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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ftdoajarticles:oai:doaj.org/article:888d0954edcd422fb700c3727f44004b 2023-05-15T14:30:01+02:00 Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr ( Salvelinus alpinus ) Fotis Pappas Christos Palaiokostas 2021-03-01T00:00:00Z https://doi.org/10.3390/ani11030899 https://doaj.org/article/888d0954edcd422fb700c3727f44004b EN eng MDPI AG https://www.mdpi.com/2076-2615/11/3/899 https://doaj.org/toc/2076-2615 doi:10.3390/ani11030899 2076-2615 https://doaj.org/article/888d0954edcd422fb700c3727f44004b Animals, Vol 11, Iss 899, p 899 (2021) reduced representation sequencing Salvelinus alpinus selective breeding GBS salmonid Veterinary medicine SF600-1100 Zoology QL1-991 article 2021 ftdoajarticles https://doi.org/10.3390/ani11030899 2022-12-31T09:40:45Z 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. Article in Journal/Newspaper Arctic charr Arctic Salvelinus alpinus Directory of Open Access Journals: DOAJ Articles Arctic Animals 11 3 899 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
reduced representation sequencing Salvelinus alpinus selective breeding GBS salmonid Veterinary medicine SF600-1100 Zoology QL1-991 |
spellingShingle |
reduced representation sequencing Salvelinus alpinus selective breeding GBS salmonid Veterinary medicine SF600-1100 Zoology QL1-991 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 Veterinary medicine SF600-1100 Zoology QL1-991 |
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 |
Article in Journal/Newspaper |
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 |
MDPI AG |
publishDate |
2021 |
url |
https://doi.org/10.3390/ani11030899 https://doaj.org/article/888d0954edcd422fb700c3727f44004b |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Salvelinus alpinus |
op_source |
Animals, Vol 11, Iss 899, p 899 (2021) |
op_relation |
https://www.mdpi.com/2076-2615/11/3/899 https://doaj.org/toc/2076-2615 doi:10.3390/ani11030899 2076-2615 https://doaj.org/article/888d0954edcd422fb700c3727f44004b |
op_doi |
https://doi.org/10.3390/ani11030899 |
container_title |
Animals |
container_volume |
11 |
container_issue |
3 |
container_start_page |
899 |
_version_ |
1766303950914453504 |