Genomic selection in algae with biphasic lifecycles: A Saccharina latissima (sugar kelp) case study
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 rangedmore »
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1958253
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Marine Science
- Additional Journal Information:
- Journal Name: Frontiers in Marine Science Journal Volume: 10; Journal ID: ISSN 2296-7745
- Publisher:
- Frontiers Media SA
- Country of Publication:
- Switzerland
- Language:
- English
Citation Formats
Huang, Mao, Robbins, Kelly R., Li, Yaoguang, Umanzor, Schery, Marty-Rivera, Michael, Bailey, David, Aydlett, Margaret, Schmutz, Jeremy, Grimwood, Jane, Yarish, Charles, Lindell, Scott, and Jannink, Jean-Luc. Genomic selection in algae with biphasic lifecycles: A Saccharina latissima (sugar kelp) case study. Switzerland: N. p., 2023.
Web. doi:10.3389/fmars.2023.1040979.
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. Genomic selection in algae with biphasic lifecycles: A Saccharina latissima (sugar kelp) case study. Switzerland. https://doi.org/10.3389/fmars.2023.1040979
Huang, Mao, Robbins, Kelly R., Li, Yaoguang, Umanzor, Schery, Marty-Rivera, Michael, Bailey, David, Aydlett, Margaret, Schmutz, Jeremy, Grimwood, Jane, Yarish, Charles, Lindell, Scott, and Jannink, Jean-Luc. Wed .
"Genomic selection in algae with biphasic lifecycles: A Saccharina latissima (sugar kelp) case study". Switzerland. https://doi.org/10.3389/fmars.2023.1040979.
@article{osti_1958253,
title = {Genomic selection in algae with biphasic lifecycles: A Saccharina latissima (sugar kelp) case study},
author = {Huang, Mao and Robbins, Kelly R. and Li, Yaoguang and Umanzor, Schery and Marty-Rivera, Michael and Bailey, David and Aydlett, Margaret and Schmutz, Jeremy and Grimwood, Jane and Yarish, Charles and Lindell, Scott and Jannink, Jean-Luc},
abstractNote = {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.},
doi = {10.3389/fmars.2023.1040979},
journal = {Frontiers in Marine Science},
number = ,
volume = 10,
place = {Switzerland},
year = {Wed Feb 22 00:00:00 EST 2023},
month = {Wed Feb 22 00:00:00 EST 2023}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3389/fmars.2023.1040979
https://doi.org/10.3389/fmars.2023.1040979
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The Accuracy of Genomic Prediction between Environments and Populations for Soft Wheat Traits
journal, September 2018
- Huang, Mao; Ward, Brian; Griffey, Carl
- Crop Science, Vol. 58, Issue 6
Seaweed aquaculture: cultivation technologies, challenges and its ecosystem services
journal, March 2017
- Kim, Jang K.; Yarish, Charles; Hwang, Eun Kyoung
- ALGAE, Vol. 32, Issue 1
Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce
journal, January 2020
- Lenz, Patrick R. N.; Nadeau, Simon; Azaiez, Aïda
- Heredity, Vol. 124, Issue 4
Scalable Sparse Testing Genomic Selection Strategy for Early Yield Testing Stage
journal, June 2021
- Atanda, Sikiru Adeniyi; Olsen, Michael; Crossa, Jose
- Frontiers in Plant Science, Vol. 12
Fine-scale population genetic structure of sugar kelp, Saccharina latissima (Laminariales, Phaeophyceae), in eastern Maine, USA
journal, January 2018
- Breton, Timothy S.; Nettleton, Jeremy C.; O'Connell, Brennah
- Phycologia, Vol. 57, Issue 1
The nitrogen bioextraction potential of nearshore Saccharina latissima cultivation and harvest in the Western Gulf of Maine
journal, February 2021
- Grebe, G. S.; Byron, C. J.; Brady, D. C.
- Journal of Applied Phycology, Vol. 33, Issue 3
Combining Partially Overlapping Multi-Omics Data in Databases Using Relationship Matrices
journal, July 2020
- Akdemir, Deniz; Knox, Ron; Isidro y. Sánchez, Julio
- Frontiers in Plant Science, Vol. 11
Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy
journal, October 2012
- Jia, Yi; Jannink, Jean-Luc
- Genetics, Vol. 192, Issue 4
Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient
journal, December 2020
- Guzinski, Jaromir; Ruggeri, Paolo; Ballenghien, Marion
- Genes, Vol. 11, Issue 12
Modeling Genotype × Environment Interaction for Genomic Selection with Unbalanced Data from a Wheat Breeding Program
journal, September 2016
- Lado, Bettina; Barrios, Pablo González; Quincke, Martín
- Crop Science, Vol. 56, Issue 5
Assessing Genomic Selection Prediction Accuracy in a Dynamic Barley Breeding Population
journal, March 2015
- Sallam, A. H.; Endelman, J. B.; Jannink, J. ‐L.
