Optimizing genomic prediction using low-density marker panels for streptococcosis resistance in red tilapia (Oreochromis spp.)

Streptococcosis is a major disease that causes huge economic losses to tilapia farming in Thailand. Breeding for Streptococcosis agalactiae resistant strains using the pedigree BLUP method has proven an effective approach to control the disease in red tilapia, but the accuracy of selection is relatively low. Genomic selection, which is based on genome-wide markers to predict genomic breeding values of selection candidates, provides a powerful approach for accelerating genetic progress and producing permanent gains in the population. We evaluated the implementation of four genomic prediction models, GBLUP, ssGBLUP, BayesB and BayesC, using 19 sets of SNP markers (ranging from 500 to 24 582 SNPs) in 886 fish challenged with S. agalactiae. The accuracy of prediction was estimated using a five-fold cross-validation approach, with 708 and 178 individuals sampled for the training and validation sets respectively. Prediction of the accuracy of each of the models was improved substantially compared with PBLUP (10%) using 1000 informative SNPs. The GBLUP model (65%), which required less computing time, outperformed the remaining models - ssGBLUP (53%), BayesB (47%) and BayesC (42%).

Selection response for Streptococcus agalactiae resistance in Nile tilapia Oreochromis niloticus

The potential of selection to improve resistance to streptococcosis was evaluated in a commercial population of Nile tilapia in Thailand. The base generation (G0) consisted of offspring from 98 sires and 149 dams using a partly nested design. At 60 days post-hatch, 30 fish from each family were injected intraperitoneally with a Streptococcosis agalactiae solution (1 × 10⁹  CFU/ml) and evaluated for 14 days. Disease resistance was recorded as the number of days from challenge until death (DD) and as a binary (BIN) trait (dead/alive) on day 14. Three models were used for genetic analyses: Cox frailty model for DD; animal model for DD; and animal model for BIN. Age at challenge was fitted as a covariate and contemporary group as fixed or random effect, depending on the model. Fish from the 18 most resistant families were selected to produce the first generation (G1). Heritability estimates for G0 were 0.22, 0.14 ± 0.02 and 0.11 ± 0.02 for the Cox, linear DD and linear BIN models, respectively. Selection response indicated that the risk of death decreased to 54%, survival time increased to 3.4 days and survival rate increased to 21%. These results suggest that genetic improvement is possible for this population.

Bioinformatics characterization of a cathepsin B transcript from the giant river prawn, Macrobrachium rosenbergii: Homology modeling and expression analysis after Aeromonas hydrophila infection

Cathepsin B is a lysosomal proteolytic enzyme that has been suggested to play a role in pathological processes of immune system. In this study, the full-length cDNA sequence of cathepsin B transcript in the giant river prawn Macrobrachium rosenbergii (MrCTSB) was obtained from 454 pyrosequencing of cDNAs from hepatopancreas and muscle. It was 1158 bp in length, containing an open reading frame (ORF) of 987 bp corresponding to 328 amino acids. The predicted molecular mass and pI of MrCTSB protein was 36.04 kDa and 4.73. The major characteristics of MrCTSB protein consisted of a propeptide of C1 peptidase family at the N-terminus and a cysteine protease (Pept_C1) domain at the C-terminus. The 3-dimentional structure of MrCTSB was constructed by computer-assisted homology modeling. The folding of MrCTSB was highly conserved to human CTSB structure and the modeled MrCTSB displayed characteristics of cysteine proteinases superfamily. The docking study was performed to investigate binding interactions between known inhibitors against MrCTSB. Known inhibitors were oriented in the groove of catalytic site cleft. They bound to subsites from S2, S1, S1', and S2', respectively, with key residues in each subsite. Challenge of juvenile prawns with Aeromonas hydrophila revealed that the MrCTSB transcript in hepatopancreas significantly increased at 60-96 h post injection (hpi). This suggested that MrCTSB may play roles in innate immunity of M. rosenbergii. Our results provide useful information for a more comprehensive study in immune-related functions of MrCTSB.

Genetic parameters for resistance against Flavobacterium columnare in Nile tilapia Oreochromis niloticus (Linnaeus, 1758)

