Genetic analysis of east and west coast populations of Penaeus monodon from India based on random amplified polymorphic DNA

The east and west coast populations of wild Penaeus monodon in India were genetically characterized by RAPD analysis using six highly polymorphic primers reported earlier. The average genetic similarities within populations, based on profiles generated by all the six primers, were 0.828 and 0.851 for the east and west coast populations, respectively, values with individual primers ranging from 0.744 to 0.889. The average genetic similarity between populations across all the primers was 0.774. The number of bands found to be polymorphic were 38 (51.35%) and 37 (50.68%) in the east and west coast populations, respectively. Primer 5 yielded the highest level of polymorphism (63.63%) in the east coast population whereas primer 3 yielded the lowest level of polymorphism (36.36%) in the west coast population. The study reveals the existence of genetic variation in P. monodon stocks providing scope for genetic improvement through selective breeding. It also provides baseline data for future work on population structure analysis of P. monodon.

Surface mucous as a source of genomic DNA from Atlantic billfishes (Istiophoridae) and swordfish (Xiphiidae)

Procedures for sampling genomic DNA from live billfishes involve manual restraint and tissue excision that can be difficult to carry out and may produce stresses that affect fish survival. We examined the collection of surface mucous as a less invasive alternative method for sourcing genomic DNA by comparing it to autologous muscle tissue samples from Atlantic blue marlin (Makaira nigricans), white marlin (Tetrapturus albidus), sailfish (Istiophorus platypterus), and swordfish (Xiphias gladius). Purified DNA from mucous was comparable to muscle and was suitable for conventional polymerase chain reaction, random amplified polymorphic DNA analysis, and mitochondrial and nuclear locus sequencing. The nondestructive and less invasive characteristics of surface mucous collection may promote increased survival of released specimens and may be advantageous for other marine fish genetic studies, particularly those involving large live specimens destined for release.

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.

An Improved molecular tool for distinguishing monoecious and dioedious Hydrilla

Two biotypes of hydrilla [Hydrilla verticillata(L.f.) Royle] occur in the United States, a dioecious type centered in the southeast and a monoecious type in the central Atlantic and northeastern states. Ecosystem managers need tools to distinguish the types as the ranges of each type expand and begin to overlap. A molecular tool using the randomly amplified polymorphic DNA (RAPD) procedure is available but its use is limited by a need for reference samples. We describe an alternative molecular tool which uses “universal primers” to sequence the trnL intron and trnL-F intergenic spacer of the chloroplast genome. This sequence yields three differences between the biotypes (two gaps and one single nucleotide polymorphism). A primer has been designed which ends in a gap that shows up only in the dioecious plant. A polymerase chain reaction (PCR) using this primer produces a product for the monoecious but not the dioecious plant.

Allozyme and RAPD variation in the eastern Pacific yellowfin tuna (Thunnus albacares)

Stock structure of eastern Pacific yellowfin tuna was investigated by analyzing allozymes and random amplified polymorphic DNAs (RAPDs) from 10 samples of 20–30 individuals each, collected between 1994 and 1996 from fishing vessels operating in the Inter-American Tropical Tuna Commission (IATTC) yellowfin regulatory area (CYRA). Allozyme analysis resolved 28 loci, eight of which were polymorphic under the 0.95 criterion: Aat-S*, Glud, Gpi-F*, Gpi-S*, La, Lgg, Pap-F*, and 6-Pgd, resulting in a mean heterozygosity over all allozyme loci of H = 0.052. Four polymorphic RAPD loci were selected for analysis, resulting in a mean heterozygosity of H = 0.43. Eight of 45 pairwise comparisons of allozyme allele frequencies among the ten samples showed significant differences after correction for multiple testing (P<0.0001), all of which involved comparisons with the Gulf of California sample. Confirmation of this signal of population structure would have management implications. No significant divergence in RAPD allele frequencies was observed among samples. Weir and Cockerham θ estimated for allozyme loci (θ=0.048; P<0.05) and RAPD loci (θ=0.030; P>0.05) revealed little population structure among samples. Mantel tests demonstrated that the genetic relationships among samples did not correspond to an isolation-by-distance model for either class of marker. Four of eight comparisons of coastal and offshore samples revealed differences of allele frequencies at the Gpi-F* locus (P<0.05), although none of these differences was significant after correction for multiple testing (P>0.001). Results are consistent with the hypothesis that the CYRA yellowfin tuna samples comprise a single genetic stock, although gene flow appears to be greater among coastal samples than between coastal and offshore samples.

