Functional feed ingredients are increasingly used in aquaculture to elevate fish growth and health to address sustainable aquaculture. Here, effects of green banana powder (GBP), with or without Lactobacillus plantarum, on growth and immune-response parameters of juvenile Nile tilapia (Oreochromis niloticus) were evaluated. Five experimental diets were used, including the control (GBP0), GBP supplemented with 25 and 50 g/kg diet (GBP25 and GBP50), plus GBP25 and GBP50, both further supplemented with L. plantarum (10(8) CFU/g; GBPL25 and GBPL50). These were tested against juvenile fish (6.44 +/- 0.13 g) for 10 weeks. Fish fed GBP50 and GBPL50 diets had higher final weights (60.60 +/- 1.59 and 60.29 +/- 0.83 g/fish, respectively) than the control fish (57.04 +/- 0.73 g/fish). Only fish fed GBP50 experienced an increase in specific growth rate (P < 0.05). This suggested that GBP supplementation improved growth of juvenile O. niloticus. In addition, fish fed GBP50 showed increased IL-1 beta expression and protease activity compared to those fed GBP0 and GBP25 diets (P < 0.05). Fish fed GBPL25 and GBPL50 diets also showed a greater expression level of HSP70 and IL-10 than the control (P < 0.05). Moreover, dietary supplementation with GBP significantly increased serum superoxide dismutase (SOD) activity (P < 0.05) while the GBPL diet resulted in a significant enhancement of lysozyme activity. Results indicated that supplementation of sufficient amounts of GBP (e.g. GBP50) and L. plantarum (e.g. GBPL25 and GBPL50) improved various immune indices of the cultured fish. Therefore, GBP is a beneficial dietary supplement for growth while its combination with L. plantarum elevates immune response parameters of O. niloticus juveniles.

Genetic diversity and population connectivity of brownstripe red snapper (Lutjanus vitta) from different petroleum platforms located in the north (N1, N2, N3, and N4), central, and south regions and two coastal locations, Songkhla and Samaesarn (Gulf of Thailand), were examined using the control region (CR) polymorphism. In total, 59 haplotypes of CR were found, and 42 of these were private haplotypes (found in only one geographic location). The haplotype no./sample size (NH/N) found in the central (0.800), south (0.741), and north (0.733) platforms was greater than that in the coastal populations (0.643 in Samaesarn and 0.682 in Songkhla). Haplotype diversity of north, central, and south platforms and coastal populations were comparable (Hd = 0.943–0.982). Nucleotide diversity within populations was estimated. The lowest and highest nucleotide diversity was observed in the north (1.293%) and south (2.850%) platforms. Larger genetic divergence was found between north–central (0.096%) and north–south platforms (0.069%) than between coastal populations (0.007%). A lack of nucleotide divergence was found between central–south platforms and between platforms and coastal populations (north–Samaesarn, central–Songkhla, and south–Songkhla). The FST estimate did not reveal significant population differentiation between all pairwise comparisons (p > 0.01 after the sequential Bonferroni’s adjustment). AMOVA confirmed a lack of intraspecific population structure of L. vitta in the Gulf of Thailand (p > 0.05). Genetic connectivity between fish from different sampling sites was noticed based on haplotype network, phylogenetic analysis, and population structure analysis. Demographic statistics revealed that L. vitta went through a sudden population expansion.

The information on genetic diversity and intraspecific population subdivision is important for the construction of appropriate fishery management and breeding programs of banana shrimp Penaeus merguiensis. Here, wild P. merguiensis in Thai waters originated from Nakhon Si Thammarat, Chonburi, Pattani, Rayong and Trat located in the Gulf of Thailand (east), and Trang and Krabi located in the Andaman Sea (west) were collected (n = 196) and genetically analyzed using Cytochrome c oxidase subunit I polymorphism. Relatively high genetic diversity (38 haplotypes, Hd and π = 0.000–0.876 & 0.000–0.024 for eastern and 0.000–0.714 & 0.000–0.002 for western populations, averaged Hd and π = 0.818 and 0.019, respectively) was observed. Nucleotide divergence between populations was 0.001 (between Trang-Krabi) –0.037 (between Nakhon Si Thammarat-the Andaman populations). FST statistics revealed genetic differentiation between all pairwise comparisons of examined populations (p < 0.0001). Analysis of molecular variance following phylogenetic grouping indicated significant variance components between individuals within populations (p < 0.0001), between populations within groups (p < 0.0001) and between phylogenetic groups (p = 0.0059). The information obtained is useful for natural resource management and for the establishment of our on-going breeding programs for genetic improvement of P. merguiensis.

