Genomic selection in algae with biphasic lifecycles: A Saccharina latissima (sugar kelp) case study

Abstract

IntroductionSugar kelp (Saccharina latissima) has a biphasic life cycle, allowing selection on both thediploid sporophytes (SPs) and haploid gametophytes (GPs).MethodsWe trained a genomic selection (GS) model from farm-tested SP phenotypic data and used a mixed-ploidy additive relationship matrix to predict GP breeding values. Topranked GPs were used to make crosses for further farm evaluation. The relationship matrix included 866 individuals: a) founder SPs sampled from the wild; b) progeny GPs from founders; c) Farm-tested SPs crossed from b); and d) progeny GPs from farm-tested SPs. The complete pedigree-based relationship matrix was estimated for all individuals. A subset of founder SPs (n = 58) and GPs (n = 276) were genotyped with Diversity Array Technology and whole genome sequencing, respectively. We evaluated GS prediction accuracy via cross validation for SPs tested on farm in 2019 and 2020 using a basic GBLUP model. We also estimated the general combining ability (GCA) and specific combining ability (SCA) variances of parental GPs. A total of 11 yield-related and morphology traits were evaluated.ResultsThe cross validation accuracies for dry weight per meter (r ranged from 0.16 to 0.35) and wet weight per meter (r ranged 0.19 to 0.35) were comparable to GS accuracy for yield traits in terrestrial crops. For morphology traits, cross validation accuracy exceeded 0.18 in all scenarios except for blade thickness in the second year. Accuracy in a third validation year (2021) was 0.31 for dry weight per meter over a confirmation set of 87 individuals.DiscussionOur findings indicate that progress can be made in sugar kelp breeding by using genomic selection.

The sugar kelp Saccharina latissima I: Recent advances in a changing climate

“…Also, novel is the application of genome-wide markers in parallel with phenotypic analysis to identify SNPs associated with traits of interest (e.g., higher growth rate) applied in NW Atlantic populations (Mao et al 2020) an approach termed genome-wide association study (GWAS). Using a genomic selection approach, breeding values of S. latissima's gametophytes were estimated and correlated with sporophytes' phenotypic traits, especially wet and dry weight per metre; however, low genetic correlations among different years are concerning and need to be further explored (Huang et al 2023). These approaches inform current attempts to establish breeding programs and, in the future, domesticate S. latissima (Yarish et al 2017;Umanzor et al 2021).…”