Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance

Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease resistant strains are highly sought after as a sustainable solution to this problem. To study the genetic basis and cellular pathways underlying disease resistance, RNA-Seq was used to characterize transcriptional responses of susceptible and resistant fish at day 4 after CyHV-3 infection

Species-Specific Marker Discovery in Tilapia

Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations

The genomic substrate for adaptive radiation in African cichlid fish

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification

Improving Salinity Tolerance in Tilapias: Past Experience and Future Prospects

With increasing scarcity of fresh water available for aquaculture, especially in arid regions, development of tilapias that tolerate high salinity would increase fish (and hence, animal protein) production. We review culture practices, nutrition, physiology, and genetics, and propose approaches to improving salinity tolerance in tilapias. Physiological studies of biochemical pathways underlying phenotypic differences in salt tolerance can lead to genetic studies of intra and interspecific variation. Molecular technology can lead to studies on osmoregulation-related biochemical pathways, for which the euryhaline tilapia is an attractive model. Functional genomics and proteomics are powerful tools for studying the molecular bases of environmental adaptation and metabolic connections to osmoregulatory physiology. Both provide avenues for discovering novel pathways related to osmoregulation with relevance to aquaculture. Dietary supplementation with NaCl and optimized acclimation protocols are immediate and practical ways to improve salt tolerance. Inter-specific variation in salinity tolerance may be used to select salt-tolerant species and develop salt-tolerant hybrids. In the long term, quantitative trait loci associated with, or genes involved in, saltwater tolerance may facilitate marker-assisted or gene-assisted selection for this trait in tilapia

Inheritance Of The White-Red (Kohaku) Color Complex In Ornamental (Koi) Carp (Cyprinus Caprio L.)

Color variability was investigated in three normal (amphimictic) and three meiotic gynogenetic progenies obtained from white-red (kohaku, according to Japanese classification) koi parents. All the amphimictic and gynogenetic progenies consisted of three color types – white, white-red and red. The ratio of colors depended on the relative coverage by red patches in the kohaku parents. The lowest percentage of red fish and highest proportion of white fish were recorded in progeny obtained from kohaku parents with relatively weak development of the red color. The percent coverage by red patches was measured in a sample of thirty or sixty white-red fish from each amphimictic progeny and the distribution of color classes within the sample was determined. The distribution of the sample, together with the white:white-red:red ratio in the total progeny, was used to estimate the color class distribution in the entire progeny (including the solid white and solid red individuals). In two of the amphimictic progenies, the fish clearly divided into two groups: non-red (solid white and white-red) and solid red fish. Appearance of these groups might be explained by the existence of some major color-determining gene(s), which determine(s) the background color (either white or red) of the individual fish. It is also suggested that the devel- opment of red patches in fish with a white body background is controlled by many genes with alleles that either maintain the white color or induce the appearance of red patches

Fertility Problems In The Second Generation Of A Four-Species Tilapia Cross

Reproductive problems were encountered in attempting to produce the second generation of a four-way cross of tilapia from interspecific F1 hybrids. The cross (Oreochromis mossambicus x O. aureus) x (Sarotherodon galilaeus x O. niloticus) successfully bred for one generation, how- ever, not even a single batch of progeny was obtained in the subsequent generation. It was con- cluded that the complex genetic structure of this cross caused the fertility problem. Any similar breeding programs that are based on multi-species crosses should take into consideration that reproductive problems may occur

DNA Barcoding of Israeli Indigenous and Introduced Cichlids

The objectives of this study were barcoding and taxonomic analysis of the five tilapiine species (Oreochromis aureus, O. niloticus, O. mossam- bicus, Sarotherodon galilaeus, and Tilapia zillii), two tilapia hybrid strains (Florida red tilapia and Philippine red tilapia), and two endemic wild cichlids (Tristramella simonis and Astatotilapia flaviijosephi) available in Israel, as well as O. urolepis hornorum. Cytochrome oxidase subunit I (COI) 619 bp sequence traces of 104 individuals were assembled, aligned, and compared (GenBank project GI 209553463). The DNA sequences of two hybrid strains were identical to those of O. hornorum and O. aureus. Absence of intra-specific variability was detected in the commercially used species, O. aureus, S. galilaeus, O. mossambicus, and O. urolepis horno- rum. Two DNA sequence variants were detected in O. niloticus originating from Ghana and Egypt. In contrast, 2-3 variants were detected in the DNA of each of the non-commercial species. Amino-acid sequences were identical in all “true tilapias” and different from the sequences in the endemic cichlids. As a whole, the protein phylogenetic tree fitted the expected conventional taxonomy as opposed to the respective DNA-based tree. Sequences FJ348047-FJ348150 were submitted to GenBank via the BOLD database (identical to FISH001-08 - FISH104-08 in this database)

Genetic basis of sex determination in fishes: Searching for master key regulator genes in the sex determination pathway of tilapias

Recent results show a striking similarity in the dynamics of expression of gonad differentiation regulators in zebrafish and mammals. Candidates for the role of master key regulators (MKRs) in tilapia were selected, based on three concepts established in the literature for non-mammal species. These three concepts are: (a) MKRs are DM-proteins or their close downstream/ upstream partners in the sex determination pathway, (b) MKRs are genes working just upstream of aromatase in the sex determination pathway, or the aromatase itself, and (c) MKRs are homologs of mammal genes which are close partners of SRY (“missing” in non-mammal verte- brates), mostly belonging to the SOX family. Coding sequences of putative genes were searched in cichlid (TIGR) and general (NCBI) databases, and in the tilapia gonad EST library (RBEST). Primers in two adjacent exons were designed, based on predicted exon-intron boundaries for each of 11 selected genes. Amplified segments of the targeted genes in two purebred tilapia species were sequenced. Seven SSLP and four SNP-based markers were identified in the can- didate genes for MKRs of sex determination and mapped to the tilapia genetic map using geno- type data of 76-90 individuals of the F2 mapping family. The mapping positions of the selected genes relative to previously reported QTL regions for sex determination are discussed

Culture Of The Australian Red-Claw Crayfish (Cherax Quadricarinatus) In Israel Crayfish Incorporation Into Intensive Tilapia Production Units

This study tested the suitability of the Australian red-claw crayfish Cherax quadricarinatus for rear- ing in an intensive culture system as a supplement to Oreochromis niloticus. Fish were grown in twelve 5.5 m3 tanks at high density (33/m3) for 133 days, alone or with crayfish at two stocking den- sities (10/m2 and 20/m2) with added shelters or with crayfish at the lower density (10/m2) without shelters. Tilapia survival ranged 90.3-95.0% with no significant differences among treatments. The growth rate of the tilapia raised with crayfish (2.05 g/day) was significantly higher than that of tilapia grown alone (1.88 g/day) probably because the fish were feeding on part of the crayfish pellets. Among treatments, there were no significant differences in fish yield. Crayfish survival was extremely low in the ‘no shelter’ treatment (2.9±2.7%) but reasonable (approximately 60%) when raised with shelters. The growth rate of the crayfish raised with shelters was significantly higher at the lower density (0.21 g/day) than at the higher density (0.18 g/day). Further research is needed on rearing tilapia and crayfish to market size in intensive systems, to establish the economic prof- itability of this culture strategy