Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass

Oikonomou, Stavroula; Kazlari, Zoi; Papapetrou, Maria; Papanna, Kantham; Papaharisis, Leonidas; Manousaki, Tereza; Loukovitis, Dimitrios; Dimitroglou, Arkadios; Kottaras, Lefteris; Gourzioti, Evgenia; Pagonis, Charalampos; Kostandis, Andreas; Tsigenopoulos, Costas S.; Chatziplis, Dimitiros

doi:10.1016/j.aqrep.2022.101178

Cited by 5 publications

(3 citation statements)

References 48 publications

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“…At the end of the trial in the D. labrax experiment (358 days), the average weight of fish was 475 g with a SGR of 0.69%/day, supporting relative good performance under the given environmental conditions in sea cages [ 32 , 35 ]. Regarding mortality, we observed an overall mortality rate of 22%, consistent with the expected mortality rate of 20% throughout the full grow-out stage for D. labrax [ 32 , 36 ].…”

Section: Discussionmentioning

confidence: 90%

Comparative analysis of blood protein fractions in two mediterranean farmed fish: Dicentrarchus labrax and Sparus aurata

Alfonso,

Fiocchi,

Toomey

et al. 2024

BMC Vet Res

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Total protein levels in fish are widely used in health and welfare studies, providing a simple and accessible measure. However, the multifaceted role of blood proteins makes it sometimes challenging to link total protein content to specific health issues, while specific protein fractions may offer more precise insights into fish biology and health, particularly in farmed fish species where such data is often lacking. Data were gathered from two experiments involving Dicentrarchus labrax and Sparus aurata, key species in European marine aquaculture. The aim was (1) to assess how different globulin fractions contribute to total protein content in blood and (2) how these contributions vary across different sampling times in healthy animals. In D. labrax, the beta1 globulin fraction emerged as the major contributor (34.16%), followed by albumin and alpha2 globulins (18.24% and 16.41%, respectively). In contrast, pre-albumins and alpha1 fractions had the least contribution (5.49% and 7.71%). S. aurata exhibited albumin as the primary contributor (23.39%), followed by beta1 and alpha2 globulins (19.71% and 19.15%, respectively), with gamma and alpha1 fractions contributing the least (5.34% and 8.63%). Notably, the study revealed relatively stable contributions of globulin fractions to total proteins within both species, albeit with minor variations over time, potentially linked to environmental and individual factors. Furthermore, larger fish displayed higher total protein levels. This research underscores the need for further investigation into the diverse factors influencing globulin contributions to total proteins, ultimately enhancing health and welfare monitoring for farmed fish species.

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Section: Discussionmentioning

confidence: 90%

Comparative analysis of blood protein fractions in two mediterranean farmed fish: Dicentrarchus labrax and Sparus aurata

Alfonso,

Fiocchi,

Toomey

et al. 2024

BMC Vet Res

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“…As a result rudd can be affected by helminths (Shukerova & Kirin, 2008;Chunchukova et al, 2019;Kvach, 2021). And as is known, the presence of parasites in the body of fish can affect their growth and morphological features (Timi & Poulin, 2020;Oikonomou et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Influence of hydrochemical factors on morphometric variability of Scardinius erythrophthalmus in a freshwater river system

Klymenko¹,

Gandziura

Biedunkova³

et al. 2022

Biosys. divers.

