Genetic identification of four Malaysian mackerel species off Coast of Peninsular Malaysia based on molecular marker

Random Amplified Polymorphic DNA (RAPD) markers and cytochrome b (Cyt-b) gene sequences were utilized to fingerprint and construct phylogenetic relationships among four species of mackerel commonly found in the Straits of Malacca namely Rastrelliger kanagurta, R. brachysoma, Decapterus maruadsi and D. russelli. The UPGMA dendogram and genetic distance clearly showed that the individuals clustered into their own genus and species except for the Decapterus. These results were also supported by partial mtDNA cytochrome b gene sequences (279 bp) which found monotypic sequence for all Decapterus studied. Cytochrome b sequence phylogeny generated through Neighbor Joining (NJ) method was congruent with RAPD data. Results showed clear discrimination between both genera with average nucleotide divergence about 25.43%. This marker also demonstrated R. brachysoma and R. kanagurta as distinct species separated with average nucleotide divergence about 2.76%. However, based on BLAST analysis, this study indicated that the fish initially identified as D. maruadsi was actually D. russelli. The results highlighted the importance of genetic analysis for taxonomic validation, in addition to morphological traits.

A Bayesian method for identification of stock mixtures from molecular marker data

Molecular markers have been demonstrated to be useful for the estimation of stock mixture proportions where the origin of individuals is determined from baseline samples. Bayesian statistical methods are widely recognized as providing a preferable strategy for such analyses. In general, Bayesian estimation is based on standard latent class models using data augmentation through Markov chain Monte Carlo techniques. In this study, we introduce a novel approach based on recent developments in the estimation of genetic population structure. Our strategy combines analytical integration with stochastic optimization to identify stock mixtures. An important enhancement over previous methods is the possibility of appropriately handling data where only partial baseline sample information is available. We address the potential use of nonmolecular, auxiliary biological information in our Bayesian model.

Real-time marker prediction and CoR estimation in optical motion capture

Optical motion capture systems suffer from marker occlusions resulting in loss of useful information. This paper addresses the problem of real-time joint localisation of legged skeletons in the presence of such missing data. The data is assumed to be labelled 3d marker positions from a motion capture system. An integrated framework is presented which predicts the occluded marker positions using a Variable Turn Model within an Unscented Kalman filter. Inferred information from neighbouring markers is used as observation states; these constraints are efficient, simple, and real-time implementable. This work also takes advantage of the common case that missing markers are still visible to a single camera, by combining predictions with under-determined positions, resulting in more accurate predictions. An Inverse Kinematics technique is then applied ensuring that the bone lengths remain constant over time; the system can thereby maintain a continuous data-flow. The marker and Centre of Rotation (CoR) positions can be calculated with high accuracy even in cases where markers are occluded for a long period of time. Our methodology is tested against some of the most popular methods for marker prediction and the results confirm that our approach outperforms these methods in estimating both marker and CoR positions. © 2012 Springer-Verlag.

Discovery of a male-biased mutant family and identification of a male-specific SCAR marker in gynogenetic gibel carp Carassius auratus gibelio

Gibel carp ( Carassius auratus gibelio) is a uniquely gynogenetic species with a minor ratio of males in natural habitats, but its male origin and sex determination mechanisms have been unknown. In this study, a male-biased mutant family was discovered from the gynogenetic gibel carp, and a male-specific SCAR marker was identified from the mutant family. Normal spermatogenesis was observed in the male testes by immuno. fluorescence histochemistry. Nearly identical AFLP profiles were observed between males and females, but a male-specific 86 bp AFLP fragment was screened by sex-pool bulked segregant analysis and individual screening. Based on the male-specific AFLP fragment, a total of 579 bp sequences were cloned by genome walking. Subsequently, a male-specific SCAR marker was designed, and the male-specific DNA fragment was confirmed to be steadily transmitted to the next generation and consistently detected only in males. (C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Microsatellite marker isolation and cultured strain identification in Carassius auratus gibelio