Genetic diversity and population differentiation of an aquaculture population of Banggai cardinalfish (Pterapogon kauderni) introduced and maintained in Phang Nga province, Southern Thailand (A1, N = 45) was examined using control region (CR) polymorphism in comparison with three wild transplanted populations from Gilimanuk Bay (Bali), collected in 2019 (W1, N = 25), Banyuwangi (East Java), collected in 2024 (W2, N = 22), and Gilimanuk Bay (Bali), collected in 2024 (W3, N = 39). In total, 14 haplotypes were identified. Haplotype 3 was found in all populations, while haplotype 4 was found in wild transplanted but not in aquaculture populations. The remaining (12) haplotypes were private haplotypes. Of these, five private haplotypes (H5, H6, H7, H8 and H9) were found only in the A1 population. Moreover, genome-wide single nucleotide polymorphisms (SNPs) in P. kauderni from A1 (N = 21), W2 (N = 15) and W3 (N = 15) populations were also analyzed by Specific Locus Amplified Fragment-Sequencing (SLAF-Seq). In total, 648,378 SNPs were identified. By analyzing both mitochondrial DNA and SNP markers, significant genetic differences were clearly found between farmed and wild transplanted populations of P. kauderni. Reduced genetic diversity was found in a farmed population from genome-wide SNPs but not mtDNA analyses.

A breeding program of Asian seabass (Lates calcarifer, also called barramundi) was established for sustainable aquaculture in Thailand. Estimated breeding values (EBVs) for growth of the base population (G0, 51 families, N = 1655) were evaluated. Fish exhibited either high (HEBV, averaged body weight = 1036.80 ± 250.80 g, N = 133) or low (LEBV, averaged body weight = 294.50 ± 167.20 g, N = 147) growth EBVs, and their parental fish (N = 26) were analyzed by Specific Locus Amplified Fragment Sequencing (SLAF-Seq). An average of 159,769 SLAF tags/sample was generated, covering 13.79-fold of the genome size, and 225,498 SNPs were applied for population genomics. Observed (Ho) and expected (He) heterozygosity values were 0.224 and 0.308, 0.178 and 0.246, and 0.184 and 0.305, respectively. Polymorphic information content (PIC) ranged from 0.205–0.251. A selective sweep was performed based on Fst, and nucleotide polymorphism (π) revealed significant differences between allelic contents of growth- and immune-related genes in HEBV and LEBV populations. Kinship analysis revealed that 84.38% of examined fish showed r values < 0.2, and population admixture analysis revealed three subpopulations in HEBV and four subpopulations in LEBV groups. Fish that possessed a single cluster were found in each subgroup of both populations, along with those exhibiting mixed ancestral clusters. This information is critically important for further applications in our ongoing seabass improvement breeding program.

To establish a new breeding program, genetic diversity of five domesticated populations and two commercial stocks of Asian seabass (Lates calcarifer) were examined. Moderate levels of genetic diversity based on microsatellite polymorphism were found. The number of alleles per locus (NA) was 3.429–11.571. Observed (Ho) and expected (He) heterozygosities were 0.416–0.772 and 0.423–0.805. FST and genetic heterogeneity analysis revealed significant genetic differences of most pairwise comparisons (P < 0.001). Genetic distance between populations was 0.000–0.703. Phylogenetic analysis divided examined populations to two genetic stocks; A: DOF-Chachoengsao 2, DOF-Songkhla, and DOF-Trang and B: Commercial Farm 1 (Phuket) and Commercial Farm 2 (Chachengsao), DOF-Chachoengsao 1 and DOF-Krabi. The base population (G0, 51 families) was established from crosses between these founder populations. Heritability and estimated breeding values (EBVs) for growth in G0 families were evaluated at 519 day post hatch (dph, mean body weight = 616.64 ± 266.80 g, N = 1655). The heritability (h2) for growth of L. calcarifer in this study was 0.386 ± 0.020. The additive genetic coefficient of variation was 28% indicating high potential of genetic improvement for growth in this population. The distribution of EBVs showed high variation both between and within families. Fish exhibiting high EBVs (SATREPS-DOF-G0-hEBVs) clustered with a phylogenetic clade A while the SATREPS-DOF-G0-lEBVs group was phylogenetically allocated to clade B. Genetic selection with +1SD criteria is expected to achieve genetic gain of 28.5% per generation. The information on genetic diversity and EBVs estimates allows efficient implementation of our ongoing breeding program of L. calcarifer.

