Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)
Background Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to ass...
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ftluke:oai:jukuri.luke.fi:10024/552326 2023-10-09T21:50:42+02:00 Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus) Carrier, Alexandra Prunier, Julien Poisson, William Trottier-Lavoie, Mallorie Gilbert, Isabelle Cavedon, Maria Pokharel, Kisun Kantanen, Juha Musiani, Marco Côté, Steeve D. Albert, Vicky Taillon, Joëlle Bourret, Vincent Droit, Arnaud Robert, Claude orcid:0000-0002-4924-946X orcid:0000-0001-6350-6373 4100111010 4100211610 Luonnonvarakeskus 14 p. true https://jukuri.luke.fi/handle/10024/552326 en eng Springer Science and Business Media LLC BMC Genomics 10.1186/s12864-022-08899-6 1471-2164 1 23 687 https://jukuri.luke.fi/handle/10024/552326 URN:NBN:fi-fe2022100761307 CC BY 4.0 karibu poro perimä SNP caribou reindeer genome single nucleotide polymorphisms SNP chip Rangifer tarandus Genotyping Next generation sequencing Genomics publication fi=A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä|sv=A1 Originalartikel i en vetenskaplig tidskrift|en=A1 Journal article (refereed), original research| fi=Publisher's version|sv=Publisher's version|en=Publisher's version| ftluke 2023-09-12T20:28:25Z Background Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. Results From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. Conclusion This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for ... Article in Journal/Newspaper caribou Rangifer tarandus Natural Resources Institute Finland: Jukuri Canada The ''Y'' ENVELOPE(-112.453,-112.453,57.591,57.591) |
institution |
Open Polar |
collection |
Natural Resources Institute Finland: Jukuri |
op_collection_id |
ftluke |
language |
English |
topic |
karibu poro perimä SNP caribou reindeer genome single nucleotide polymorphisms SNP chip Rangifer tarandus Genotyping Next generation sequencing Genomics |
spellingShingle |
karibu poro perimä SNP caribou reindeer genome single nucleotide polymorphisms SNP chip Rangifer tarandus Genotyping Next generation sequencing Genomics Carrier, Alexandra Prunier, Julien Poisson, William Trottier-Lavoie, Mallorie Gilbert, Isabelle Cavedon, Maria Pokharel, Kisun Kantanen, Juha Musiani, Marco Côté, Steeve D. Albert, Vicky Taillon, Joëlle Bourret, Vincent Droit, Arnaud Robert, Claude Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus) |
topic_facet |
karibu poro perimä SNP caribou reindeer genome single nucleotide polymorphisms SNP chip Rangifer tarandus Genotyping Next generation sequencing Genomics |
description |
Background Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. Results From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. Conclusion This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for ... |
author2 |
orcid:0000-0002-4924-946X orcid:0000-0001-6350-6373 4100111010 4100211610 Luonnonvarakeskus |
format |
Article in Journal/Newspaper |
author |
Carrier, Alexandra Prunier, Julien Poisson, William Trottier-Lavoie, Mallorie Gilbert, Isabelle Cavedon, Maria Pokharel, Kisun Kantanen, Juha Musiani, Marco Côté, Steeve D. Albert, Vicky Taillon, Joëlle Bourret, Vincent Droit, Arnaud Robert, Claude |
author_facet |
Carrier, Alexandra Prunier, Julien Poisson, William Trottier-Lavoie, Mallorie Gilbert, Isabelle Cavedon, Maria Pokharel, Kisun Kantanen, Juha Musiani, Marco Côté, Steeve D. Albert, Vicky Taillon, Joëlle Bourret, Vincent Droit, Arnaud Robert, Claude |
author_sort |
Carrier, Alexandra |
title |
Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus) |
title_short |
Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus) |
title_full |
Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus) |
title_fullStr |
Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus) |
title_full_unstemmed |
Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus) |
title_sort |
design and validation of a 63k genome-wide snp-genotyping platform for caribou/reindeer (rangifer tarandus) |
publisher |
Springer Science and Business Media LLC |
url |
https://jukuri.luke.fi/handle/10024/552326 |
long_lat |
ENVELOPE(-112.453,-112.453,57.591,57.591) |
geographic |
Canada The ''Y'' |
geographic_facet |
Canada The ''Y'' |
genre |
caribou Rangifer tarandus |
genre_facet |
caribou Rangifer tarandus |
op_relation |
BMC Genomics 10.1186/s12864-022-08899-6 1471-2164 1 23 687 https://jukuri.luke.fi/handle/10024/552326 URN:NBN:fi-fe2022100761307 |
op_rights |
CC BY 4.0 |
_version_ |
1779313773684719616 |