Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)
Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic...
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ftmdpi:oai:mdpi.com:/2076-2615/11/3/899/ 2023-08-20T04:03:16+02:00 Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus) Fotis Pappas Christos Palaiokostas agris 2021-03-21 application/pdf https://doi.org/10.3390/ani11030899 EN eng Multidisciplinary Digital Publishing Institute Aquatic Animals https://dx.doi.org/10.3390/ani11030899 https://creativecommons.org/licenses/by/4.0/ Animals; Volume 11; Issue 3; Pages: 899 reduced representation sequencing Salvelinus alpinus selective breeding GBS salmonid Text 2021 ftmdpi https://doi.org/10.3390/ani11030899 2023-08-01T01:20:08Z Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding. Text Arctic charr Arctic Salvelinus alpinus MDPI Open Access Publishing Arctic Animals 11 3 899 |
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MDPI Open Access Publishing |
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ftmdpi |
language |
English |
topic |
reduced representation sequencing Salvelinus alpinus selective breeding GBS salmonid |
spellingShingle |
reduced representation sequencing Salvelinus alpinus selective breeding GBS salmonid Fotis Pappas Christos Palaiokostas Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus) |
topic_facet |
reduced representation sequencing Salvelinus alpinus selective breeding GBS salmonid |
description |
Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding. |
format |
Text |
author |
Fotis Pappas Christos Palaiokostas |
author_facet |
Fotis Pappas Christos Palaiokostas |
author_sort |
Fotis Pappas |
title |
Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus) |
title_short |
Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus) |
title_full |
Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus) |
title_fullStr |
Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus) |
title_full_unstemmed |
Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus) |
title_sort |
genotyping strategies using ddrad sequencing in farmed arctic charr (salvelinus alpinus) |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2021 |
url |
https://doi.org/10.3390/ani11030899 |
op_coverage |
agris |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Salvelinus alpinus |
op_source |
Animals; Volume 11; Issue 3; Pages: 899 |
op_relation |
Aquatic Animals https://dx.doi.org/10.3390/ani11030899 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/ani11030899 |
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Animals |
container_volume |
11 |
container_issue |
3 |
container_start_page |
899 |
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1774713656183881728 |