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Howard C, Taylor JF, Migaud H, Gutierrez AP, Bekaert M. Comparison of Diploid and Triploid Atlantic Salmon ( Salmo salar) Physiological Embryonic Development. Animals (Basel) 2023; 13:3352. [PMID: 37958107 PMCID: PMC10647732 DOI: 10.3390/ani13213352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Diploid and triploid Atlantic salmon show distinct physiological differences including heart, brain, and digestive system morphology, propensity for certain deformities, temperature tolerance as eggs and once hatched, and different nutritional requirements. Whilst several studies have looked in detail at the rate of embryogenesis in diploid salmon, no study has compared the rate of embryogenesis between ploidies from fertilisation to hatch. This study based its assessment on a seminal paper by Gorodilov (1996) and used the same techniques to compare the rate at which triploid and diploid embryos developed morphological characteristics. Whilst no significant difference was found, this study provides well-needed justification for the assumption that both ploidies develop at the same rate and gives scientific weight to studies which involve manipulation at these stages of development. Two factors that did differ, however, were the timing of hatch, and mortality. Triploids hatched more quickly than diploids and reached 50% hatch at a significantly earlier point. Triploids also suffered from a significantly higher rate of mortality.
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Affiliation(s)
- Callum Howard
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
- AquaBioTech Group, 1761 Mosta, Malta
| | - John F. Taylor
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
- AquaMaof Aquaculture Technologies Ltd., Rosh Ha’ayin 4809245, Israel
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
- Mowi Scotland, Glen Nevis Business Park, Fort William PH33 6RX, UK
| | - Alejandro P. Gutierrez
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
- Center for Aquaculture Technologies, San Diego, CA 92121, USA
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
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Cádiz MI, López ME, Díaz-Domínguez D, Cáceres G, Marin-Nahuelpi R, Gomez-Uchida D, Canales-Aguirre CB, Orozco-terWengel P, Yáñez JM. Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3395-3404. [PMID: 34339816 DOI: 10.1016/j.ygeno.2021.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/26/2022]
Abstract
Domestication processes and artificial selection are likely to leave signatures that can be detected at a molecular level in farmed rainbow trout (Oncorhynchus mykiss). These signatures of selection are genomic regions that contain functional genetic variants conferring a higher fitness to their bearers. We genotyped 749 rainbow trout from a commercial population using a rainbow trout Axiom 57 K SNP array panel and identified putative genomic regions under selection using the pcadapt, Composite Likelihood Ratio (CLR) and Integrated Haplotype Score (iHS) methods. After applying quality-control pipelines and statistical analyses, we detected 12, 96 and 16 SNPs putatively under selection, associated with 96, 781 and 115 candidate genes, respectively. Several of these candidate genes were associated with growth, early development, reproduction, behavior and immune system traits. In addition, some of the SNPs were found in interesting regions located in autosomal inversions on Omy05 and Omy20. These findings could represent a genome-wide map of selection signatures in farmed rainbow trout and could be important in explaining domestication and selection for genetic traits of commercial interest.
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Affiliation(s)
- María I Cádiz
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - María E López
- Department of Aquatic Resources, Swedish University of Agricultural Sciences, Drottningholm, Sweden
| | | | - Giovanna Cáceres
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago 8820808, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile
| | - Rodrigo Marin-Nahuelpi
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Daniel Gomez-Uchida
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | - Cristian B Canales-Aguirre
- Centro i~Mar, Universidad de Los Lagos, Camino Chinquihue 6 km, Puerto Montt, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile
| | | | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Avenida Santa Rosa 11735, La Pintana, 8820808 Santiago, Chile; Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción, Chile.
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Vo TTM, Nguyen TV, Amoroso G, Ventura T, Elizur A. Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar). BMC Genomics 2021; 22:545. [PMID: 34271869 PMCID: PMC8285899 DOI: 10.1186/s12864-021-07884-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/28/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3' mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3' mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes. RESULTS In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR. CONCLUSIONS Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3' mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for duox2 and duoxa1.
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Affiliation(s)
- Thu Thi Minh Vo
- GeneCology Research Centre, University of the Sunshine Coast, Queensland, Sunshine Coast, Australia.,School of Science, Technology and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia.,School of Biotechnology, International University, Viet Nam National University, 700000, Ho Chi Minh City, Vietnam
| | - Tuan Viet Nguyen
- Centre for AgriBiosciences, AgriBio, Agriculture Victoria, Victoria, 3083, Bundoora, Australia
| | | | - Tomer Ventura
- GeneCology Research Centre, University of the Sunshine Coast, Queensland, Sunshine Coast, Australia. .,School of Science, Technology and Engineering, University of the Sunshine Coast, Sunshine Coast, Queensland, Australia.
| | - Abigail Elizur
- GeneCology Research Centre, University of the Sunshine Coast, Queensland, Sunshine Coast, Australia.
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Smedley M, Migaud H, McStay E, Clarkson M, Bozzolla P, Campbell P, Taylor J. Impact of dietary phosphorous in diploid and triploid Atlantic salmon ( Salmo salar L.) with reference to early skeletal development in freshwater. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2018; 490:329-343. [PMID: 29681666 PMCID: PMC5905282 DOI: 10.1016/j.aquaculture.2018.02.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 05/28/2023]
Abstract
In order to assess the effect of dietary phosphorus (P) in reducing vertebral malformations and improving freshwater (FW) performance in triploid Atlantic salmon (Salmo salar), both triploid and diploid Atlantic salmon were fed three different dietary P inclusion levels (low: 4.9, medium: 7.7, and high: 9.7 g available P kg-1) from first feeding until smolt. Somatic and skeletal response was assessed at fry (~0.5 g), parr (~5 g) and smolt (~45 g) stages. Triploid parr initially grew faster on the high P diet, while groups fed low P resulted in a significantly higher weight at smolt. Image analysis of double stained Alcian blue and Alizarin red S fry revealed that low P fed triploid fish presented less well mineralised vertebrae, and significantly more malformed vertebrae in both parr and smolt stages following x-ray radiographic assessment. Triploid parr fed high and medium P had similar numbers of malformed vertebrae relative to their diploid counterparts but greater numbers than at smolt. Low P fed triploids had the highest prevalence of jaw and vertebral malformations as well as the highest number of deformed vertebrae in the central caudal vertebral region, which was more pronounced at parr than at smolt. Shorter vertebrae dorso-ventral lengths were observed throughout the spinal column (R1-R4) in parr fed low P and only in the caudal region (R3) at smolt. In parr, both ploidies showed reduced phosphate homeostasis protein fgf23 gene expression in vertebrae when fed low P diets, while triploids showed greater down-regulation of osteogenic factors (alp, opn and igf1r) between diets relative to diploids, suggesting possible greater active suppression of mineralisation and reduced osteogenic potential in triploids. No effects of diet or ploidy on gene expression were evident at smolt. Comparisons between development stages suggest early P supplementation in triploids is crucial for skeletal development. Ultimately, reducing vertebral deformities observed at smolt with higher P supplementation in triploids could contribute towards improving skeletal performance and welfare of the stocks in the marine phase.
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Affiliation(s)
- M.A. Smedley
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - H. Migaud
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - E.L. McStay
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - M. Clarkson
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - P. Bozzolla
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | | | - J.F. Taylor
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
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