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We isolated 18 novel microsatellite loci from the walking catfish (Clarias batrachus), and examined their cross-amplification in seven additional catfish species from three families. Sixteen of the 18 microsatellites were polymorphic in the source species (allele number: 2–10/locus and expected heterozygosity: 0.30–0.87). Moreover, nine of these 18 primer pairs cross-amplified specific and polymorphic products from the genome of at least six of the seven other catfish species tested. However, the success rate of cross-species amplification varied from locus to locus, indicating that cross-species amplification of microsatellites is locus-dependent.

Here we report the isolation and characterization of 17 polymorphic loci isolated from a partial genomic DNA library of grass carp ( Ctenopharyngodon idellus ) enriched for CA repeats. We tested variability of these microsatellites on 24 unrelated individuals collected in China. All microsatellites were polymorphic. The average allele number was 7.9 per locus, ranging from four to 13. The observed heterozygosity was from 0.46 to 0.88 with an average of 0.71, whereas the average expected heterozygosity was 0.78. Sixteen of the 17 microsatellites conformed to Hardy–Weinberg equilibrium, and inherited independently. These microsatellites can be used to study genetic diversity and population structure of wild populations, and facilitate selective breeding of cultured broodstocks.

Asian green mussels (Perna viridis) belonging to the family Mytilidae are native to the coastal and tropical marine waters of the Indo-Pacific region. Ten polymorphic microsatellites were isolated and their polymorphisms were determined in 36 individuals. The average allele number of the 10 microsatellites was 11.7/locus with a range of two to 24 and the expected heterozygosity averaged at 0.69, ranging from 0.18 to 0.94. Eight out of 10 microsatellites agreed with the Hardy–Weinberg equilibrium and showed independent segregation. These microsatellites will facilitate the studying of the genetic diversity and population structure of the green mussel in and outside of the Indo-Pacific region of Asia.

The ribbonfish, Trichiurus haumela , is an important marine foodfish species. Supply of this fish relies on capture from the wild. No information about genetic diversity and population structure of wild stocks is available. Therefore, we developed the first set of 10 polymorphic microsatellites. The average allele number was 13.2 per locus ranging from six to 20. The expected heterozygosity was 0.84, whereas the observed heterozygosity was 0.71. This set of microsatellites provides a tool for assessing genetic diversity and population structure of this species.

The orchid genus Vanda includes more than 70 monopodial species and numerous hybrids. The aim of this study was to develop microsatellite markers for this horticultural valuable genus. Thirteen polymorphic microsatellite markers were isolated from the variety Vanda Miss Joaquim and were characterized in four Vanda species, 11 Vanda hybrids, and one Aranda intergenus hybrid. Populations from three species were also analysed. Number of alleles ranged from two to 19. For the V. sumatrana population, the expected heterozygosity ranged from 0 to 0.76 (mean 0.31) and the observed heterozygosity ranged from 0 to 1 (mean 0.36). All the varieties tested were distinct from one another (similarity index < 0.8). These microsatellites could be used for studying genetic diversity and population structure of wild populations within the orchid genus Vanda, as well as for distinguishing cultured Vanda varieties.

The aim of this study was to develop simple sequence repeat (SSR) markers for Dendrobium varieties/species, many of which have medicinal and horticultural values. Two genomic DNA libraries of Dendrobium Sonia enriched with GA repeats and CA repeats were constructed. Fourteen polymorphic SSR markers were identified when screened against 42 popular commercial Dendrobium hybrids. The average allele number was 12.0 ± 1.9 and the observed heterozyosity was averaged at 0.70. All 42 hybrids tested, except for two tissue culture mutants, were uniquely identified with the markers used. Sibling hybrids were closely clustered. Hybrids were also closer to parents. These SSR markers can be used for molecular ecology research, genetic mapping and marker-assisted breeding. They can also help protection for new Dendrobium varieties.

Eleven polymorphic microsatellites were isolated from an important foodfish species, silver pomfret ( Pampus argenteus ). The loci showed different variation patterns in 24 unrelated P. argenteus individuals, with a mean number of alleles of 11.5 and a mean expected heterozygosity of 0.85. Eight of the 11 loci conformed to Hardy–Weinberg equilibrium. All and six of the 11 markers amplified specific and polymorphic products in Chinese pomfret ( Pampus sinesis ) and dark pomfret ( Pamus cinereus ), respectively. These markers should be useful for population genetic analysis and biodiversity studies of P. argenteus and other pomfret species .