- The Plant Genome, Vol. 8, Issue 1
Simulation of sugar kelp (Saccharina latissima) breeding guided by practices to accelerate genetic gains
journal, January 2022
- Huang, Mao; Robbins, Kelly R.; Li, Yaoguang
- G3 Genes|Genomes|Genetics, Vol. 12, Issue 3
Mariculture of the Asian kelp Undaria pinnatifida and the native kelp Saccharina latissima along the Atlantic coast of Southern Europe: An overview
journal, April 2016
- Peteiro, César; Sánchez, Noemí; Martínez, Brezo
- Algal Research, Vol. 15
Combined effects of seasonal variation and drying methods on the physicochemical properties and antioxidant activity of sugar kelp (Saccharina latissima)
journal, August 2018
- Sappati, Praveen Kumar; Nayak, Balunkeswar; VanWalsum, G. Peter
- Journal of Applied Phycology, Vol. 31, Issue 2
Shrinkage Estimation of the Realized Relationship Matrix
journal, November 2012
- Endelman, Jeffrey B.; Jannink, Jean-Luc
- G3: Genes|Genomes|Genetics, Vol. 2, Issue 11
Functional properties of the isomorphic biphasic algal life cycle
journal, June 2006
- Thornber, C. S.
- Integrative and Comparative Biology, Vol. 46, Issue 5
Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers
journal, August 2020
- Mao, Xiaowei; Augyte, Simona; Huang, Mao
- Frontiers in Marine Science, Vol. 7
Fermentation of sugar kelp (Saccharina latissima)—effects on sensory properties, and content of minerals and metals
journal, July 2019
- Bruhn, Annette; Brynning, Gunhild; Johansen, Aase
- Journal of Applied Phycology, Vol. 31, Issue 5
Efficiency of multi-trait, indirect, and trait-assisted genomic selection for improvement of biomass sorghum
journal, December 2017
- Fernandes, Samuel B.; Dias, Kaio O. G.; Ferreira, Daniel F.
- Theoretical and Applied Genetics, Vol. 131, Issue 3
Improving SNP discovery by base alignment quality
journal, February 2011
- Li, H.
- Bioinformatics, Vol. 27, Issue 8
Accuracy of genomic selection in European maize elite breeding populations
journal, November 2011
- Zhao, Yusheng; Gowda, Manje; Liu, Wenxin
- Theoretical and Applied Genetics, Vol. 124, Issue 4
Genomic selection across multiple breeding cycles in applied bread wheat breeding
journal, April 2016
- Michel, Sebastian; Ametz, Christian; Gungor, Huseyin
- Theoretical and Applied Genetics, Vol. 129, Issue 6
Introduction to a Special Issue on Genotype by Environment Interaction
journal, September 2016
- de Leon, Natalia; Jannink, Jean-Luc; Edwards, Jode W.
- Crop Science, Vol. 56, Issue 5
Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP
journal, January 2011
- Endelman, Jeffrey B.
- The Plant Genome Journal, Vol. 4, Issue 3
Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelpSaccharina latissima(Laminariales, Phaeophyta)
journal, April 2018
- Luttikhuizen, Pieternella C.; van den Heuvel, Freek H. M.; Rebours, Céline
- Ecology and Evolution, Vol. 8, Issue 8
Genomic Selection for Yield and Seed Composition Traits Within an Applied Soybean Breeding Program
journal, July 2019
- Stewart-Brown, Benjamin B.; Song, Qijian; Vaughn, Justin N.
- G3 Genes|Genomes|Genetics, Vol. 9, Issue 7
Speciation in the exposed intertidal zone: the case of Saccharina angustissima comb. nov . & stat. nov . (Laminariales, Phaeophyceae)
journal, January 2018
- Augyte, Simona; Lewis, Louise; Lin, Senjie
- Phycologia, Vol. 57, Issue 1
Opportunities, challenges and future directions of open-water seaweed aquaculture in the United States
journal, September 2019
- Kim, JangKyun; Stekoll, Michael; Yarish, Charles
- Phycologia, Vol. 58, Issue 5
Fast and accurate long-read alignment with Burrows–Wheeler transform
journal, January 2010
- Li, Heng; Durbin, Richard
- Bioinformatics, Vol. 26, Issue 5
Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers
journal, September 2010
- Crossa, José; Campos, Gustavo de los; Pérez, Paulino
- Genetics, Vol. 186, Issue 2
Genomic selection in plant breeding: from theory to practice
journal, February 2010
- Jannink, J. -L.; Lorenz, A. J.; Iwata, H.
