Identification of sex-specific expression markers in the giant tiger shrimp (Penaeus monodon)

Isolation and characterization of male-specific DNA markers in the rock bream Oplegnathus fasciatus

Sex-specific DNA markers applicable were very useful for elucidating the sex-determination mechanism and sex control in fishes. In the present study, amplified fragment-length polymorphism (AFLP) approach with 144 primer combinations was employed to identify sex-specific markers in the rock bream. Four male-specific AFLP fragments were identified which were designated as Opl286, Opl237, Opl422, and Opl228. Further sequence analysis of the sex markers' genomic region revealed subtle differences between the males and females. We identified four male-specific single-nucleotide polymorphisms (SNPs) and a deletion of 8 bp in marker Opl286, six male-specific SNPs in marker Opl237, three male-specific SNPs in marker Opl422, and eight male-specific SNPs and 1 bp inversions in marker Opl228. Specific primers were designed based on the nucleotide variation in the sequences to develop a simple polymerase chain reaction method for identifying the genetic sex of rock bream. As a result, three out of the four male-specific markers were converted into SNP markers. The male-specific AFLP markers and AFLP-derived SNP markers were tested in 100 individuals collected from three locations around the coast of Zhoushan, yielding reproducible sex identification. These male-specific DNA markers are a useful tool for the identification of the sex-determining locus in rock bream and for guiding artificial breeding programs.

Genetic diversity of wild and domesticated stocks of Thai abalone, Haliotis asinina (Haliotidae), analyzed by single-strand conformational polymorphism of AFLP-derived markers

Amplified fragment length polymorphism (AFLP) analysis was carried out on representative individuals of wild Haliotis asinina using 64 primer combinations. Nine polymorphic AFLPs were cloned and sequenced. Sequence-specific primers were designed from six AFLP-derived fragments. Three sequence-characterized amplified region (SCAR) markers (HaSCAR(320), HaSCAR(295), HaSCAR(327)) were selected for genotyping of 8-month-old domesticated stocks of H. asinina cultured separately at Sichang Marine Science Research and Training Station (N = 95) and at a hatchery in Trang province (N = 40) using single-strand conformational polymorphism analysis. Genotypes of wild abalone originating from Talibong Island (N = 25), Cambodia (N = 22), and the P(0) progeny established from Samet Island founders (N = 20) were also investigated. Significant genetic differentiation (P<0.0001 for the exact test and F(ST) = 0.8759-0.8919, P<0.001) between abalone from the Gulf of Thailand (Cambodia and Samet Island--east) and the Andaman Sea (Talibong Island--west) were observed. This demonstrated the strong biogeographic structure of H. asinina in Thai waters. Non-overlapping composite genotypes for wild abalone from different coastal regions allow us to determine founder contributions in domesticated abalone stocks. Almost all Sichang Marine Science Research and Training Station and the Trang province hatchery stocks exhibited the east coast genotypes (97% of the 135 samples). We suggest that abalone from the east coast population have better survival rates under cultivated conditions than those from the west coast population.

Suppression subtractive hybridization (SSH) for isolation and characterization of genes related to testicular development in the giant tiger shrimp Penaeus monodon

Suppression subtractive hybridization (SSH) cDNA libraries of the giant tiger shrimp, Penaeus monodon, were constructed. In total, 178 and 187 clones from the forward and reverse SSH libraries, respectively, of P. monodon were unidirectionally sequenced. From these, 37.1% and 53.5% Expressed Sequence Tags (ESTs) significantly matched known genes (E-value < 1e-04). Three isoforms of P. monodon progestin membrane receptor component 1: PM-PGMRC1-s (1980 bp), PM-PGMRC1-m (2848 bp), and PM-PGMRC1-l (2971 bp), with an identical ORF of 573 bp corresponding to a deduced polypeptide of 190 amino acids, were successfully identified by RACE-PCR. Interestingly, PMPGMRC1 showed a greater expression level in testes of juvenile than broodstock P. monodon (P < 0.05). Dopamine administration (10(-6) mol/shrimp) resulted in up-regulation of PMPGMRC1 in testes of juveniles at 3 hrs post treatment (P < 0.05), but had no effect on PM-Dmc1 (P > 0.05).

Molecular characterization and expression profiles of cyclin A and cyclin B during ovarian development of the giant tiger shrimp Penaeus monodon

The meiotic maturation of oocytes is regulated by maturation promoting factor (MPF), a complex of cdc2 (Cdk1) and cyclin B and other Cdk/cyclin complexes. To better understand molecular aspects governing reproductive maturation of the giant tiger shrimp (Penaeus monodon), the full length cDNAs and genomic organization of cyclins A and B (PMCyA and PMCyB) were characterized. A single form of PMCyA contained an open reading frame (ORF) of 1326 bp corresponding to a deduced protein of 441 amino acids. Its genomic sequence contained 5 exons, 4 introns and untranslated regions (UTRs) spanning 2586 bp in length. In contrast, PMCyB possessed three isoforms with an identical ORF of 1206 bp (401 amino acids) but three different 3' UTR lengths of 416, 543 and 1117 bp, respectively. Their respective genomic sequences were composed of 8 exons, 7 introns and UTRs covering 4181, 4307 and 4940 bp. Expression levels of both PMCyA and PMCyB in ovaries of broodstock were much greater than those of juveniles (P<0.05). During ovarian development and after spawning of normal shrimp broodstock, PMCyA was not differentially expressed (P>0.05) whereas the level of PMCyB in stage IV was greater than that of stage I ovaries (P<0.05). Unilateral eyestalk ablation, a technique commonly used to induce spawning in P. monodon female brooders, had no effects on transcription of PMCyB (P>0.05) but resulted in a lower expression of PMCyA at stage IV of ovarian development of this economically important species (P<0.05).

Identification, characterization and expression of sex-related genes in testes of the giant tiger shrimp Penaeus monodon

Isolation and characterization of genes involving gonadal development are an initial step towards understanding reproductive maturation and sex determination of the giant tiger shrimp (Penaeus monodon). In the present study, 896 clones from the testis cDNA library were sequenced. A total of 606 ESTs (67.6%) significantly matched sequences in the GenBank (E-value <1e-04) whereas 290 ESTs (32.4%) were newly unidentified transcripts. The full length cDNA of genes functionally involved in testicular development including cyclophilin A (PMCYA), small ubiquitin-like modifier 1 (PMSUMO-1), ubiquitin conjugating enzyme E2, dynactin subunit 5, cell division cycle 2 (cdc2) and mitotic checkpoint BUB3 were discovered. In addition, Tra-2, a gene involving sex determination cascades, was successfully characterized by RACE-PCR and first reported in crustaceans. Expression analysis indicated that a homologue of low molecular weight neurofilament protein XNF-L (termed P. monodon testis-specific transcript 1, PMTST1; N=8 for each sex) was only expressed in testes but not ovaries. PMCYA, thyroid hormone receptor-associated protein complex 240 kDa component (Trap240), multiple inositol polyphosphate phosphatase 2 (MIPP2) and heat shock-related 70 kDa protein 2 (HSP70-2), but not PMSUMO-1, PMTra-2 and prohibitin2 were differentially expressed between ovaries and testes of P. monodon. Expression of PMTST1 was up-regulated but that of the remaining genes in testes of P. monodon broodstock was down-regulated after shrimp were molted (P<0.05). Significant reduction of PMSUMO-1 and increment of prohibitin2 transcripts in domesticated broodstock (P<0.05) suggested that these reproductively related genes may be used as biomarkers to evaluate reduced degrees of the reproductive maturation in domesticated P. monodon.