Characterization of reproduction-related genes is crucial for comprehending molecular mechanisms involved in ovarian development of banana shrimp (Penaeus merguiensis). Here, genes expressed in different ovarian (immature, vitellogenic and mature) stages were characterized by RNA-Seq. In total, 12 libraries were established and 88.56 Gb (6.91-8.04 Gb/sample) clean data were obtained for overall samples. The Q30 values were between 94.14 and 94.86 %. The N50 values were 2763 bp for transcripts and 2536 bp for unigenes. A total of 2208 differentially expressed genes (DEGs) were identified, comprising 1203 up-regulated and 1005 down-regulated genes. Identified genes were annotated and functionally categorized. DEGs in protein synthesis, metabolism and biogenesis levels were abundant suggested that the development of immature ovaries to further stages requires energy and nutrient accumulation. Expression of DEGs in Cellular process, Environmental information processing, Genetic information processing, and Metabolism in immature ovaries increased in vitellogenic ovaries and decreased in mature ovaries. This reflects the rapid accumulation of various proteins during the vitellogenic stage. The identified DEGs in mature ovaries suggest that signal transduction pathways are crucial during the final ovarian maturation of P. merguiensis. Gene expression was further analyzed by qRT-PCR. PmMknk1, PmTtc3 and PmSult1C4 were upregulated in vitellogenic and mature ovaries (P < 0.05). In addition, PmCcnF, PmBmp2, PmFoxA1, PmChst5 and PmVtg were upregulated in mature ovaries (P < 0.05). This suggested their important role in ovarian development and maturation. The information is crucial for further studies on reproductive maturation of P. merguiensis.

Improvement of growth performance and disease resistance of cultured species is an important objective of the aquaculture industry. In this study, solid-state fermentation (SSF) was applied for increasing the nutritional value of rice bran with baker's yeast (Saccharomyces cerevisiae). Four diets containing different levels of fermented rice bran (FRB) at 0, 100, 200 and 300 g/kg (FRB0, FRB10, FRB20 and FRB30, respectively) were tested using juvenile Nile tilapia Oreochromis niloticus (average body weight = 5.22 +/- 0.02 g) for 56 days. Compared to FRB0, all diets improved growth performance of the experimental fish (P<0.05). Intestinal amylase and protease amounts were significantly increased (P<0.05). The experimental fish were intraperitoneally injected with Streptococcus agalactiae and the cumulative mortality rate was monitored for 10 days. All FRB-supplemented diets resulted in greater survival rates in challenge fish. The FRB20 and FRB30 diets promoted expression of insulin-like growth factor I (IGF-I) transcripts and enhanced non-specific immunity; lysozyme and antioxidant enzyme activities; myeloperoxidase (MPO), catalase (CAT), and superoxide dismutase (SOD) (P<0.05). The expression level of interleukin 8 (IL-8) was down-regulated in fish fed FRB20 and FRB30 (P<0.05) but IL-10 was up-regulated in fish fed FRB10 and FRB30 (P<0.05) while IL-1 beta was up-regulated in fish fed FRB20 (P<0.05). The expression of complementary 3 (C3) transcripts was significantly increased while nuclear factor-kappa B (NF-kappa B) was decreased in fish fed all FRB-supplemented diets (P<0.05). Conventional histology revealed increased villus height following FRB30 treatment (P<0.05). These results suggest the beneficial use of FRB supplementation on growth, immune defense and stress tolerance for juvenile O. niloticus.