Microsatellites have become the preferred molecular markers for strain selection and genetic breeding in fish. In this study a total of 105 microsatellites were isolated and identified in gibel carp (Carassius auratus gibelio) by microsatellite sequence searches in GenBank and other databases and by screening and sequencing of positive clones from the genomic library enriched for AG and GATA repeats. Moreover, nineteen microsatellites were randomly selected to design locus-specific primer pairs, and these were successfully used to identify and discriminate different cultured strains of gibel carp including strains A, D, L, and F. Three different types of microsatellite pattern were distinguished by the number and length of fragments amplified from the 19 primer pairs, and some microsatellite primer pairs were found to produce different microsatellite patterns among strains and strain-specific fragments. In addition, some duplicated alleles were also detected in two microsatellite patterns. Therefore, the current study provides direct molecular markers to discriminate among different cultured strains for selective breeding and aquaculture practice of gibel carp.

Characterization of a highly conserved microsatellite marker with utility potentials in cyprinid fishes

A microsatellite locus, MFW1, originating from common carp is highly conserved in flanking nucleotides but variable in repeat length in some fishes from different families of the Cypriniformes. This orthologous locus is polymorphic in approximately 58% of the species tested in the order and is inherited by Mendelian law. It proved to be a potentially good marker in population genetics and in the cyprinid species-breeding programme in which no microsatellite markers were available.

Genetic structure of Chinese sucker population Myxocyprinus asiaticus in the Yangtze River based on mitochondrial DNA marker

The sequencing analysis of the mitochondrial DNA control region (mtCR DNA) was performed to assess the genetic divergence and population structure of the Chinese sucker Myxocyprinus asiaticus (Cypriniformes Catostomidae) using four sample lots from natural populations of the Yangtze River. The mtCR DNA sequences of approximately 920 base pairs were obtained. A total of 223 nucleotide positions were polymorphic, and these defined 39 haplotypes. Of the 39 haplotypes, 37 (90%) were not shared, and among the populations as a whole there was little sharing of haplotypes. The average haplotype diversity (0.958) and the average nucleotide diversity (0.052) indicated a higher level of genetic diversity of Chinese sucker through the river. Analysis of molecular variation (AMOVA) of data revealed significant partitioning of variance (P<0.001) among populations (60.29%), and within populations (39.71%). The topology according to the neighbor joining and maximum parsimony methods showed mosaic composition of the 39 haplotypes, suggesting that the populations wore not completely divergent. The pairwise F statistic values, however, indicated that the population structuring existed to some extent among the geographic populations. There was a positive relationship between the aquatic distance and the genetic distance (Fst) among the populations (P<0.05). Based on our data, it is suggested that genetic drift, gene flow, and stochastic events are the possible factors influencing the population structure and genetic variation.

Genetic heterogeneity analysis and RAPD marker detection among four forms of Atrina pectinata Linnaeus

Pen shell (Atrina pectinata Linnaeus) can be distinguished into four forms based on the morphololgic characteristics. Genetic similarity, and heterogeneity were analyzed among the four forms by random amplified polymorphic DNA (RAPD) technique using 24 10-nucleotide-long primers. Of these primers, 22 pruners produced well-identifiable RAPD band patterns. Significant differences in RAPD band patterns were revealed among the four forms. A total of 198 polymorphic fragments were scored from 22 pruners. and they are specific for one form, shared by two or three forms. Several pruners, such as S451, S453 S463 S464, S470. S473 and S474, produced abundant band patterns and provided sufficient information for reliable discrimination of the four forms. The average genetic distances and phylogenetic relationships were calculated and analyzed according to the distinguishable fragments. The data indicate that pen shells of form G and form Y are similar not only among individuals within the same form, but also between individuals from the two forms, and that shells of form T and form S are highly divergent. The constructed phylogenetic free matches the average genetic distances. Three clusters were clearly distinguishable, in which two were corresponding to form S and form T respectively and one included forms G and Y. This Study will be benefit to further studies oil the taxonomy and selective breeding of Pinnid species. It is suggested that the four forms of pen shell should be categorized to at least two species taxonomically.