Columnaris disease is a major cause of mortality in tilapia hatcheries and commonly occurs during the summer season in Thailand. One way of reducing the problem is by selective breeding for increased disease resistance. The objective of this study was to estimate quantitative genetic parameters for resistance against columnaris in the Chitralada 4 strain of Nile tilapia. Data from 43 full-sib families (2,580 records) of fry (age = 32 ± 4 days post-hatch) were used in the analyses. Initially, fry were subjected to bath challenge with Flavobacterium columnare (LD₅₀ concentration = 1.2 × 10⁶  CFU/ml) for 14 days. Disease resistance was defined as the number of days from challenge until death (DD) or as a binary trait (dead/alive) on day 14. Linear animal and sire-dam models were used for DD, while threshold animal, threshold sire-dam, binary linear animal and binary linear sire-dam models were used for binary outcomes. Covariate effect of age, fixed effect of challenge day and random effects of the individual animals or sires and dams were included in the models. Mean survival was 32.4 ± 11.6%, and survival rates of the best and poorest families were 70% and 8%, respectively. The highest estimate of heritability (0.30 ± 0.025) was obtained under the threshold sire-dam model. Heritability estimates for DD (0.16 ± 0.034 and 0.17 ± 0.046) were comparable to those obtained from the threshold animal (0.15 ± 0.031) and the binary linear (0.14 ± 0.045 and 0.15 ± 0.044) models. The linear animal and sire-dam models for DD and the threshold sire-dam models performed equally with similar values of r_EBV (0.629, 0.628 and 0.627) and accuracy of selection (0.793, 0.793 and 0.791). This study reveals the potential of selective breeding to increase disease resistance to F. columnare in the studied population of Nile tilapia.

cDNA sequence and protein bioinformatics analyses of MSTN in African catfish (Clarias gariepinus)

Myostatin, also known as growth differentiation factor 8, has been identified as a potent negative regulator of skeletal muscle growth. The purpose of this study was to characterize and predict function of the myostatin gene of the African catfish (Cg-MSTN). Expression of Cg-MSTN was determined at three growth stages to establish the relationship between the levels of MSTN transcript and skeletal muscle growth. The partial cDNA sequence of Cg-MSTN was cloned by using published information from its congener walking catfish (Cm-MSTN). The Cg-MSTN was 1194 bp in length encoding a protein of 397 amino acids. The deduced MSTN sequence exhibited key functional sites similar to those of other members of the TGF-β superfamily, especially, the proteolytic processing site (RXXR motif) and nine conserved cysteines at the C-terminal. Expression of MSTN appeared to be correlated with muscle development and growth of African catfish. Protein bioinformatics revealed that the primary sequence of Cg-MSTN shared 98 % sequence identity with that of walking catfish Cm-MSTN with only two different residues, [Formula: see text]. and [Formula: see text]. The proposed model of Cg-MSTN revealed the key point mutation [Formula: see text] causing a 7.35 Å shorter distance between the N- and C-lobes and an approximately 11° narrow angle than those of Cm-MSTN. The substitution of a proline residue near the proteolytic processing site which altered the structure of myostatin may play a critical role in reducing proteolytic activity of this protein in African catfish.

cDNA structure and the effect of fasting on myostatin expression in walking catfish (Clarias macrocephalus, Günther 1864)

We cloned and sequenced the myostatin (MSTN) gene of walking catfish and characterized its expression under different conditions. The full cDNA sequence of MSTN was 1,784 bp, containing an open reading frame of 1,191 bp, which encoded 396 amino acids. The deduced MSTN sequence contained functional sites similar to other members of TGF-β superfamily, including the proteolytic processing site and nine conserved cysteines in the C-terminal. Walking catfish MSTN mRNA was strongly expressed in skeletal muscle and brain tissues, consistent with the expression profiles of MSTN-1 isoform in other teleosts. Temporal expression analysis revealed that the MSTN was expressed at the highest levels in 1-week-old larvae and adults, but was lowest in early juveniles. A fasting-re-feeding experiment was used to evaluate the effects of starvation on growth and MSTN expression in juvenile walking catfish for 28 days. MSTN transcript levels increased significantly (threefold) after 7 days of fasting (P < 0.05) compared with the fed control. Subsequently, MSTN expression levels decreased 1.6-fold when fasting was extended to 14 days. Although re-feeding decreased the MSTN expression relative to the levels of the fed control, the period was not long enough for growth recovery of the juveniles. Our results supported a role of MSTN as a negative regulator of muscle growth and, possibly, a role in energy conservation in fish.

Sixteen EST-linked microsatellite markers in Günther's walking catfish, Clarias macrocephalus

Twenty-seven new microsatellite sequences were identified by screening 2029 expressed sequence tags from Günther's walking catfish, Clarias macrocephalus. Sixteen loci were polymorphic with the number of alleles ranging from two to 16 per locus and the observed and expected heterozygosities ranging from 0.4667 to 0.9333 and from 0.427 to 0.8819 per locus, respectively. Cross-species amplifications of all 16 primer pairs were tested in four other species of catfish including Clarias gariepinus, Pangasius hypophthalmus, Pangasius larnaudii and Pangasianodon gigas. Eleven loci were found to amplify in other species, with the number of polymorphic loci ranging from one in P. larnaudii to nine in C. gariepinus.