High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species.
High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species.
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DOI：
10.1186/1471-2164-14-176
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发表时间：
2013-03-15
期刊：
影响因子：
4.4
通讯作者：
Burke T
中科院分区：
文献类型：
--
作者：
Dawson DA;Ball AD;Spurgin LG;Martín-Gálvez D;Stewart IR;Horsburgh GJ;Potter J;Molina-Morales M;Bicknell AW;Preston SA;Ekblom R;Slate J;Burke T
微卫星被广泛用于许多遗传学研究。与单核苷酸多态性（SNP）和测序基因分型方法相比，它们容易在低DNA质量/浓度的样品（例如博物馆/非侵入性样品）中分型，并且能够快速、廉价地鉴定物种、杂交种、克隆和倍性。微卫星还具有用于基因分型的所有类型的标记的最高跨物种效用，但是，尽管如此，当从单个物种分离时，只有相对小的比例将是有用的。任何类型的标记开发都需要技能和时间。足够的“现成的”标记，适用于基因分型广泛的物种的可用性不仅可以节省资源，但也独特地使新的比较类群之间的多样性在同一套基因座。其他标记类型无法启用此功能。因此，我们开发了一套鸟类微卫星标记增强跨物种的效用。我们选择了两个遗传上遥远的物种中具有大量重复单位的高度保守序列。24个引物组设计的同源序列，具有至少8个重复单位，在斑马雀（Taeniopygia guttata）和鸡（原鸡）。每个引物序列与斑胸草雀完全匹配，并且在考虑简并碱基后，与鸡至少86%相似。我们评估了引物集的效用基因分型个人属于八雀形目和四个非雀形目物种。大多数新的保守鸟类微卫星（CAM）标记在所有12个测试物种中扩增（平均94%在雀形目和95%在非雀形目）。这个新的标记集是特别高的实用性雀形目，平均68%的位点多态性每种，相比之下，42%的非雀形目物种。当与先前描述的保守位点相结合时，这组新的保守标记将不仅减少微卫星分离的必要性和费用，用于广泛的遗传研究，包括鸟类亲子关系和种群分析，而且现在还将使不同物种（和种群）之间的遗传多样性的比较在同一组位点，没有或减少偏见。最后，这里使用的方法可以适用于其他类群，其中适当的基因组序列是可用的。
Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient “off-the-shelf” markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
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影响因子：
4.4
作者：
CRITTENDEN, LB;PROVENCHER, L;DODGSON, JB
通讯作者：
DODGSON, JB
影响因子：
1.1
作者：
Bicknell, Anthony W. J.;Dawson, Deborah A.;Votier, Stephen C.
通讯作者：
Votier, Stephen C.
影响因子：
2.2
作者：
Bourke, Brian P.;Frantz, Alain C.;Burke, Terry A.
通讯作者：
Burke, Terry A.
影响因子：
4.9
作者：
Balloux, F;Amos, W;Coulson, T
通讯作者：
Coulson, T
影响因子：
2.4
作者：
Gaerke, C.;Ytournel, F.;Simianer, H.
通讯作者：
Simianer, H.