Quantitative trait loci for precocious parr maturation, early smoltification, and adult maturation in double-backcrossed trans-Atlantic salmon (Salmo salar)

• Four transAtlantic salmon families were genotyped for 320 (or 121) SNPs.
• Genome level significant QTL for early smolting on Ssa05, Ssa08, Ssa13, and Ssa23.
• Precocious parr maturation QTL on Ssa05, Ssa07, Ssa09, Ssa10, Ssa12, Ssa16, and Ssa20.
• Chromosome level QTL adult maturity on Ssa21 and Ssa23 and length on Ssa05 and Ssa24.
• QTL for adult maturity were on homologous chromosomes to those in rainbow trout.

Quantitative trait loci (QTL) for age at smoltification and adult maturation have been mapped in several salmonid species but less is known about precocious male parr maturity. Phenotypic information on length at age, precocious male parr maturation (paedogenesis), early smoltification, and adult sexual maturation was recorded for four double-backcross families of F1 European/North American trans-Atlantic salmon that had been genotyped for 320 (family A) or 121 (families B, C and D) single nucleotide polymorphisms (SNPs). The locations of QTL for early smoltification and for precocious parr and adult maturation in Atlantic salmon (Salmo salar) were identified and then compared with QTL in homologous chromosomal arms of rainbow trout (Oncorhynchus mykiss). Novel QTL for precocious male parr maturation on Ssa05, Ssa07, Ssa09, Ssa10, Ssa12, Ssa16 and Ssa20 were significant at the genome-wide level as were QTL for early smolting detected on chromosomes Ssa05, Ssa08, Ssa13, and Ssa23. As predicted, precocious male parr were significantly less likely to become early smolts. Two QTL for adult sexual maturation on chromosomes Ssa21 and Ssa23 were significant at the chromosome-wide level as were QTL for adult length on Ssa05 and Ssa24. Separate analysis of family A resulted in novel QTL being detected on Ssa01q for early smolting, Ssa17 and Ssa22 for precocious maturation, and on Ssa03 and Ssa20 for length at the early smolt measuring period. The two chromosomes (Ssa21 and Ssa23) that contained QTL for adult maturation were homologous to two chromosomes (Omy22 and Omy4) that contain QTL for adult maturation in rainbow trout.