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.