Genomics Era on Breeding Aquaculture Stocks

Martsikalis, Petros V.; Gkafas, Georgios A.; Palaiokostas, Christos; Exadactylos, Athanasios

doi:10.1007/978-3-030-05603-2_4

Cited by 8 publications

(4 citation statements)

References 61 publications

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“…Many studies have shown that a population-based case-control design can be more powerful than a family-based study design in identifying genes predisposing both for qualitative and quantitative traits [ 34 , 35 ]. In recent years, only a few studies regarding next generation sequencing for gene expression analysis in early life stages (embryonic and/ or larval stages) of Solea solea and Solea senegalensis were carried out.…”

Section: Introductionmentioning

confidence: 99%

Hox genes polymorphism depicts developmental disruption of common sole eggs

Kavouras¹,

Malandrakis

Danis

et al. 2019

Open Life Sciences

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In sole aquaculture production, consistency in the quality of produced eggs throughout the year is unpredictable. Hox genes have a crucial role in controlling embryonic development and their genetic variation could alter the phenotype dramatically. In teleosts genome duplication led paralog hox genes to become diverged. Direct association of polymorphism in hoxa1a, hoxa2a & hoxa2b of Solea solea with egg viability indicates hoxa2b as a potential genetic marker. High Resolution Melt (HRM) analysis was carried out in 52 viable and 61 non-viable eggs collected at 54±6 hours post fertilization (hpf). Allelic and genotypic frequencies of polymorphism were analyzed and results illustrated a significantly increased risk for non-viability for minor alleles and their homozygous genotypes. Haplotype analysis demonstrated a significant recessive effect on the risk of non-viability, by increasing the odds of disrupting embryonic development up to three-fold. Phylogenetic analysis showed that the paralog genes hoxa2a and hoxa2b, are separated distinctly in two clades and presented a significant ω variation, revealing their diverged evolutionary rate.

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Section: Introductionmentioning

confidence: 99%

Hox genes polymorphism depicts developmental disruption of common sole eggs

Kavouras¹,

Malandrakis

Danis

et al. 2019

Open Life Sciences

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“…Conclusively, our results revealed that ambicolorated juveniles exhibit a divergent function mainly of the central nervous system at the synaptic level. In the present work, using high throughput sequencing techniques make it easier to compare holistically the expression patterns of biochemical and molecular networks and to identify critical differences in a short period of time during different stages of ontogenesis between the two above-mentioned categories [ 76 ]. The gene ontology enrichment analysis and the analysis carried out through the “Reactome” database demonstrated the major biochemical and molecular pathways that appear to be affected.…”

Section: Discussionmentioning

confidence: 99%

Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Kavouras

Malandrakis

Blom

et al. 2021

Animals

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In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

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“…Certainly, there should be exceptions to the general case where species are single interbreeding populations; such cases include phylogeographic divisions present within species [54] that can have their own complicated evolutionary fate [121,147,177] and those with shared, or overlapping barcode clusters due to a complicated history of species formation and mtDNA introgression ( [30] (Figures 2 and 3); see also discussion in Section 2), or even a more complex scenario with introgression-reticulation and genome mosaicism [121]. Actual exceptions from the general assumption that may arise due to the lack of divergence or its small value to be detected by current MM techniques are also expected [178]. For example, if a species originates by the geographic mode (D1) with long-term accumulation of substitutions in isolation, then all the above-explained expectations come true, but when the event of speciation depends on the action of regulatory alterations, chromosomal changes, etc.…”

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confidence: 99%

Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society

Kartavtsev

2021

Animals

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Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the “source” taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.

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Genomics Era on Breeding Aquaculture Stocks

Cited by 8 publications

References 61 publications

Hox genes polymorphism depicts developmental disruption of common sole eggs

Hox genes polymorphism depicts developmental disruption of common sole eggs

Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society

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