title: Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).
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.
authors.affiliation: School of Biosciences, Hatherly Laboratories, University of Exeter, Prince of Wales Rd, Exeter EX4 4PS, UK.
authors.forename: J S
authors.initials: JS
authors.lastname: Ellis
authors.forename: J
authors.initials: J
authors.lastname: Gilbey
authors.forename: A
authors.initials: A
authors.lastname: Armstrong
authors.forename: T
authors.initials: T
authors.lastname: Balstad
authors.forename: E
authors.initials: E
authors.lastname: Cauwelier
authors.forename: C
authors.initials: C
authors.lastname: Cherbonnel
authors.forename: S
authors.initials: S
authors.lastname: Consuegra
authors.forename: J
authors.initials: J
authors.lastname: Coughlan
authors.forename: T F
authors.initials: TF
authors.lastname: Cross
authors.forename: W
authors.initials: W
authors.lastname: Crozier
authors.forename: E
authors.initials: E
authors.lastname: Dillane
authors.forename: D
authors.initials: D
authors.lastname: Ensing
authors.forename: C
authors.initials: C
authors.lastname: García de Leániz
authors.forename: E
authors.initials: E
authors.lastname: García-Vázquez
authors.forename: A M
authors.initials: AM
authors.lastname: Griffiths
authors.forename: K
authors.initials: K
authors.lastname: Hindar
authors.forename: S
authors.initials: S
authors.lastname: Hjorleifsdottir
authors.forename: D
authors.initials: D
authors.lastname: Knox
authors.forename: G
authors.initials: G
authors.lastname: Machado-Schiaffino
authors.forename: P
authors.initials: P
authors.lastname: McGinnity
authors.forename: D
authors.initials: D
authors.lastname: Meldrup
authors.forename: E E
authors.initials: EE
authors.lastname: Nielsen
authors.forename: K
authors.initials: K
authors.lastname: Olafsson
authors.forename: C R
authors.initials: CR
authors.lastname: Primmer
authors.forename: P
authors.initials: P
authors.lastname: Prodohl
authors.forename: L
authors.initials: L
authors.lastname: Stradmeyer
authors.forename: J-P
authors.initials: JP
authors.lastname: Vähä
authors.forename: E
authors.initials: E
authors.lastname: Verspoor
authors.forename: V
authors.initials: V
authors.lastname: Wennevik
authors.forename: J R
authors.initials: JR
authors.lastname: Stevens
mesh_terms: D000483:Alleles; D000818:Animals; D003247:Conservation of Natural Resources; D040961:Genetic Drift; D014644:Genetic Variation; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics*; D058889:Molecular Typing / Q000295:instrumentation / Q000379:methods* / Q000592:standards*; D020317:Salmo salar / Q000235:genetics*; D057188:Workflow