A quantitative genetic analysis of size-related traits in cultivated sugar kelp (Saccharina latissima)

Sugar kelp (Saccharina latissima) is a commercially important kelp with great potential for sustainable biomass production. To evaluate the potential for genetic improvement through breeding we analyzed size-related traits in a three-generation selection experiment based on mixed hybridization and mass selection. A base population (F0), composed of 159 wild individuals, was crossed to create the F1 generation, and the longest individuals from F1 were selected to produce the F2selected population. Genomic relationship matrices (GRMs) were constructed using short read-backed haplotypes obtained by Genotyping-by-Sequencing, and different haplotype filtering thresholds were compared. The best-performing GRM (made with markers from 7724 loci) slightly outperformed a pedigree-based matrix when applied to a prediction model. Narrow sense heritability estimates varied between traits, with blade length and blade width exhibiting low to moderate heritability (0.17–0.28), while stipe length was highly heritable (0.46–0.48) and fresh weight was not significantly heritable. Inbreeding depression was significant, with selfed and apomictic individuals showing reduced performance in F1 (0.43–0.80 phenotypic SD across traits) and F2selected (0.19–0.35). Despite selection for longer individuals in F1, the average estimated breeding value for blade length did not increase in F2selected. We identified two main problems associated with the use of mixed hybridization and phenotypic mass selection in our experiment: (1) the best phenotypes might not have high breeding values, and (2) unintended selection may negatively impact the trait being selected for. Our results underscore the value of genomic tools and refined breeding protocols to achieve genetic progress in S. latissima breeding.