Mapping transmission ratio distortion QTLs in a turbot farmed population

Transmission ratio distortion (TRD) occurs when alleles from one parent are preferentially transmitted to offspring, resulting in deviations from Mendelian expectations. Recent methodological advances allow the evaluation of two independent TRD scenarios that reflect different inheritance mechanisms: genotype-based models (additive and dominant distortion effects) and allele-based models (sire- or dam-specific effects). Genotypic models are thought to better capture TRD mechanisms acting at diploid developmental stages (postfertilisation), whereas allelic models are more appropriate for TRD occurring at the haploid (gametic) level. Although TRD has been extensively studied in plants and mammals, fish remain an underexplored yet highly promising model due to their high fecundity, which enables the analysis of thousands of offspring from a single mating pair. The objective of this study was to characterise TRD patterns in a farmed turbot population and to identify genomic regions and candidate genes associated with viability and survival. The analysed population comprised 1 391 individuals from 36 full-sib families derived from 23 sires and 23 dams. Genotyping was performed using RAD-sequencing, yielding 18 097 single-nucleotide polymorphism (SNP) markers. TRD analyses were conducted using TRDscreen v.1.07 software, which implements a frequentist approach. Models were compared using the Akaike Information Criterion, and statistical significance of distortion parameters was assessed using a strict Bonferroni correction for multiple testing. Candidate regions were explored using the BioMart tool based on the turbot database in Ensembl, and the over-representation of biological processes was evaluated with the Gene List Analysis tool from the PANTHER database. A total of 127 SNPs showed significant deviations from Mendelian inheritance. The majority of which were detected under the genotype-based additive model, consistent with TRD mechanisms acting after fertilisation. These SNPs defined 66 candidate genomic regions encompassing 668 genes, with notable clustering on chromosomes 5, 6, 12 and 13. Functional enrichment and network analyses identified seven significantly overrepresented biological processes, including growth, chromatin organisation and nucleotide metabolism, oocyte meiosis, necrotic process, and ribosome and mitochondrial process. These processes are closely associated with disruptive mechanisms affecting development and survival. In conclusion, the use of a genotype-based approach is particularly relevant in turbot, indicating that the main problem in turbot is related to survival (diploid stages) rather than to fertility (haploid cells).