Population connectivity among Dry Tortugas, Florida, and Caribbean populations of mutton snapper (Lutjanus analis), inferred from multiple microsatellite loci

Determining patterns of population connectivity is critical to the evaluation of marine reserves as recruitment sources for harvested populations. Mutton snapper (Lutjanus analis) is a good test case because the last known major spawning aggregation in U.S. waters was granted no-take status in the Tortugas South Ecological Reserve (TSER) in 2001. To evaluate the TSER population as a recruitment source, we genotyped mutton snapper from the Dry Tortugas, southeast Florida, and from three locations across the Caribbean at eight microsatellite loci. Both Fstatistics and individual-based Bayesian analyses indicated that genetic substructure was absent across the five populations. Genetic homogeneity of mutton snapper populations is consistent with its pelagic larval duration of 27 to 37 days and adult behavior of annual migrations to large spawning aggregations. Statistical power of future genetic assessments of mutton snapper population connectivity may benefit from more comprehensive geographic sampling, and perhaps from the development of less polymorphic DNA microsatellite loci. Research where alternative methods are used, such as the transgenerational marking of embryonic otoliths with barium stable isotopes, is also needed on this and other species with diverse life history characteristics to further evaluate the TSER as a recruitment source and to define corridors of population connectivity across the Caribbean and Florida.

Identification of larval sea basses (Centropristis spp.) using ribosomal DNA-specific molecular assays

The identification of sea bass (Centropristis) larvae to species is difficult because of similar morphological characters, spawning times, and overlapping species ranges. Black sea bass (Centropristis striata) is an important fishery species and is currently considered to be overfished south of Cape Hatteras, North Carolina. We describe methods for identifying three species of sea bass larvae using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) assays based on species-specific amplification of rDNA internal transcribed spacer regions. The assays were tested against DNA of ten other co-occurring reef fish species to ensure the assay's specificity. Centropristis larvae were collected on three cruises during cross-shelf transects and were used to validate the assays. Seventy-six Centropristis larva were assayed and 69 (91%) were identified successfully. DNA was not amplified from 5% of the larvae and identification was inconclusive for 3% of the larvae. Those assays can be used to identify sea bass eggs and larvae and will help to assess spawning locations, spawning times, and larval dispersal.

Genetic diversity study of Caspian brown trout (Salmo trutta caspius Kessler, 1877) population in five rivers in the southern part of Caspian Sea, Iran

