Genomic selection in organisms with biphasic lifecycles: a Saccharina latissima (sugar kelp) case study
Genomic selection in organisms with biphasic lifecycles: a Saccharina latissima (sugar kelp) case study
Abstract Sugar kelp (Saccharina latissima) has a biphasic life cycle, allowing selection on both the diploid sporophytes (SPs) and haploid gametophytes (GPs). 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. Top-ranked 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 on farm-tested SPs in two years 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. 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 for dry weight per meter over a confirmation set of 87 individuals was 0.31.
Aydlett Margaret、Huang Mao、Li Yaoguang、Grimwood Jane、Yarish Charles、Jannink Jean-Luc、Schmutz Jeremy、Robbins Kelly R、Lindell Scott、Marty-Rivera Michael、Bailey David、Umanzor Schery
Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic InstitutionSection of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell UniversityDepartment of Ecology & Evolutionary Biology, University of ConnecticutHudsonAlpha Institute for BiotechnologyDepartment of Ecology & Evolutionary Biology, University of ConnecticutSection of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University||United States Department of Agriculture-Agriculture Research ServiceHudsonAlpha Institute for BiotechnologySection of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell UniversityApplied Ocean Physics and Engineering Department, Woods Hole Oceanographic InstitutionDepartment of Ecology & Evolutionary Biology, University of ConnecticutApplied Ocean Physics and Engineering Department, Woods Hole Oceanographic InstitutionDepartment of Ecology & Evolutionary Biology, University of Connecticut||College of Fisheries and Ocean Sciences, University of Alaska Fairbanks
农业科学技术发展生物科学研究方法、生物科学研究技术水产、渔业
Aydlett Margaret,Huang Mao,Li Yaoguang,Grimwood Jane,Yarish Charles,Jannink Jean-Luc,Schmutz Jeremy,Robbins Kelly R,Lindell Scott,Marty-Rivera Michael,Bailey David,Umanzor Schery.Genomic selection in organisms with biphasic lifecycles: a Saccharina latissima (sugar kelp) case study[EB/OL].(2025-03-28)[2025-06-30].https://www.biorxiv.org/content/10.1101/2022.08.01.502376.点此复制
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