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

Thumbnail Image
Date
2023-02-22
Authors
Huang, Mao
Robbins, Kelly R.
Li, Yaoguang
Umanzor, Schery
Marty-Rivera, Michael
Bailey, David
Aydlett, Margaret
Schmutz, Jeremy
Grimwood, Jane
Yarish, Charles
Lindell, Scott
Jannink, Jean-Luc
Alternative Title
Date Created
Location
DOI
10.3389/fmars.2023.1040979
Related Materials
Replaces
Replaced By
Keywords
Sugar kelp (Saccharina latissima)
Genomic selection (GS)
Genotyping
Phenotyping
Brown algae
Biphasic cycle
Breeding
Abstract
Introduction Sugar kelp ( Saccharina latissima ) has a biphasic life cycle, allowing selection on both thediploid sporophytes (SPs) and haploid gametophytes (GPs). Methods We 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. Results The 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. Discussion Our findings indicate that progress can be made in sugar kelp breeding by using genomic selection.
Description
© The Author(s), 2023. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Huang, M., Robbins, K., Li, Y., Umanzor, S., Marty-Rivera, M., Bailey, D., Aydlett, M., Schmutz, J., Grimwood, J., Yarish, C., Lindell, S., & Jannink, J.-L. Genomic selection in algae with biphasic lifecycles: a Saccharina latissima (sugar kelp) case study. Frontiers in Marine Science, 10, (2023): 1040979, https://doi.org/10.3389/fmars.2023.1040979.
Embargo Date
Citation
Huang, M., Robbins, K., Li, Y., Umanzor, S., Marty-Rivera, M., Bailey, D., Aydlett, M., Schmutz, J., Grimwood, J., Yarish, C., Lindell, S., & Jannink, J.-L. (2023). Genomic selection in algae with biphasic lifecycles: a Saccharina latissima (sugar kelp) case study. Frontiers in Marine Science, 10, 1040979.
Cruises
Cruise ID
Cruise DOI
Vessel Name
Except where otherwise noted, this item's license is described as Attribution 4.0 International