Genes exhibiting differential expression patterns between large-sized (average body weight 17.57 +/- 1.8 g and 40.97 +/- 4.0 g for 3- and 5-month-old juveniles in a total of 342 and 356 samples, respectively) and small-sized (average body weight 10.01 +/- 0.76 g and 22.86 +/- 2.51 g, respectively) juvenile giant tiger shrimps (Penaeus monodon) were isolated by complementary DNA-amplified fragment length polymorphism (cDNA-AFLP). In total, 368 primer combinations were screened against the first-strand cDNA of the different groups of 3- and 5-month-old P. monodon. Over 146 differentially expressed or size-specific markers were derived using 59 selective primer combinations. A total of 70 candidate cDNA-AFLP markers-19 size-specific and 51 showing differential expression-were further cloned, sequenced, and blasted against the GenBank database. Twenty-five markers were found to comprise newly identified sequences (E-values >10(-4)). Quantitative real-time PCR and Single-strand conformational polymorphism (SSCP) analyses of the products generated with the SCAR/cDNA-AFLP primers were further undertaken. Interestingly, the relative expression levels of the products of primers E(+3)4M(+3)14-550-PDI, E(+3)5M(+3)10-350-Unk, E(+2)9/M(+2)11-350-CHK, E(+3)4/M(+3)1-380-phosphotysosyl, and E(+3)8/M(+3)15-800-fucosidase were significantly upregulated in the hepatopancreas of large-sized juvenile shrimp compared with that is small-sized animals. In contrast, the relative expression levels of the products generated by E(+3)1M(+3)8-480-InositolOxy and E(+2)9/M(+2)11-330-vitelline membrane were significantly upregulated in small-sized P. monodon. The consistency of our results was further assessed in 1-month-old aquaculture-raised P. monodon. Single nucleotide polymorphisms were identified using SSCP at different positions in the sequences of fragments of the different groups generated with the primers E(+3)4M(+3)14-550-PDI and E(+3)5M(+3)10-350-Unk. Our results indicated that cDNA-AFLP has the potential for use in the isolation of functionally important transcripts in P. monodon.

Biomonitoring and environmental impact assessment of marine ecosystems are important for the effective management of petroleum platform activity. Eukaryote biodiversity in water and sediment near petroleum platforms in the Gulf of Thailand was surveyed using environmental DNA (eDNA) based on 18S ribosomal DNA variable region 4 (18S rDNA-V4), the full-length 18S rDNA gene (18S rDNA-FL), and cytochrome c oxidase subunit 1 (COI). Water and sediment samples were collected from three platforms. The water sample was also collected from a reference site located farther south, away from the platforms. Both 18S rDNA markers outperformed COI. A total of 1144 and 889 species were found in water and sediment when analyzed by 18S rDNA-V4, and 519 species were found in sediment when analyzed by 18S rDNA-FL. Only 99 species were found in water samples when analyzed by COI. Alpha-diversity (Shannon and Simpson Evenness) indices were significantly different in water (p < 0.05), but not in sediment (p > 0.05). Beta-diversity (PCoA and NDMS) revealed significant species components between different petroleum platforms (p < 0.01). Species distribution revealed biological connectivity between eukaryotes from different platforms suggesting the importance of platforms on ecological impacts. This study also illustrates the possible application of eDNA for monitoring ecological toxicity around petroleum platforms.

The basic information on genetic diversity is important for the construction of a breeding scheme leading to the sustainable farming activity of banana shrimp Fenneropenaeus merguiensis. Here, its genetic variability was examined (N = 584). Species authentication was performed by cytochrome oxidase subunit I (COI) polymorphism (N = 77). Microsatellite analysis revealed limited genetic diversity (average no. of alleles per locus, NA = 4.857-5.571) in the previous domesticated stocks. Subsequently, specimens from different geographic locations including Trat, Rayong, Chonburi, Pattani and Nakhon Si Thammarat on the Gulf of Thailand (east) and Trang and Krabi on the Andaman Sea (west) were genetically analyzed. Relatively high levels of genetic diversity (NA = 7.857–23.429) and heterozygosity (Ho = 0.500–0.733) were observed. Genetic differentiation was found between all pairwise comparisons (P < 0.001) except Trat-Nakhon Si Thammarat (P > 0.0071). Phylogenetic analysis allocated wild F. merguiensis to three groups, A (Gulf of Thailand), B (Trang) and C (Krabi). Admixture analysis did not reveal large mixing between different lineages of genotypes in each population. However, the Krabi population (west) mainly showed the eastern genetic lineage. A new domestication program was established by selecting shrimp from different genetic groups. High genetic diversity was found in founders (NA = 27.714 and AR = 14.137) and brooders of the second generation (NA = 24.571 and AR = 12.835). Currently, genome-wide association study (GWAS) of G2 shrimp exhibiting large and small sizes from four families is being carried out to analyze growth-related SNPs in this species.

