In the context of the Greek-funded research project MeagreGen, w e genetically analyzed more than 900 samples from eleven meagre broodstocks using microsatellite markers, eight of which were from breeders of AVRAMAR SA , as well as three other stocks and their offspring . Meagre is a fast-grow ing sciaenid species that has recently gained significant interest in aquaculture diversification and the industry’s sustainability. The estimated heterozygosity values were generally low (0.40 to 0.84), as was the number of alleles per site (average 3.58). Structure and DAPC analyses suggested that th e populations may be optimally grouped into five groups. We analyzed the relatedness results using two selected methods to demonstrate that there is no strong kinship relationship between the stocks. Conversely, we found parent-offspring and/or full-sibling relationships within the stocks (Nousias et al., 2021) .
We also initiated the first massive production of genetic data in meagre with genomic and transcriptomic sequences. In total, over 38 million base pair s (bp) were sequenced with the ONT MinION platform (long-read sequences), and more than 3 million sequences with an average length of 12,640 bp, providing 54.5× coverage of the genome. Additionally, o ver 166 million sequences of 150 bp were sequenced using the Illumina platform (short-length and high-fidelity sequences) , providing 30.9× coverage of the genome. Moreover , the transcriptome sequencing generated over 100 million sequences that were used for constructing the transcriptome of the species. At the end, t he first high-quality reference genome as well as the first gene predictions were delivered for meagre . The genome has a total length of 696 megabases (Mb) and includes 1,012 highly relevant sequences. More than 93% of the genome is included in the 24 largest scaffolds, which correspond to the 24 chromosomes of the species (Papadogiannis et al., 2023) .
Subsequently , we conducted the first complete genomic evaluation of the species for body weight, length and growth parameters using more than 800 offspring genotyped with a double-digest RAD sequencing protocol . Parentage assignment was performed using SNP markers and a quantitative trait locus (QTL) associated with growth, and explaining approximately 3.25 % of the phenotypic variance was detected in chromosome 17. Using pedigree and genomic relationship matrix, moderate to high heritability estimates along with high genetic/genomic correlations between all studied traits were detected except for the initial body weight. The predicted performance of the breeding values estimation was higher with the genomic than the pedigree relationship matrix for body weight and growth (Oikonomou et al., 2025). Lastly, other significant or minor QTLs for head centroid size and skeletal deformities, such as lordosis and pugheadedness, were identified by integrating data from geometric morphometrics , and their use was evaluated as an improvement target in breeding programs. Finally, we propose the application of genomic selection (GS) over MAS, which has advantages over the classical polygenic effects based on pedigree, because it predicts the breeding value for each phenotype with greater accuracy, reduces the generation interval with positive effects on genetic progress, and helps maintain homozygosity at low levels under breeding conditions.
References
Nousias O, Tzokas K, Papaharisis L, Ekonomaki K, Chatziplis D, Batargias C, Tsigenopoulos CS (2021) Genetic Variability, Population Structure, and Relatedness Analysis of Meagre Stocks as an Informative Basis for New Breeding Schemes. Fishes 6(4): 78, https://doi.org/10.3390/fishes6040078
Oikonomou S, Tasiouli K, Tsaparis D, Manousaki T, Vallecillos A, Oikonomaki K, Tzokas K, Katribouzas N, Batargias C, Chatziplis D, Tsigenopoulos CS (2025) Genomic evaluation for body weight, length and growth estimates in meagre Argyrosomus regius . Aquaculture, 595(P2), 741622. https://doi.org/10.1016/j.aquaculture.2024.741622
Papadogiannis V, Manousaki T, Nousias O, Tsakogiannis A, Kristoffersen JB, Mylonas CC, Batargias C, Chatziplis D, Tsigenopoulos CS (2023) Chromosome genome assembly for the meagre, Argyrosomus regius , reveals species adaptations and sciaenid sex-related locus evolution, Frontiers in Genetics, section Evolutionary and Population Genetics, 10: 1081760, https://doi.org/10.3389/fgene.2022.1081760
Acknowledgements
The study received funding from the Hellenic Republic through the "MeagreGen" project under the call "Special Actions – AQUACULTURE” in the Operational Program "Competitiveness, Entrepreneurship and Innovation 2014-2020".