Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction
Pacific oysters are a key aquaculture species globally, and genetic improvement via selective breeding is a major target. Genomic selection has the potential to expedite genetic gain for key target traits of a breeding program, but has not yet been evaluated in oyster. The recent development of SNP...
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ftunivstirling:oai:dspace.stir.ac.uk:1893/31438 2023-05-15T15:58:17+02:00 Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction Gutierrez, Alejandro P Matika, Oswald Bean, Tim P Houston, Ross D Natural Environment Research Council Biotechnology and Biological Sciences Research Council Roslin Institute Weymouth Laboratory 2018 application/pdf http://hdl.handle.net/1893/31438 https://doi.org/10.3389/fgene.2018.00391 http://dspace.stir.ac.uk/bitstream/1893/31438/1/fgene-09-00391.pdf en eng Frontiers Media SA Gutierrez AP, Matika O, Bean TP & Houston RD (2018) Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction. Frontiers in Genetics, 9, Art. No.: 391. https://doi.org/10.3389/fgene.2018.00391 391 http://hdl.handle.net/1893/31438 doi:10.3389/fgene.2018.00391 30283494 WOS:000445068200001 2-s2.0-85055143232 1643543 http://dspace.stir.ac.uk/bitstream/1893/31438/1/fgene-09-00391.pdf © 2018 Gutierrez, Matika, Bean and Houston. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. http://creativecommons.org/licenses/by/4.0/ CC-BY genomic selection Pacific oyster growth GBLUP SNP array Journal Article VoR - Version of Record 2018 ftunivstirling https://doi.org/10.3389/fgene.2018.00391 2022-06-13T18:42:43Z Pacific oysters are a key aquaculture species globally, and genetic improvement via selective breeding is a major target. Genomic selection has the potential to expedite genetic gain for key target traits of a breeding program, but has not yet been evaluated in oyster. The recent development of SNP arrays for Pacific oyster (Crassostrea gigas) raises the opportunity to test genomic selection strategies for polygenic traits. In this study, a population of 820 oysters (comprising 23 full-sibling families) were genotyped using a medium density SNP array (23 K informative SNPs), and the genetic architecture of growth-related traits [shell height (SH), shell length (SL), and wet weight (WW)] was evaluated. Heritability was estimated to be moderate for the three traits (0.26 ± 0.06 for SH, 0.23 ± 0.06 for SL and 0.35 ± 0.05 for WW), and results of a GWAS indicated that the underlying genetic architecture was polygenic. Genomic prediction approaches were used to estimate breeding values for growth, and compared to pedigree based approaches. The accuracy of the genomic prediction models (GBLUP) outperformed the traditional pedigree approach (PBLUP) by ∼25% for SL and WW, and ∼30% for SH. Further, reduction in SNP marker density had little impact on prediction accuracy, even when density was reduced to a few hundred SNPs. These results suggest that the use of genomic selection in oyster breeding could offer benefits for the selection of breeding candidates to improve complex economic traits at relatively modest cost. Article in Journal/Newspaper Crassostrea gigas Pacific oyster University of Stirling: Stirling Digital Research Repository Pacific Frontiers in Genetics 9 |
institution |
Open Polar |
collection |
University of Stirling: Stirling Digital Research Repository |
op_collection_id |
ftunivstirling |
language |
English |
topic |
genomic selection Pacific oyster growth GBLUP SNP array |
spellingShingle |
genomic selection Pacific oyster growth GBLUP SNP array Gutierrez, Alejandro P Matika, Oswald Bean, Tim P Houston, Ross D Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction |
topic_facet |
genomic selection Pacific oyster growth GBLUP SNP array |
description |
Pacific oysters are a key aquaculture species globally, and genetic improvement via selective breeding is a major target. Genomic selection has the potential to expedite genetic gain for key target traits of a breeding program, but has not yet been evaluated in oyster. The recent development of SNP arrays for Pacific oyster (Crassostrea gigas) raises the opportunity to test genomic selection strategies for polygenic traits. In this study, a population of 820 oysters (comprising 23 full-sibling families) were genotyped using a medium density SNP array (23 K informative SNPs), and the genetic architecture of growth-related traits [shell height (SH), shell length (SL), and wet weight (WW)] was evaluated. Heritability was estimated to be moderate for the three traits (0.26 ± 0.06 for SH, 0.23 ± 0.06 for SL and 0.35 ± 0.05 for WW), and results of a GWAS indicated that the underlying genetic architecture was polygenic. Genomic prediction approaches were used to estimate breeding values for growth, and compared to pedigree based approaches. The accuracy of the genomic prediction models (GBLUP) outperformed the traditional pedigree approach (PBLUP) by ∼25% for SL and WW, and ∼30% for SH. Further, reduction in SNP marker density had little impact on prediction accuracy, even when density was reduced to a few hundred SNPs. These results suggest that the use of genomic selection in oyster breeding could offer benefits for the selection of breeding candidates to improve complex economic traits at relatively modest cost. |
author2 |
Natural Environment Research Council Biotechnology and Biological Sciences Research Council Roslin Institute Weymouth Laboratory |
format |
Article in Journal/Newspaper |
author |
Gutierrez, Alejandro P Matika, Oswald Bean, Tim P Houston, Ross D |
author_facet |
Gutierrez, Alejandro P Matika, Oswald Bean, Tim P Houston, Ross D |
author_sort |
Gutierrez, Alejandro P |
title |
Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction |
title_short |
Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction |
title_full |
Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction |
title_fullStr |
Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction |
title_full_unstemmed |
Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction |
title_sort |
genomic selection for growth traits in pacific oyster (crassostrea gigas): potential of low-density marker panels for breeding value prediction |
publisher |
Frontiers Media SA |
publishDate |
2018 |
url |
http://hdl.handle.net/1893/31438 https://doi.org/10.3389/fgene.2018.00391 http://dspace.stir.ac.uk/bitstream/1893/31438/1/fgene-09-00391.pdf |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
Gutierrez AP, Matika O, Bean TP & Houston RD (2018) Genomic Selection for Growth Traits in Pacific Oyster (Crassostrea gigas): Potential of Low-Density Marker Panels for Breeding Value Prediction. Frontiers in Genetics, 9, Art. No.: 391. https://doi.org/10.3389/fgene.2018.00391 391 http://hdl.handle.net/1893/31438 doi:10.3389/fgene.2018.00391 30283494 WOS:000445068200001 2-s2.0-85055143232 1643543 http://dspace.stir.ac.uk/bitstream/1893/31438/1/fgene-09-00391.pdf |
op_rights |
© 2018 Gutierrez, Matika, Bean and Houston. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fgene.2018.00391 |
container_title |
Frontiers in Genetics |
container_volume |
9 |
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1766394013331488768 |