Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture ...production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.
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FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Tilapia is one of the most commercially valuable species in aquaculture with over 5 million tonnes of Nile tilapia, Oreochromis niloticus, produced worldwide every year. It has become increasingly ...important to keep track of the inheritance of the selected traits under continuous improvement (e.g. growth rate, size at maturity or genetic gender), as selective breeding has also resulted in genes that can hitchhike as part of the process. The goal of this study was to generate a Local Ancestry Interence workflow that harnessed existing tilapia genotyping-by-sequencing studies, such as Double Digest RAD-seq derived Single-Nucleotide Polymorphism markers. We developed a workflow and implemented a suite of tools to resolve the local ancestry of each chromosomal locus based on reference panels of tilapia species of known origin. We used tilapia species, wild populations and breeding programmes to validate our methods. The precision of the pipeline was evaluated on the basis of its ability to identify the genetic makeup of samples of known ancestry. The easy and inexpensive application of local ancestry inference in breeding programmes will facilitate the monitoring of the genetic profile of individuals of interest, the tracking of the movement of genes from parents to offspring and the detection of hybrids and their origin.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Nile tilapia has proven to be sensitive to change phenotypic sex upon exposure to steroid hormone and high temperature during the critical period of gonad differentiation. It is more difficult to ...feminize XY males than to masculinize XX females. High temperature feminization has also been observed in very few cases in Nile tilapia. Therefore, this study was designed to increase the feminization rates using combined treatments of estrogen hormone (either diethylstilbestrol, DES, or 17α-ethynylestradiol, EE2) and high temperature (36 oC) during the sensitive period of gonad differentiation in Nile tilapia. The parents genotype of the crosses was XX♀ × XY♂; XX♀ × YY♂ and XX♀ × XX♂. Progenies from each cross were exposed to one of six types of treatments: (i) combined treatment of estrogen hormone (DES or EE2) and high temperature (36 oC) (ii) hormone (DES or EE2) alone as positive control (iii) 36 oC as positive control and (iv) 28 oC as negative control. The sexual genotype was confirmed using tightly sex-linked markers located in linkage groups (LG) 1, LG20 and LG23. Both of the combined treatments of estrogen hormone (either DES or EE2) and high temperature induced significant feminization compared with hormone alone in all the crosses except XX (all female progeny). The combined hormone and high temperature treatment using DES showed 100% feminization rate in mixed sex group. On the other hand, high temperature treatment with EE2 showed 75% (100 mg/kg feed) and 65% (150 mg/kg feed) feminization rate in mixed sex group whereas in XY progeny group c. 19% (100 mg/kg feed) and c. 22% (150 mg/kg feed) feminization percentage were observed. However, the survival rate in the negative control ranged from 79% to 96% whereas the EE2-high temperature combined treatment showed higher survival rate (ranged from 79% to 94%) than in the DES-high temperature combined treatment (46.88% in mixed sex group). Similarly, survival rate was also higher in EE2 alone (ranged from 73% to 96%) than in DES alone treatment (c. 66%). DES hormone alone showed higher percentage of feminization (57.14%) than EE2 whereas EE2 hormone alone showed variable results and induced feminization (38.89%) in only one of the batches produced (mixed sex progeny treated with 150 mg/kg feed). High temperature masculinization was observed in one of the mixed sex crosses produced (40%) and in the XX cross (30%). This is the first study demonstrating that combined treatment of estrogen hormone and elevated temperature induced higher feminization rates in Nile tilapia than hormone alone, despite the generally opposite effect of the estrogen hormone and high temperature on gonad differentiation pathways in Nile tilapia.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Stock enhancement of Atlantic salmon (Salmo salar L.), a fish of considerable economic and social importance, is commonplace. Supportive-breeding is a well-recognised method of enhancement which, ...when compared with traditional hatchery practices, is thought to reduce the severity of selection pressures on broodstock fish. Critically, in supportive-breeding programmes, the eggs and sperm used in the breeding process are taken from wild adult fish originating from the same catchment that resulting juvenile fish are subsequently stocked into, thereby avoiding problems associated with a lack of local adaptation in the stocked fish. Previous studies have indicated that sex bias during the hatchery process may result in reduced genetic diversity of the offspring. Utilising 16 microsatellite loci and two expressed sequence tag (EST) loci, we examined progeny from two hatcheries located on the rivers Exe and Tamar in southwest England, assessing the genetic diversity and parental contribution at each. Two strains were assessed within each hatchery. Genetic diversity was found to be reduced in offspring compared with that of the parent fish. This is likely the result of utilising a small number of broodstock in combination with parental bias. In the four hatchery strains studied (Bar, LEx, Lyd and TXL), parental contribution ranged between 2.1 and 29.2%, 12.2–51.0%, 2.0–70.0% and 4.0–40.0%, respectively. If this practice is to be continued, efforts should be made to improve adherence to national rearing guidelines by increasing the number of broodstock fish utilised and ensuring a more balanced contribution of all adults during the crossing process. Ultimately, we suggest a need to review the suitability of current national Atlantic salmon hatchery guidelines, particularly with regard to their use and relevance in small European rearing systems.
•Hatchery-bred fish are unrepresentative of broodstock used for supportive breeding.•Juveniles do not exhibit genetic diversity on a par with that of the wild population.•The appropriateness of UK national hatchery guidelines and practices is considered.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
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