For study the genetic diversity of Caspian brown trout population in five rivers in the southern part of Caspian Sea in Iran 182 number generators in the fall and winter of 1390 were collected in Chalus, Sardab Rud, Cheshmeh Kileh, Kargan Rud and Astara rivers. Then about 3-5 g of soft and fresh tissue from the bottom fin fish removed and were fixed in ethanol 96°. Genomic DNA was extracted by using ammonium acetate, then quantity and quality of the extracted DNA were determined by using spectrophotometry and horizontal electrophoresis in 1% agarose gel. The polymerase chain reaction was performed by using 16 SSR primers and sequencing primers (D-Loop) and the quality of PCR products amplified by SSR method were performed by using horizontal electrophoresis in 2% agarose gel. Alleles and their sizes were determined by using vertical electrophoresis in 6% polyacrylamide gel and silver nitrate staining method. Gel images were recorded by gel documentarian, the bands were scored by using Photo- Capt software and statistical analysis was performed by using Gene Alex and Pop Gene software. Also the PCR sequencing products after quality assessment by usinghorizontal electrophoresis in 1.5% agarose gel were purified and sent to South Korea Bioneer Corporation for sequencing. Sequencing was performed by chain termination method and the statistical analysis was performed by using Bio- Edit, Mega, Arlequin and DNA SP software. The SSR method, 5 pairs of primers produced polymorphic bands and the average real and effective number of alleles were calculated 5.60±1.83 and 3.87±1.46 in the Cheshmeh Kileh river and 7.60±1.75 and 5.48±1.32 in the Karganrud river and the mean observed and expected heterozygosity were calculated 0.44 ±0.15 and 0.52 ±0.16 in the Cheshmeh Kileh river and 0.50 ±0.11 and 0.70±0.13 in the Karganrud river. Analysis of Molecular Variance results showed that significant differences in genetic diversity between and within populations and between and within individuals in the studied rivers (P<0.01). The sequencing method identified 35 different haplotype, the highest number of polymorphic position (251) and haplotype (14) were observed in the Chalus river. The highest mean observed number of alleles (2.24±0.48) was calculated in the Sardabrud river, the highest mean observed heterozygosity (1.00±0.03) was calculated in the Chalus river and the highest mean nucleotide diversity (0.13±0.07) was observed in the Sardabrud river and mean haplotype diversity was obtained (1) in three studied rivers. The overall results show that there are no same population of this fish in the studied rivers and Karganrud and Chalus rivers in the SSR and sequencing methods had the highest levels of genetic diversity.

Genetic diversity of Bartail flathead (Platycephalus indicus (Linnaeus,1758)) using AFLP markers in Persian Gulf

Platycephalus indicus is a large benthic fish that inhabits temperate and tropical coastal waters of the Indo-West Pacific and found on sand or mud bottom in vary shallow area of estuary and near shore to depth of 25m. This species is dominant species of platycephalidae family, in Khuzestan, Bushehr and Hormozgan provinces and mainly is captured by bottom trawl, gillnet and moshta in Hormozgan. This study was designed to evaluate population variation and differentiation of bartail flathead (Platycephalus indicus (Linnaeus, 1785))in the Iranian waters of Persian Gulf using the morphometric and meristic characters and by AFLP marker. . A total 180 fish specimens were collected by gill net from six station(khor mosa, bahrekan, shif, motaf, charak and bandar abbas) that was 30 individual related to every station in Iranian shores of Persian Gulf . 28 morphometric factors and 11meristic specialties were measured and morphometric factors was standardized with Beacham formula. Univariate analysis of variance (One-way ANOVA) revealed significant differences with varying degrees between the means for 21 standardized morphometric measurements and 6 meristic counts that showed high significant differences between the six stations sampling. Discriminate function analysis (DFA) or the overall random assignment of individuals into their original groups was for morphometric and meristic characters was 47.9% and 53.9% respectively. The data were subjected to a principle component analysis (PCA) which grouped in eight and four factors for morphometric and meristic charactersrespectively.. Genetic diversity of six populations of bartail flathead (Platycephalus indicus) was investigated using amplified fragment length polymorphism (AFLP). A total of 118 reproducible bands amplified with ten AFLP primer combinations were obtained from 42 fishes that were collected from six different locations in the northern of Persian Gulf. The percentage of polymorphic bands was 57.06%. Average of Nei’s genetic diversity was 0.200±0.008, and Average of Shannon’s index was 0.300±0.011. The results of AMOVA analysis indicated that 66% of the genetic variation contained within populations and 34% occurred among populations and gene flow was 0.6454.The estimated level of population differentiation asmeasured by average Fst value across all loci was 0.327. Plotting discriminant functions 1 and 2 and UPGMA dendrograms based on Euclidian distance and genetic distance also showed at least five separate populations of bartail flathead in the northern Persian Gulf.