a comparison of snps and microsatellites as linkage mapping markers lessons from the zebra finch (taeniopygia guttata)比较单核苷酸多态性和微卫星链接映射标记教训斑胸草雀(taeniopygia guttata).pdfVIP

Ball et al. BMC Genomics 2010, 11:218 /1471-2164/11/218 R E S E A R C H A R T I C L E Open Access Research article A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata) Alexander D Ball*, Jessica Stapley, Deborah A Dawson, Tim R Birkhead, Terry Burke and Jon Slate 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)