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New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds

Dawson, Deborah A.; Horsburgh, Gavin J.; Kupper, Clemens; Stewart, Ian R. K.; Ball, Alexander D.; Durrant, Kate L.; Hansson, Bengt LU ; Bacon, Ida; Bird, Susannah and Klein, Akos, et al. (2010) In Molecular Ecology Resources 10(3). p.475-494
Abstract
We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When... (More)
We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa. (Less)
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keywords
AVES, cross-species utility, microsatellite, expressed sequence tag (EST), conserved, Passerine
in
Molecular Ecology Resources
volume
10
issue
3
pages
475 - 494
publisher
Wiley-Blackwell
external identifiers
  • wos:000276407300008
  • scopus:77952671387
ISSN
1755-098X
DOI
10.1111/j.1755-0998.2009.02775.x
language
English
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yes
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3066b229-2575-4ec8-8e90-849d4102675b (old id 1603688)
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2010-05-17 14:15:42
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2018-05-29 11:39:44
@article{3066b229-2575-4ec8-8e90-849d4102675b,
  abstract     = {We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa.},
  author       = {Dawson, Deborah A. and Horsburgh, Gavin J. and Kupper, Clemens and Stewart, Ian R. K. and Ball, Alexander D. and Durrant, Kate L. and Hansson, Bengt and Bacon, Ida and Bird, Susannah and Klein, Akos and Krupa, Andrew P. and Lee, Jin-Won and Martin-Galvez, David and Simeoni, Michelle and Smith, Gemma and Spurgin, Lewis G. and Burke, Terry},
  issn         = {1755-098X},
  keyword      = {AVES,cross-species utility,microsatellite,expressed sequence tag (EST),conserved,Passerine},
  language     = {eng},
  number       = {3},
  pages        = {475--494},
  publisher    = {Wiley-Blackwell},
  series       = {Molecular Ecology Resources},
  title        = {New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds},
  url          = {http://dx.doi.org/10.1111/j.1755-0998.2009.02775.x},
  volume       = {10},
  year         = {2010},
}