The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis

Jonker R, Zhang Q, Van Hooft P, Loonen MJJE, Van der Jeugd HP, Crooijmans RPMA, Groenen MAM, Prins HHT, Kraus RHS (2012)
PLoS ONE 7(7): e38412.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ; ; ; ;
Abstract / Bemerkung
Migratory birds are of particular interest for population genetics because of the high connectivity between habitats and populations. A high degree of connectivity requires using many genetic markers to achieve the required statistical power, and a genome wide SNP set can fit this purpose. Here we present the development of a genome wide SNP set for the Barnacle Goose Branta leucopsis, a model species for the study of bird migration. We used the genome of a different waterfowl species, Mallard Anas platyrhynchos, as a reference to align Barnacle Goose second generation sequence reads from an RRL library and detected 2188 SNPs genome wide. Furthermore, we used chimeric flanking sequences, merged from both Mallard and Barnacle Goose DNA sequence information, to create primers for validation by genotyping. Validation with a 384 SNP genotyping set resulted in 374 (97%) successfully typed SNPs in the assay, of which 358 (96%) were polymorphic. Additionally, we validated our SNPs on relatively old (30 years) museum samples, which resulted in a success rate of at least 80%. This shows that museum samples could be used in standard SNP genotyping assays. Our study also shows that the genome of a related species can be used as reference to detect genome wide SNPs in birds, because genomes of birds are highly conserved. This is illustrated by the use of chimeric flanking sequences, which showed that the incorporation of flanking nucleotides from Mallard into Barnacle Goose sequences lead to equal genotyping performance when compared to flanking sequences solely composed of Barnacle Goose sequence.
Erscheinungsjahr
Zeitschriftentitel
PLoS ONE
Band
7
Zeitschriftennummer
7
Seite
e38412
ISSN
eISSN
PUB-ID

Zitieren

Jonker R, Zhang Q, Van Hooft P, et al. The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis. PLoS ONE. 2012;7(7):e38412.
Jonker, R., Zhang, Q., Van Hooft, P., Loonen, M. J. J. E., Van der Jeugd, H. P., Crooijmans, R. P. M. A., Groenen, M. A. M., et al. (2012). The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis. PLoS ONE, 7(7), e38412. doi:10.1371/journal.pone.0038412
Jonker, R., Zhang, Q., Van Hooft, P., Loonen, M. J. J. E., Van der Jeugd, H. P., Crooijmans, R. P. M. A., Groenen, M. A. M., Prins, H. H. T., and Kraus, R. H. S. (2012). The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis. PLoS ONE 7, e38412.
Jonker, R., et al., 2012. The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis. PLoS ONE, 7(7), p e38412.
R. Jonker, et al., “The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis”, PLoS ONE, vol. 7, 2012, pp. e38412.
Jonker, R., Zhang, Q., Van Hooft, P., Loonen, M.J.J.E., Van der Jeugd, H.P., Crooijmans, R.P.M.A., Groenen, M.A.M., Prins, H.H.T., Kraus, R.H.S.: The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis. PLoS ONE. 7, e38412 (2012).
Jonker, Rudy, Zhang, Qiong, Van Hooft, Pim, Loonen, Maarten J. J. E., Van der Jeugd, Henk P., Crooijmans, Richard P. M. A., Groenen, Martien A. M., Prins, Herbert H. T., and Kraus, Robert H. S. “The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis”. PLoS ONE 7.7 (2012): e38412.

10 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays.
von Thaden A, Cocchiararo B, Jarausch A, Jüngling H, Karamanlidis AA, Tiesmeyer A, Nowak C, Muñoz-Fuentes V., Sci Rep 7(1), 2017
PMID: 28883428
Population-level consequences of complementary sex determination in a solitary parasitoid.
de Boer JG, Groenen MA, Pannebakker BA, Beukeboom LW, Kraus RH., BMC Evol Biol 15(), 2015
PMID: 26025754
Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.
Greminger MP, Stölting KN, Nater A, Goossens B, Arora N, Bruggmann R, Patrignani A, Nussberger B, Sharma R, Kraus RH, Ambu LN, Singleton I, Chikhi L, van Schaik CP, Krützen M., BMC Genomics 15(), 2014
PMID: 24405840
Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms.
Kraus RH, van Hooft P, Megens HJ, Tsvey A, Fokin SY, Ydenberg RC, Prins HH., Mol Ecol 22(1), 2013
PMID: 23110616
SNP discovery using Paired-End RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae).
Vandepitte K, Honnay O, Mergeay J, Breyne P, Roldán-Ruiz I, De Meyer T., Mol Ecol Resour 13(2), 2013
PMID: 23231662
Circannual transitions in gene expression: lessons from seasonal adaptations.
Schwartz C, Andrews MT., Curr Top Dev Biol 105(), 2013
PMID: 23962845
Reference-free SNP discovery for the Eurasian beaver from restriction site-associated DNA paired-end data.
Senn H, Ogden R, Cezard T, Gharbi K, Iqbal Z, Johnson E, Kamps-Hughes N, Rosell F, McEwing R., Mol Ecol 22(11), 2013
PMID: 23432348
Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar).
Johnston SE, Lindqvist M, Niemelä E, Orell P, Erkinaro J, Kent MP, Lien S, Vähä JP, Vasemägi A, Primmer CR., BMC Genomics 14(), 2013
PMID: 23819691
Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis.
Jonker RM, Kraus RH, Zhang Q, van Hooft P, Larsson K, van der Jeugd HP, Kurvers RH, van Wieren SE, Loonen MJ, Crooijmans RP, Ydenberg RC, Groenen MA, Prins HH., Mol Ecol 22(23), 2013
PMID: 24118391

37 References

Daten bereitgestellt von Europe PubMed Central.

R: A language and environment for statistical computing.
AUTHOR UNKNOWN, 2009
A physical map of the chicken genome.
Wallis JW, Aerts J, Groenen MA, Crooijmans RP, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, McGrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang SP, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, de Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Schein J, Hillier L, Mardis ER, Wilson RK, Warren WC., Nature 432(7018), 2004
PMID: 15592415
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
A review on SNP and other types of molecular markers and their use in animal genetics.
Vignal A, Milan D, SanCristobal M, Eggen A., Genet. Sel. Evol. 34(3), 2002
PMID: 12081799
Relatedness and nesting dispersion within breeding populations of Greater White-fronted Geese.
Fowler AC, Eadie JM, Ely CR., 2004
Fine-scale spatial structuring in cackling Canada geese related to reproductive performance and breeding philopatry.
Fowler AC., 2005
Isolation, characterisation and predicted genome locations of Light-bellied Brent goose (Branta bernicla hrota) microsatellite loci (Anatidae, Aves).
Harrison XA, Dawson DA, Horsburgh GJ, Tregenza T, Bearhop S., 2010
Highly accurate SNP genotyping from historical and low-quality samples
MORIN PHILLIPA, MCCARTHY MELISSA., Mol. Ecol. Notes 7(6), 2007
PMID: IND43974548
Comparative painting reveals strong chromosome homology over 80 million years of bird evolution.
Shetty S, Griffin DK, Graves JA., Chromosome Res. 7(4), 1999
PMID: 10461874
Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks.
Kraus RH, Kerstens HH, van Hooft P, Megens HJ, Elmberg J, Tsvey A, Sartakov D, Soloviev SA, Crooijmans RP, Groenen MA, Ydenberg RC, Prins HH., BMC Evol. Biol. 12(), 2012
PMID: 22462721

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 22808008
PubMed | Europe PMC

Suchen in

Google Scholar