title: A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata).
abstract: BACKGROUND
  Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence.
  
  
  RESULTS
  We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy.
  
  
  CONCLUSIONS
  When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable.
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK. a.d.ball@sheffield.ac.uk
authors.forename: Alexander D
authors.initials: AD
authors.lastname: Ball
authors.forename: Jessica
authors.initials: J
authors.lastname: Stapley
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Dawson
authors.forename: Tim R
authors.initials: TR
authors.lastname: Birkhead
authors.forename: Terry
authors.initials: T
authors.lastname: Burke
authors.forename: Jon
authors.initials: J
authors.lastname: Slate
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D046369:Finches / Q000235:genetics*; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide