Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.)

H...............H

Show simple item record

dc.contributor.author Ellis, J. S.
dc.contributor.author Gilbey, J.
dc.contributor.author Armstrong, A.
dc.contributor.author Balstad, T.
dc.contributor.author Cauwelier, E.
dc.contributor.author Cherbonnel, C.
dc.contributor.author Consuegra, Sofia
dc.contributor.author Coughlan, J.
dc.contributor.author Cross, T. F.
dc.contributor.author Crozier, W.
dc.contributor.author Dillane, E.
dc.contributor.author Ensing, D.
dc.contributor.author Garcia de Leaniz, C.
dc.contributor.author Garcia-Vazquez, E.
dc.contributor.author Griffiths, A. M.
dc.contributor.author Hindar, K.
dc.contributor.author Hjorleifsdottir, S.
dc.contributor.author Knox, D.
dc.contributor.author Machado-Schiaffino, G.
dc.contributor.author McGinnity, P.
dc.contributor.author Meldrup, D.
dc.contributor.author Nielsen, E. E.
dc.contributor.author Olafsson, K.
dc.contributor.author Primmer, C. R.
dc.contributor.author Prodohl, P.
dc.contributor.author Stradmeyer, L.
dc.contributor.author Vaha, J. -. P.
dc.contributor.author Verspoor, E.
dc.contributor.author Wennevik, V.
dc.contributor.author Stevens, J. R.
dc.date.accessioned 2011-06-06T14:27:10Z
dc.date.available 2011-06-06T14:27:10Z
dc.date.issued 2011-03
dc.identifier.citation Ellis , J S , Gilbey , J , Armstrong , A , Balstad , T , Cauwelier , E , Cherbonnel , C , Consuegra , S , Coughlan , J , Cross , T F , Crozier , W , Dillane , E , Ensing , D , Garcia de Leaniz , C , Garcia-Vazquez , E , Griffiths , A M , Hindar , K , Hjorleifsdottir , S , Knox , D , Machado-Schiaffino , G , McGinnity , P , Meldrup , D , Nielsen , E E , Olafsson , K , Primmer , C R , Prodohl , P , Stradmeyer , L , Vaha , J P , Verspoor , E , Wennevik , V & Stevens , J R 2011 , ' Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.) ' Genetica , vol 139 , no. 3 , pp. 353-367 . en
dc.identifier.issn 1573-6857
dc.identifier.other PURE: 166287
dc.identifier.other dspace: 2160/6935
dc.identifier.uri http://hdl.handle.net/2160/6935
dc.identifier.uri http://www.springerlink.com/content/q53114553698k6q7/ en
dc.description Ellis, J. S., Gilbey, J., Armstrong, A., Balstad, T., Cauwelier, E., Cherbonnel, C., Consuegra, S., Coughlan, J., Cross, T. F., Crozier, W., Dillane, E., Ensing, D., Garcia de Leaniz, C., Garcia-Vazquez, E., Griffiths, A. M., Hindar, K., Hjorleifsdottir, S., Knox, D., Machado-Schiaffino, G., McGinnity, P., Meldrup, D., Nielsen, E. E., Olafsson, K., Primmer, C. R., Prodohl, P., Stradmeyer, L., Vaha, J-P., Verspoor, E., Wennevik, V., Stevens, J. R. (2011). Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.). Genetica, 139 (3), 353-367. IMPF: 02.14 en
dc.description.abstract Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size (‘size shifts’), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species. en
dc.format.extent 15 en
dc.language.iso eng
dc.relation.ispartof Genetica en
dc.subject Atlantic salmon en
dc.subject Microsatellite en
dc.subject Calibration en
dc.subject Standardization en
dc.subject Genotyping error en
dc.subject Conservation en
dc.title Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.) en
dc.type Text en
dc.type.publicationtype Article (Journal) en
dc.identifier.doi http://dx.doi.org/10.1007/s10709-011-9554-4
dc.contributor.institution Institute of Biological, Environmental and Rural Sciences en
dc.description.status Peer reviewed en


Files in this item

Files Size Format View

There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record

Search Cadair


Advanced Search

Browse

My Account