A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata).
A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata).
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DOI：
10.1186/1471-2164-11-218
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发表时间：
2010-04-01
期刊：
影响因子：
4.4
通讯作者：
Slate J
中科院分区：
文献类型：
--
作者：
Ball AD;Stapley J;Dawson DA;Birkhead TR;Burke T;Slate J
遗传连锁图是寻找数量性状基因座（QTL）的重要工具。为了使基因组覆盖最大化并提供均匀间隔的标记分布，有时使用不同类型的遗传标记的组合。本研究利用单核苷酸多态性（SNPs）和微卫星标记构建了斑胸草雀（Taeniopygia guttata）4条染色体（1、1A、2和9）的连锁图谱。为了评估每种标记的有效性和准确性，我们比较了分别使用每种标记类型和组合使用两种标记类型构建的地图。通过与组装的斑胸草雀基因组序列进行比较，验证了连锁图标记顺序。我们发现，标记顺序是不太可靠的，连锁图长度膨胀微卫星地图相对于SNP地图，显然是由于两种类型的标记之间的错误率不同。提供了关于如何最大限度地减少错误影响的指南。特别是，我们表明，当这两种类型的标记相结合的传统过程中建立连锁图谱，其中最翔实的标记被添加到地图上的第一，必须修改，以提高地图的准确性。当使用多种类型和大量的标记来创建密集的连锁图谱时，在添加其他可能更容易出错的标记（微卫星）之前，应使用最不容易出错的位点（SNP）而不是最有信息量的位点来创建框架图谱。这引发了人们对之前使用传统构建过程创建的微卫星连锁图谱中标记顺序和预测重组率的准确性的质疑，然而，只要遵循合适的错误检测策略，基于微卫星的图谱可以继续被视为合理可靠的。
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. 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. 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.
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影响因子：
2.6
作者：
Calderon, P. L.;Pigozzi, M. I.
通讯作者：
Pigozzi, M. I.
影响因子：
64.8
作者：
Dib, C;Faure, S;Weissenbach, J
通讯作者：
Weissenbach, J
DOI：
10.1111/j.1471-8286.2005.00906.x
发表时间：
2005-06-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
Dawson, DA;Hunter, FM;Burke, T
通讯作者：
Burke, T
影响因子：
9.8
作者：
Brinkmann, B;Klintschar, M;Rolf, B
通讯作者：
Rolf, B
影响因子：
4.9
作者：
Davis, CS;Strobeck, C
通讯作者：
Strobeck, C