Pigmentation genes expressed in skin, body muscle and tail of Thai-flag compared with Blue, White and Red varieties of Siamese fighting fish Betta splendens were identified. In total, 22,919 new unigenes were found. Pearson correlation and PCA analysis revealed that expression profiles of genes in muscle, skin and tail across solid color variety were similar. In contrast, those in skin and red tail part of Thai-flag were closely related but they showed different expression profiles with the white tail part. Moreover, 21,347-64,965 SNPs were identified in exonic regions of identified genes. In total, 28,899 genes were differentially expressed between paired comparisons of libraries where 13,907 genes (48.12 %) were upregulated and 14,992 genes (51.88 %) were downregulated. DEGs between paired libraries were 106-5775 genes relative to the compared libraries (56-2982 and 50-2782 for upregulated and downregulated DEGs). Interestingly, 432 pigmentation genes of B. splendens were found. Of these, 297 DEGs showed differential expression between varieties. Many DEGs in melanogenesis (Bsmcr1r, Bsmcr5r, and Bsslc2a15b), tyrosine metabolism (Bstyr, Bstyrp1b and Bsdct), stripe repressor (BsAsip1 and BsAsip2b), pteridine (Bsgch2) and carotenoid (BsBco2) biosynthesis were downregulated in the Thai-flag compared with solid color varieties. Expression of Bsbco1l, Bsfrem2b, Bskcnj13, Bszic2a and Bspah in skin, muscle and tail of Thai-flag, Blue, Red and White varieties was analyzed by qRT-PCR and revealed differential expression between fish varieties and showed anatomical tissue-preferred expression patterns in the same fish variety. The information could be applied to assist genetic-based development of new B. splendens varieties in the future.

The full-length transcript of cytochrome b5 (PmCytb5) in the giant tiger shrimp (Penaeus monodon) was characterized. It was 1539 bp with an open reading frame (ORF) of 432 bp deducing to 143 amino acids. The deduced PmCytb5 protein contained predicted cytochrome b5-like heme/steroid binding domain (Cytb5, positions 17-91) and a transmembrane domain (positions 120-139). In non-ablated wild adults, PmCytb transcript was significantly increased in mature ovaries while it was earlier upregulated in late vitellogenic stage in eyestalk-ablated shrimp (P<0.05). Progesterone injection (0.1 μg/g) induced the expression of PmCytb5 at 48 hours post injection (hpi, P<0.05) but serotonin (50 μg/g) did not alter its expression (P>0.05) in domesticated adults. The cytoplasmic PmCytb5 protein was upregulated from immature ovaries in the early vitellogenic stage and comparably expressed in subsequent stages in non-ablated wild broodstock. In eyestalk-ablated wild broodstock, a similar expression profile was observed but its expression was further increased in late vitellogenic, and mature stages. The membrane PmCytb5 protein was upregulated in late vitellogenic and mature stages in the former but expressed at a similar level in different ovarian stages in eyestalk-ablated broodstock. Results suggested the important role of PmCytb5 in ovarian development of P. monodon.

Characterization of genes exhibiting differential expression profiles during ovarian development is important for understanding reproductive maturation of the giant tiger shrimp (Penaeus monodon). Here, the partial cDNAs of P. monodon cAMP-dependent protein kinase, catalytic subunit 1 (PmPkaC1) and adenylyl cyclase-associated protein 1-like (PmCap1-l) were studied. They were more preferentially expressed in ovaries than testes of cultured juveniles and wild broodstock. PmPkaC1 mRNA in ovaries of non-ablated broodstock was significantly increased during vitellogenesis (P<0.05). However, unilateral eyestalk ablation (the removal of one eyestalk) resulted in a significant reduction of its expression (P<0.05). PmCap1-l was not differentially expressed during ovarian development in wild non-ablated broodstock. It was up-regulated in mature ovaries following eyestalk ablation (P<0.05). The PmCap1-l transcript in each ovarian stage of the former was significantly lower than that of the latter (P<0.05). The levels of ovarian PmPkaC1 and vitellogenin 1 (PmVtg1) treated in vitro with 17-20β-DHP (0.1, 1.0 and 10.0 μg/ml for 24 h) was not significantly different from the control (P>0.05). Nevertheless, the expression of PmCap1-l was increased in ovaries treated with 0.1 and 10 μg/ml 17-20β-DHP at 24 hours post treatment (hpt, P<0.05).