- Briefings in Functional Genomics, Vol. 9, Issue 2
Skinny kelp (Saccharina angustissima) provides valuable genetics for the biomass improvement of farmed sugar kelp (Saccharina latissima)
journal, August 2022
- Li, Yaoguang; Umanzor, Schery; Ng, Crystal
- Journal of Applied Phycology, Vol. 34, Issue 5
Cryptic genetic variation: evolution's hidden substrate
journal, March 2014
- Paaby, Annalise B.; Rockman, Matthew V.
- Nature Reviews Genetics, Vol. 15, Issue 4
Genetic Gain from Phenotypic and Genomic Selection for Quantitative Resistance to Stem Rust of Wheat
journal, July 2015
- Rutkoski, J.; Singh, R. P.; Huerta-Espino, J.
- The Plant Genome, Vol. 8, Issue 2
Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle
journal, January 2011
- Brito, Fernanda V.; Neto, José; Sargolzaei, Mehdi
- BMC Genetics, Vol. 12, Issue 1
On the Accuracy of Genomic Selection
journal, June 2016
- Rabier, Charles-Elie; Barre, Philippe; Asp, Torben
- PLOS ONE, Vol. 11, Issue 6
Genomic Selection in Plant Breeding: A Comparison of Models
journal, January 2012
- Heslot, Nicolas; Yang, Hsiao-Pei; Sorrells, Mark E.
- Crop Science, Vol. 52, Issue 1
Genome-Wide Mapping of Cytosine Methylation Revealed Dynamic DNA Methylation Patterns Associated with Sporophyte Development of Saccharina japonica
journal, September 2021
- Yang, Xiaoqi; Wang, Xiuliang; Yao, Jianting
- International Journal of Molecular Sciences, Vol. 22, Issue 18
Growth and agarose characteristics of isomorphic gametophyte (male and female) and sporophyte of Gracilaria dura and their marker assisted selection
journal, August 2011
- Gupta, Vishal; Baghel, Ravi S.; Kumar, Manoj
- Aquaculture, Vol. 318, Issue 3-4
Prospects for upgrading by the European kelp sector
journal, November 2020
- van den Burg, Sander; Selnes, Trond; Alves, Liliana
- Journal of Applied Phycology, Vol. 33, Issue 1
European aquaculture of sugar kelp (Saccharina latissima) for food industries: iodine content and epiphytic animals as major problems
journal, November 2015
- Lüning, Klaus; Mortensen, Leiv
- Botanica Marina, Vol. 58, Issue 6
A reaction norm model for genomic selection using high-dimensional genomic and environmental data
journal, December 2013
- Jarquín, Diego; Crossa, José; Lacaze, Xavier
- Theoretical and Applied Genetics, Vol. 127, Issue 3
Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica
journal, May 2015
- Zhang, Jing; Liu, Tao; Feng, Rongfang
- PLOS ONE, Vol. 10, Issue 5
The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes
journal, February 2012
- Clark, Samuel A.; Hickey, John M.; Daetwyler, Hans D.
- Genetics Selection Evolution, Vol. 44, Issue 1
The cultivation of European kelp for bioenergy: Site and species selection
journal, September 2015
- Kerrison, Philip D.; Stanley, Michele S.; Edwards, Maeve D.
- Biomass and Bioenergy, Vol. 80
Genomic imprinting: parental influence on the genome
journal, January 2001
- Reik, Wolf; Walter, Jörn
- Nature Reviews Genetics, Vol. 2, Issue 1
Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
journal, April 2001
- Meuwissen, T. H. E.; Hayes, B. J.; Goddard, M. E.
- Genetics, Vol. 157, Issue 4
Characterization of newly developed expressed sequence tag-derived microsatellite markers revealed low genetic diversity within and low connectivity between European Saccharina latissima populations
journal, March 2016
- Guzinski, Jaromir; Mauger, Stéphane; Cock, J. Mark
- Journal of Applied Phycology, Vol. 28, Issue 5
Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers
journal, March 2021
- Roque, Breanna M.; Venegas, Marielena; Kinley, Robert D.
- PLOS ONE, Vol. 16, Issue 3
Relationships among analytical methods used to study genotypic variation and genotype-by-environment interaction in plant breeding multi-environment experiments
journal, July 1994
- Cooper, M.; DeLacy, I. H.