Crimson red snapper (Lutjanus erythropterus) is an important marine foodfish species in Asia with great potentials for aquaculture. We isolated nine polymorphic microsatellites, among which eight were tetranucleotide repeats, and one was CA-microsatellite. The average allele number present in 48 individuals was 11.1/locus, ranging from three to 33. The expected heterozygosity ranged from 0.49 to 0.97 with an average of 0.74. Six of the nine markers conformed to the Hardy–Weinberg expectations. No pairwise markers showed the possibility of linkage. Protocols for two multiplex polymerase chain reactions (PCRs), each amplifying two and seven markers, respectively, were presented. The developed microsatellites and optimized multiplex PCRs will be useful for studying population structure of wild stocks and parentage assignment for cultured populations.

We isolated 12 polymorphic microsatellites from an important marine food fish Larimichthys polyactis and characterized them in 32 unrelated individuals. Among the 12 microsatellites, four were tetranucleotide repeats and eight were dinucleotide repeats. The allele number ranged from five to 25 with an average of 15.4/locus; average expected heterozygosity was 0.81, ranging from 0.57 to 0.95, whereas the observed heterozygosity ranged from 0.34 to 1.00 (average: 0.78). Nine of the 12 markers conformed to Hardy–Weinberg equilibrium and showed no sign of linkage. These microsatellites will be useful for population genetic studies and selective breeding programs of this species.

The red coral grouper, Plectropomus maculatus , is a high value marine food fish species. We isolated the first set of 10 polymorphic microsatellites and examined their polymorphism in two related species: the Malabar grouper Epinephelus malabaricus and the brown-marbled grouper Epinephelus fuscoguttatus . The average allele number of these 10 microsatellite DNA loci is 9.1/locus with a range of four to 17, whereas the expected heterozygosity ranged from 0.18 to 0.94, averaging 0.76. Five of the 10 markers amplified polymorphic and specific products in E. malabaricus , whereas only four were amplified in E. fuscoguttatus . These microsatellites could be applicable to captive breeding and to the studies on genetic diversity and population structure of grouper wild stocks.

The green swordtail (Xiphophorus hellerii; Poeciliidae) is a popular ornamental freshwater fish species. Fourteen microsatellites were isolated from a green swordtail genomic library enriched for CA-repeats. Thirteen microsatellites were polymorphic in green swordtail; interestingly four of them were tetranucleotide-type. Cross-species amplification showed that 10 of the 14 microsatellites were polymorphic in guppy (Poecilia reticulata; Poeciliidae) as well. No significant directional difference of allele length was seen between the two species at any of the loci tested.

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.

The first set of six polymorphic microsatellites was isolated from a partial genomic DNA library of an important marine food fish Gnathanodon specious , and was characterized in 28 unrelated individuals. The allele number ranged from three to 12 with an average of seven/ locus; average expected heterozygosity was 0.57 ranging from 0.10 to 0.87, whereas the observed heterozygosity ranged from 0.11 to 0.96 (average: 0.57). All six markers conform to Hardy–Weinberg and linkage equilibria. These markers will be useful for accessing genetic population structure of wild populations and for selective breeding program in fish farms.

The goldfish (Carassius auratus auratus; Cyprinidae) is not only an important ornamental fish species, but also a useful model for biological studies. The sequence of goldfish genes present in the public database was searched for short tandem repeats, and 11 polymorphic microsatellites were detected within eight important genes. Two microsatellites were located in coding regions of the c-myc and GAP-43 genes, respectively, whereas the others were mainly located in 5′ and 3′ untranscribed regions of other genes, such as gonadotropin and activin. The average allele number of these microsatellites was 5.5 per locus with a range between 3 and 9. These microsatellites will be useful for ecological and population genetic studies of this species, as well as for the ornamental fish industry.

Six microsatellites were detected in the IGF-II, GH2, prolactin I and insulin genes of Mozambique tilapia (Oreochromis mossambicus) and Nile tilapia (Oreochromis niloticus) by screening DNA sequences deposited to GenBank. Genotyping of 24 individuals from each species revealed that all six microsatellites were polymorphic in both species. In Mozambique tilapia the number of alleles ranged from 3 to 17 (average 9.8), whereas in Nile tilapia the range was 4–21 (average 10.5). The range of expected heterozygosity values were 0.44–0.95 (average 0.79) in Mozambique tilapia, and 0.52–0.96 (average 0.73) in Nile tilapia.