The basic information on genetic diversity of wild and hatchery-propagated stocks of tropical abalone, Haliotis asinina is important for the construction of a breeding scheme leading to the sustainable culturing activity of this species. In this study, 2,876 expressed sequence tags (ESTs) were in silico analyzed and 178 EST sequences contained microsatellite motifs. Four loci (DW455, DW503, PHe177, and PT102) of type I and two loci (Haμ9 and Haμ10) of type II microsatellites were applied for genetic diversity studies. The mean number of alleles per locus and observed heterogeneity in wild populations were 4.167 and 0.483, and 4.833 and 0.528 for CAME (east coast) and TRGW (west coast) while those of hatchery-propagated samples were 3.000 and 0.708, 4.500 and 0.479, 5.167 and 0.524, and 6.333 and 0.527 for PHIH (2nd generation, G2; Philippines), SAMH (G1), SMaRT-TRGH (G8) and SMaRT-SICH (G8), respectively. The numbers of alleles, observed heterozygosity and effective population sizes suggested no severe reduction of genetic diversity in our breeding program of H. asinina. However, reduced Ne was observed in the cultured stocks from the Philippines (PHIH). FST-statistics and the exact test between pairs of samples revealed significant genetic differences between all pairwise comparisons of samples in this study.

To establish sustainable resources and founder populations for genetic improvement of the Siamese fighting fish Betta splendens, genetic diversity in wild and hatchery stocks was examined using mitochondrial (mt) DNA genes cytochrome b (cytb), 16S ribosomal DNA (16S rDNA), and cytochrome oxidase subunit I (COI), and eight microsatellite loci. Based on mtDNA sequences, restrictive levels of polymorphism (0, 3, and 1 substitutions) were observed in this study. For analysis of microsatellites, fluorescent multiplex PCR was developed, and subsequently identifying moderate levels of observed (Ho = 0.4488) and expected (He = 0.6627) heterozygosities and a high number of alleles per locus (15.125 alleles) for overall samples. Comparison of Siamese fighting fish from different sources revealed large genetic differences between pairs of farmed fish (eight groups) and between wild (three geographic locations) and farmed fish (P < 0.0031 following Bonferroni correction). This suggested limited exchanges of genetic resources between commercial farms. When different color varieties of B. splendens were compared, large genetic distances and significant FST estimates and genetic heterogeneity were found (P < 0.0031). Effective population sizes (Ne) were estimated and two farms (NP2-2BS and BK1-4BS) showed Ne greater than 10. Among color varieties, Multi-colors and Blue revealed reasonable Ne (large and 27.9), but lower Ne values (3.6–8.4) were found for the remaining color varieties. These results indicate an urgent need for the establishment of gene pool resources of B. splendens for effective genetic improvement of Siamese fighting fish in Thailand.

Transcriptome comparison was performed to identify genes expressed in skin, muscle and tails of mono-color (Red, Blue, Black, White and Yellow), bi-color (Cambodian) and multi-color (Marble) varieties of Siamese fighting fish Betta splendens. In total, 163,140 unigenes covering 26.348 Gb were found. Of these, 93,899 (57.55 %) unigenes significantly matched at least one database. In total, 5039 differentially expressed genes (DEGs) were found where 2415 genes (47.93 %) showed higher expression and 2624 genes (52.07 %) showed lower expression for all pairwise comparisons. DEGs between paired color varieties were 133-443. Of these, 38-220 genes were more highly expressed while 37-280 genes were more lowly expressed relative to the compared varieties. A total of 897 sequences (148 genes) significantly matched pigmentation-related genes of Danio rerio (E-value < 1e-06). Of these, 19 DEGs were identified. Examples are tyrosinase-related protein 1a (BsTyrp1a), epidermal growth factor receptor (BsEgfr) and neurofibronin 1a (BsNf1a). Moreover, 711,123 SNPs were identified and 1365 of these were located in pigmentation-related genes. Interestingly, an A > C-474 SNP in the gene BsTrpm7 and an indel (position 3571) in the BsItgb1a gene were found only in Cambodian. A C > T-2520 SNP in BsFzd4 and 10 of 11 SNPs in BsTyrp1a were found only in Black. Different expression levels (P < 0.05) were found for tyrosinase (BsTyr), BsTyrp1a, BsNf1a and BsEgf1 among skin, body muscle and tails of the same variety and among the same tissues of different varieties (Red, Green, Blue, Black, Cambodian and Multi-colors, N = 5 each).

