applied 454‐sequencing approach on specifically enriched sublibraries proved to be quite competitive in terms of success rates and number of finally applicable loci.     

Isolation and characterization of 21 microsatellite loci in Lycium chinense and cross-amplification in Lycium barbarum

The present study reports isolation and characterization of 21 polymorphic microsatellite markers developed from Lycium chinense Mill. These markers produced a total of 86 alleles across 30 L. chinense accessions, with an average of 4.1 alleles per locus. Values for observed heterozygosity and polymorphism information content ranged from 0.03 to 0.81 (mean = 0.35) and from 0.03 to 0.78 (mean = 0.31), respectively. At the significance threshold (P < 0.05), 12 loci deviated from Hardy–Weinberg equilibrium, whereas significant linkage disequilibrium values were observed between 52 pairs of loci. All loci were successfully amplified for all L. barbarum accessions. These newly developed polymorphic microsatellite markers will be very useful for programming in the genetic conservation and classification of L. chinense and L. barbarum.     

Isolation and characterization of polymorphic microsatellite loci for the study of paternity and population structure in the little penguin Eudyptula minor

We isolated and characterized eight novel microsatellite loci in the little penguin Eudyptula minor, using nonradioactive polymerase chain reaction‐based techniques to screen GA and GAAA repeats from enriched genomic DNA libraries. All eight loci were polymorphic and seven were variable in our main study population (mean H_E = 0.613, mean N_A = 7.14). Cross‐amplification using a microsatellite primer developed in Spheniscus demersus (African penguin) yielded one additional polymorphic locus. This locus combined with six of the little penguin loci is suitable for paternity assignment in little penguins (exclusion probability for seven unlinked loci = 0.993).     

A multiplex panel of microsatellite markers for widespread sub‐Saharan rodents of the genus Mastomys

We isolated and characterized 12 polymorphic microsatellite loci in the sub‐Saharan rodent Mastomys huberti. We tested cross‐species amplification of all these loci in three closely related Mastomys species: M. coucha, M. erythroleucus and M. natalensis. Multiplex panels comprising 11 loci were developed and their application to a set of individuals in each species allowed clear and easy characterization of allele sizes. Statistics from 31 M. huberti coming from one locality in Mali showed no deviation from Hardy–Weinberg equilibrium except for one locus, and no significant linkage disequilibria between loci.     

Development of EST‐derived microsatellite markers for Arabidopsis lyrata subspecies petraea (L.)

A set of expressed sequence tag–simple sequence repeat (EST‐SSR) loci has been developed for Arabidopsis lyrata ssp. petraea. From 768 root cDNA clones, 126 microsatellites, including di‐, tri‐, tetra‐ and pentanucleotide repeat motifs were identified and primers were designed to 24 EST‐SSRs. Eleven loci were subsequently screened on 150 individuals sampled from five natural populations, which revealed three to nine alleles per locus (mean 5.36) and expected heterozygosity (H_E) estimates ranging from 0.046 to 0.698. Significant deviations from random mating were observed at 10 EST‐SSR loci, likely due to inbreeding (global F_IS = 0.151) and population structure (global F_ST = 0.246).     

Ten new polymorphic microsatellite loci for North American river otters (Lontra canadensis) and their utility in related mustelids

We describe 10 novel North American river otter (Lontra canadensis) polymorphic microsatellite loci. Individuals from two river drainages in New York were sampled, and the number of alleles per locus ranged from two to 12 (Drainage 1) and two to 10 (Drainage 2). Observed heterozygosities ranged from 0.21 to 0.83 (Drainage 1) and 0.20 to 0.80 (Drainage 2). Preliminary screening revealed that loci amplified in five other mustelids [Martes pennanti (n = 6), Martes fiona (n = 8), Mustela frenata (n = 8), Mustela erminea (n = 8) and Mustela vison (n = 5)].     

Polymorphic microsatellite markers isolated from partially enriched genomic library of Chitala chitala

A total eight polymorphic microsatellite loci were obtained from genomic library of Indian feather back, Chitala chitala (order Osteoglossiformes, family Notopteridae) and the 46 samples were analysed to determine genetic variation. The mean number of alleles per locus ranged from 4.50 to 5.25, and expected heterozygosity ranged from 0.124 to 0.852. Deviation from Hardy–Weinberg equilibrium expectations (P < 0.002) was observed at loci Cch2, Cch9 (Bhaghirathi) and Cch9 (Brahmaputra). The identified microsatellite loci were found promising for population genetics studies of C. chitala and related species Notopterus notopterus (family Notopteridae).     

Isolation and characterization of eight microsatellite loci for the Neotropical freshwater catfish Pimelodella chagresi (Teleostei: Pimelodidae)

We report eight (CA)_10?35 unlinked microsatellite loci from the Neotropical freshwater catfish, Pimelodella chagresi (Siluriformes: Pimelodidae). These loci were characterized with 23 individuals collected in Panama. Number of alleles per locus varied from 7 to 23 (mean = 12.9) and observed heterozygosity ranged from 0.522 to 0.909 (mean = 0.732). These loci will be used to investigate the existence of cryptic species within the P. chagresi clade, and to study fine‐scale population structure.     

Microsatellite primers for three Western Atlantic Farfantepenaeus prawn species

Microsatellite loci were identified for three closely related penaeid species, Farfantepenaeus subtilis, F. paulensis and F. sp., from genomic libraries enriched for CA repeats. Seven out of nine highly polymorphic loci detected were amplified across all three species. Between four and 64 alleles were recorded per locus (average = 36). The average observed heterozygosity ranged from 0.094 to 0.897 (mean = 0.613), while the expected heterozygosity ranged from 0.091 to 0.985 (mean = 0.822).