Genetic and molecular factors regulating growth and morphology in Senegalese sole (Solea senegalensis)

Body shape and growth are two crucial traits in aquaculture, as they directly influence the productivity capacity and market value of farmed species. This is especially relevant in flatfish, where the specific morphology of each specie is a distinctive factor for consumers. Both traits, growth and morphology, are complex trait regulated by genetic factors, phenotypic plasticity, and other life cycle aspects, such as reproduction. This thesis aims to explore the phenotypic and genetic factors controlling morphology and growth in Senegalese sole (Solea senegalensis) through an integrative approach that includes morphological, skeletal, transcriptomic, and genomic analyses. In the first chapter, Elliptic Fourier Descriptors (EFDs) and other morphometric variables were used to assess morphological variation and calculate its genetic estimates. Principal component analysis identified four symmetric and four asymmetric components that affected main body regions (head, body, and caudal fin) and were modulated by sex, the evaluation batch, and amoeba lesions. Symmetric components, that explained 68.8% of total variation and were related to the body's adjustment to an ellipse and caudal fin positioning, showed moderate to high heritability with high genetic correlations with ellipse descriptors. Asymmetric components related caudal fin position exhibited low heritability, while and head orientation, The heritability of the components related to caudal fin were low, while the heritability for the head orientation component was moderate, suggesting indirect selection for correlated variables as a more efficient approach with greater intergenerational progress. These data confirm the potential of EFDs in genetic selection programs to comprehensively evaluate morphological variation in sole. In the second chapter, the skeletal features, transcriptomic profiles, and genomic regions associated with body ellipticity (ELL) were investigated. High-ellipticity soles had a higher number of vertebrae, longer vertebral bodies and intervertebral spaces, and absence of skeletal malformations. Females showed a wider ventral region than males, and differences in the length of the urostyle relative to the axial skeleton. Differential expression analysis revealed a high number of differentially expressed transcripts (DETs) associated with sex in muscle, liver, and pterygiophores. A subset of 31 ubiquitous DETs between ellipticity groups were identified in at least two tissues. Functional analysis identified cell structure, locomotion, hormonal regulation, and immune response as the main enriched pathways. A bulk segregant analysis (BSR-Seq) identified five genomic regions associated with ELL. The regions on linkage groups 5 and 14 included the candidate genes malt1 and vtg3, also ubiquitous DETs, and the gen bmpr1b close to malt1, suggesting that inflammatory processes and BMP signaling pathways could contribute to modifying the axial skeleton and, consequently, the body ellipticity. Finally, this thesis examined the genetic architecture of growth, with a special emphasis on sexual dimorphism, a critical factor modulating both growth and morphology in soles. Phenotypic data showed significant differences between growth groups. Sexual dimorphism was confirmed with females being generally heavier, with less ELL, and wider ventral regions than males. Differential expression analysis showed a marked effect of sex in muscle and liver, with more than 50% of the DETs co-regulated by sex and growth. Functional analysis revealed complex interaction between transcriptional networks, particularly in muscle and liver. Pathways related to energy provision, cell cycle, and signaling were highly associated with growth. The analysis of sex-specific DETs and growth × sex interactions highlighted pathways involved in lipid metabolism, autophagy, cell cycle, DNA and RNA metabolism, ribosome biogenesis, energy provision, and homeostasis as the most relevant pathways driving sexual dimorphism. The variant analysis identified eleven genomic windows, associated with growth, that include several candidate genes, also differentially expressed (pptc7, taz, abcd1, tfe3, nfix, ptcd2, prkaa1), and related to mitochondrial homeostasis and activity, energy production, and musculoskeletal system. Altogether, these results have important implications for improving productivity, commercialization, and sustainability in aquaculture, allowing the optimization of genetic breeding programs towards more efficient and better-targeted strategies for improving growth and morphology.

Author dc:creator

• Gayo de Linos, Patricia

Advisor dc:contributor.advisor

• Manchado Campaña, Manuel

Statement dc:rights

• Attribution-NonCommercial-NoDerivatives 4.0 Internacional

Licence dc:rights.uri

• http://creativecommons.org/licenses/by-nc-nd/4.0/

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/10498/36268

OAI identifier oai:identifier

oai:rodin.uca.es:10498/36268