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Studying fish growth is a complex task because growth depends on many factors. The process of fish growth is influenced by ecological factors of the water environment. Each species of fish has growth characteristics and characteristic changes in this process as a result of the action of natural and anthropogenic factors. We investigated the morphometric features of Scardinius erythrophthalmus in the hydroecosystem conditions of the Horyn River. Fish were caught by amateur fishing methods during 2018–2021 in the section of the hydrographic system of the Horyn River within the Rivne Plateau, which is the northern part of the Volhynian Upland , namely the Horyn River and its tributaries – the Zamchysko River, the Ustia River, and the Stubelka River. The catches included fish aged from 0+ (one-year-olds) to 5+ (five-year-olds). Growth variability was studied for fish aged 1+ to 4+ because their numbers were sufficient for statistical evaluation. We noticed clear features of the morphometric variability of the fish. According to the coefficient of variation for the general populations of S. erythrophthalmus from different rivers, there was mostly significant variability of such growth characteristics as the largest and smallest fish body height, total length, Smith length and short body length of fish. We also noticed the similarity of the morphometric variability of fish of different ages for the Horyn River and Stubelka River and Zamchisko River and Ustia River. The analysis and evaluation of the surface water quality of these rivers was also similar. Thus, Horyn and Stubla districts had a transitional state from II to III quality class, and the Zamchysko River and Ustya River districts had a transitional state from III to IV quality class. We conducted a multivariate regression and it revealed statistical significance and a close correlation between the coefficients of variation of the growth characteristics of fish with the phosphate content in the water (with an average value of the weighting coefficients of 0.50 ± 0.06), nitrite nitrogen (0.39 ± 0.10) and nitrate nitrogen (0.84 ± 0.34). The calculation of the specific growth of fish by full length revealed that the intensity of growth is the highest between the first and second year of life of fish for small rivers (Zamchysko River, Ustya River, Stubelka River) and between the second and third year for the Horyn River. The results presented in the article are valuable and describe the local variation in the morphometric variability of S. erythrophthalmus. This expanded the understanding of the influence of ecological factors of the aquatic environment on the formation of growth characteristics of this species of fish. In the future, our research will continue and study the linear growth of natural fish populations against the background of changes in the ecological and hydrological conditions of the studied region

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“…The development of the whole-genome resequencing technology provides a large number of SNPs for genetic mapping, which enables whole-genome association and linkage analyses, such as genome-wide association analysis (GWAS), quantitative trait locus (QTL) mapping and bulked sample analysis (BSA) [ 37 , 38 , 39 ]. In aquaculture, GWAS, as a crucial genetic mapping method, has been widely applied to easily measurable quality traits such as growth [ 40 , 41 , 42 ] and nutrition [ 43 , 44 ], while studies on heat tolerance have been limited due to the difficulties in accurately assessing phenotypes. Previous studies of genetic mapping of heat tolerance in oysters have only been conducted on screening temperature-adapted genes between wild C. gigas and C. angulata [ 31 ] and the identification of the regulatory architecture of heat-responsive genes through eQTL in backcross populations between C. gigas and C. angulata [ 45 ], lacking the identification of genomic markers related to heat tolerance at the whole-genome level in hybrid populations between C. gigas and C. angulata .…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Analysis of Heat Tolerance in F2 Progeny from the Hybridization between Two Congeneric Oyster Species

Du,

Jiang,

Wang

et al. 2023

IJMS

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As the world’s largest farmed marine animal, oysters have enormous economic and ecological value. However, mass summer mortality caused by high temperature poses a significant threat to the oyster industry. To investigate the molecular mechanisms underlying heat adaptation and improve the heat tolerance ability in the oyster, we conducted genome-wide association analysis (GWAS) analysis on the F2 generation derived from the hybridization of relatively heat-tolerant Crassostrea angulata ♀ and heat-sensitive Crassostrea gigas ♂, which are the dominant cultured species in southern and northern China, respectively. Acute heat stress experiment (semi-lethal temperature 42 °C) demonstrated that the F2 population showed differentiation in heat tolerance, leading to extremely differentiated individuals (approximately 20% of individuals die within the first four days with 10% survival after 14 days). Genome resequencing and GWAS of the two divergent groups had identified 18 significant SNPs associated with heat tolerance, with 26 candidate genes located near these SNPs. Eleven candidate genes that may associate with the thermal resistance were identified, which were classified into five categories: temperature sensor (Trpm2), transcriptional factor (Gata3), protein ubiquitination (Ube2h, Usp50, Uchl3), heat shock subfamily (Dnajc17, Dnaja1), and transporters (Slc16a9, Slc16a14, Slc16a9, Slc16a2). The expressional differentiation of the above genes between C. gigas and C. angulata under sublethal temperature (37 °C) further supports their crucial role in coping with high temperature. Our results will contribute to understanding the molecular mechanisms underlying heat tolerance, and provide genetic markers for heat-resistance breeding in the oyster industry.

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Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass

Cited by 5 publications

References 48 publications

Comparative analysis of blood protein fractions in two mediterranean farmed fish: Dicentrarchus labrax and Sparus aurata

Comparative analysis of blood protein fractions in two mediterranean farmed fish: Dicentrarchus labrax and Sparus aurata

Influence of hydrochemical factors on morphometric variability of Scardinius erythrophthalmus in a freshwater river system

Genome-Wide Association Analysis of Heat Tolerance in F2 Progeny from the Hybridization between Two Congeneric Oyster Species

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