Genome-wide association study of morphometric and metabolic characteristics in European populations of the sugar kelp Saccharina latissima.

Abstract

The sugar kelp Saccharina latissima is a promising candidate for sustainable aquaculture in the North Atlantic and Northeast Pacific, but genetic improvement has been hindered by a limited understanding of the genetic basis of economically important traits. We conducted a genome-wide association study (GWAS) for this species using 202 self-fertilized pseudo-F1 individuals derived from 12 of 13 sampled populations spanning northern and southern European genetic clusters. Individuals were genotyped with ddRAD-seq-derived single nucleotide polymorphism markers and phenotyped in a common-garden experiment for four morphological traits (blade length, blade width, blade area, and stipe length) and six metabolic traits related to nitrogen metabolism. We identified 18 significant marker-trait associations, with individual loci explaining 1.37% to 10.93% of phenotypic variance (PVE). Rather than major-effect quantitative trait locus (QTL), the associated loci each accounted for a small-to-moderate proportion of trait variance, the largest being for nitrogen-metabolism traits (up to 10.93% PVE), and a single locus on chromosome 17 influenced both blade length and blade area. Marker-based heritability was high for morphological traits (0.75-0.99) but ranged widely for metabolic traits (0-0.99), with large standard errors throughout. Cross-validated genomic selection models yielded predictive abilities of 0.21-0.59 across traits, the only exception being for protein content, for which both heritability and predictive ability were effectively null. Overall, these results indicate a mixed genetic architecture, comprising moderate-effect loci amenable to marker-assisted selection and polygenic traits better suited to genomic selection, and they provide a foundation for genomics-assisted breeding in kelp aquaculture.