- Theoretical and Applied Genetics, Vol. 88, Issue 5
Systematic Procedures for Calculating Inbreeding Coefficients
journal, February 1949
- Emik, L. Otis; Terrill, Clair E.
- Journal of Heredity, Vol. 40, Issue 2
Accuracy and Training Population Design for Genomic Selection on Quantitative Traits in Elite North American Oats
journal, July 2011
- Asoro, Franco G.; Newell, Mark A.; Beavis, William D.
- The Plant Genome, Vol. 4, Issue 2
Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava
journal, July 2020
- Rabbi, Ismail Yusuf; Kayondo, Siraj Ismail; Bauchet, Guillaume
- Plant Molecular Biology, Vol. 109, Issue 3
Enhancing Hybrid Prediction in Pearl Millet Using Genomic and/or Multi-Environment Phenotypic Information of Inbreds
journal, January 2020
- Jarquin, Diego; Howard, Reka; Liang, Zhikai
- Frontiers in Genetics, Vol. 10
Genomic selection for wheat traits and trait stability
journal, June 2016
- Huang, Mao; Cabrera, Antonio; Hoffstetter, Amber
- Theoretical and Applied Genetics, Vol. 129, Issue 9
The variant call format and VCFtools
journal, June 2011
- Danecek, P.; Auton, A.; Abecasis, G.
- Bioinformatics, Vol. 27, Issue 15
Key Considerations for the Use of Seaweed to Reduce Enteric Methane Emissions From Cattle
journal, December 2020
- Vijn, Sandra; Compart, Devan Paulus; Dutta, Nikki
- Frontiers in Veterinary Science, Vol. 7
Stability of Genomic Selection prediction models across ages and environments
journal, September 2011
- Resende, Marcio FR; Muñoz Del Valle, Patricio R.; Acosta, Juan J.
- BMC Proceedings, Vol. 5, Issue S7
Changes in the Composition of Atlantic Salmon upon the Brown Seaweed (Saccharina latissima) Treatment
journal, November 2019
- Kirkholt, Even Moen; Dikiy, Alexander; Shumilina, Elena
- Foods, Vol. 8, Issue 12
Comparative analysis of morphometric traits of farmed sugar kelp and skinny kelp, Saccharina spp., strains from the Northwest Atlantic
journal, March 2021
- Umanzor, Schery; Li, Yaoguang; Bailey, David
- Journal of the World Aquaculture Society, Vol. 52, Issue 5
Commercial cultivation and bioremediation potential of sugar kelp, Saccharina latissima, in Danish waters
journal, January 2015
- Marinho, Gonçalo S.; Holdt, Susan L.; Birkeland, Mads J.
- Journal of Applied Phycology, Vol. 27, Issue 5
Use of genomic selection in breeding rice (Oryza sativa L.) for resistance to rice blast (Magnaporthe oryzae)
journal, July 2019
- Huang, Mao; Balimponya, Elias G.; Mgonja, Emmanuel M.
- Molecular Breeding, Vol. 39, Issue 8
Factors Affecting Accuracy From Genomic Selection in Populations Derived From Multiple Inbred Lines: A Barley Case Study
journal, March 2009
- Zhong, Shengqiang; Dekkers, Jack C. M.; Fernando, Rohan L.
- Genetics, Vol. 182, Issue 1
Improving gaseous biofuel yield from seaweed through a cascading circular bioenergy system integrating anaerobic digestion and pyrolysis
journal, August 2020
- Deng, Chen; Lin, Richen; Kang, Xihui
- Renewable and Sustainable Energy Reviews, Vol. 128
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
The use of unbalanced historical data for genomic selection in an international wheat breeding program
journal, December 2013
- Dawson, Julie C.; Endelman, Jeffrey B.; Heslot, Nicolas
- Field Crops Research, Vol. 154
Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments
journal, November 2012
- Windhausen, Vanessa S.; Atlin, Gary N.; Hickey, John M.
- G3 Genes|Genomes|Genetics, Vol. 2, Issue 11
Polar lipid profile of Saccharina latissima, a functional food from the sea
journal, May 2019
- Rey, Felisa; Lopes, Diana; Maciel, Elisabete
- Algal Research, Vol. 39
Cultivation of a morphologically distinct strain of the sugar kelp, Saccharina latissima forma angustissima, from coastal Maine, USA, with implications for ecosystem services
journal, April 2017
- Augyte, Simona; Yarish, Charles; Redmond, Sarah
- Journal of Applied Phycology, Vol. 29, Issue 4