Effects of ammonia challenge on expression of ferritin (LvFer) transcripts in Pacific white shrimp Litopenaeus vannamei were examined. One family of second generation (G2) of a growth-improved stock was generated and subjected to a non-lethal ammonia stress test (control, 10 and 20 mg/l ammonia-N). The expression level of LvFer transcripts in hemocytes and hepatopancreas of L. vannamei juveniles during a 72 h trial was significantly changed after exposed to 20 mg/l ammonia-N compared to the control (unchanged water). In addition, a lethal dose challenge (32.15 mg/l ammonia-N) was carried out. The expression levels of LvFer transcripts in susceptible (died before 72 h post treatment, hpt) was significantly lower than that of tolerant (survived after 72 hpt) shrimp (P < 0.05). One single nucleotide polymorphism (SNP, T>G 208) was found in the LvFer gene segment. Real-time PCR amplification of specific alleles (real-time PASA) was successfully developed for genotyping of a T>G 208 SNP. The expression level of juveniles in the tested family carrying a T/T 208 genotype was greater than those carrying a T/G 208 genotype. Association analysis was further tested in a genetically improved stock (4 full-sib families). Juveniles with a T/T 208 genotype showed a greater average body weight and total length than those with a T/G 208 genotype. The expression level of LvFer can be further applied for selection of ammonia-tolerant families while its SNP can be used for selection of shrimp families with a better growth performance in our on-going breeding program of L. vannamei.

White scar oyster Crassostrea belcheri is a commercially important bivalve species in Thailand. Appropriate genetic markers are needed for effective management to elevate its production efficiency. Type II microsatellites of C. belcheri were identified and characterized using an Illumina paired-end shotgun sequencing. A total of 14,743,710 reads were generated for which 198,849 reads containing microsatellites and 217,998 microsatellite loci were found. Twenty out of 60 microsatellite loci (33.33%) were polymorphic and these microsatellites were further tested against DNA bulks (N = 10 each) originating from 7 different geographic locations in Thai waters. Results indicated that newly developed microsatellites can be used for genetic diversity analysis of C. belcheri. Genotyping of C. belcheri collected from Surat Thani (Gulf of Thailand; N = 50) were performed. The number of alleles per locus ranged from 2 to 12 (average = 4.95). Observed and expected heterozygosities ranged from 0.0000 to 0.9400 (average = 0.3419) and 0.1139 to 0.8190 (average = 0.5844), respectively. Genome information and 20 newly isolated microsatellites will facilitate further studies in population genetics, stock management, and genetic improvement of C. belcheri in Thailand.

The basic information on genetic diversity and population structure is essential for the construction of appropriate management schemes leading to sustainable fisheries of the blue swimming crab (Portunus pelagicus). Here, genetic heterogeneity of P. pelagicus (N=174) was examined by single-strand conformational polymorphism (SSCP) analysis of mitochondrial cytochrome c oxidase subunit I (PpCOI270). Seven SSCP genotypes were found across all investigated samples. The average genetic distance between pairs of geographic samples was 0.0014-0.7247. Significant geographic heterogeneity (P<0.05) and restricted levels of female gene flow between paired samples (0.03-1.60 individuals per generation) were observed except between Chanthaburi Prachuap Kriri Khan and Ranong Krabi (P>0.05; 6.54 and 16.17 individuals per generation) located in the same coastal regions. Therefore, the gene pool of P. pelagicus in Thai waters was genetically differentiated to different stocks even though it is biologically regarded as a potential dispersal species. Five geographic samples of P. pelagicus in Thai waters could be differentiated to three genetic stocks; Chanthaburi and Suratthani (stock A), Prachuap Khiri Khan (stock B) and Ranong and Krabi (stock C).