Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).
Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).
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DOI：
10.1186/1471-2164-12-150
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发表时间：
2011-03-16
期刊：
影响因子：
4.4
通讯作者：
Groenen MA
中科院分区：
文献类型：
--
作者：
Kraus RH;Kerstens HH;Van Hooft P;Crooijmans RP;Van Der Poel JJ;Elmberg J;Vignal A;Huang Y;Li N;Prins HH;Groenen MA
下一代测序技术允许以低成本获得目前缺乏的大多数经济和生态上重要的生物体的基因组序列信息。野鸭的基因组数据是有限的。绿头鸭除了是一种重要的农业和社会物种外，也是禽流感远距离传播的重点物种。为了大规模鉴定SNP，我们对野生野鸭DNA进行了Illumina测序，并将我们的数据与正在进行的驯化同种的基因组和EST测序进行了比较。这是首次对水禽进行此类研究。产生了超过10亿个碱基对的序列信息，导致野鸭基因组的简化代表文库的16倍覆盖率。将序列读数与驯化鸭参考基因组草案进行比对，并允许在我们的绿头鸭序列数据集中检测超过122，000个SNP。此外，与野生野鸭相比，家鸭参考上的近62，000个核苷酸位置显示出不同的核苷酸。在我们的数据中鉴定的大约20，000个SNP与在测序的家鸭或EST测序项目中鉴定的SNP共享。共享的SNP被认为是高度可靠的，并用于对非共享的SNP进行质量基准测试。对364个SNP的代表性样本进行基因分型，SNP转换率为99.7%。SNP发现库中次要等位基因计数和观察到的次要等位基因频率的相关性为0.72。我们在野生野鸭中发现了近150，000个SNP，这可能会在基因分型中产生良好的结果。其中，在我们的野生野鸭序列中检测到约101，000个SNP，在野生鸭和家鸭数据之间检测到约49，000个SNP。在约101，000个SNPs中，我们发现野生野鸭和测序的家鸭之间共有约20，000个SNPs的子集，表明遗传差异较低。总SNP集（122，000 + 62，000 = 184，000个SNP）和经验证的子集之间的质量度量的比较显示两个集的相似特征。这表明我们已经检测到大量（约150，000）准确推断的野鸭SNP，这将有利于鸟类进化研究，生态研究（例如解开迁徙连接）和工业育种计划。
Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.
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影响因子：
3.7
作者：
Ramos AM;Crooijmans RP;Affara NA;Amaral AJ;Archibald AL;Beever JE;Bendixen C;Churcher C;Clark R;Dehais P;Hansen MS;Hedegaard J;Hu ZL;Kerstens HH;Law AS;Megens HJ;Milan D;Nonneman DJ;Rohrer GA;Rothschild MF;Smith TP;Schnabel RD;Van Tassell CP;Taylor JF;Wiedmann RT;Schook LB;Groenen MA
通讯作者：
Groenen MA
影响因子：
4.4
作者：
Paul M;Tavornpanich S;Abrial D;Gasqui P;Charras-Garrido M;Thanapongtharm W;Xiao X;Gilbert M;Roger F;Ducrot C
通讯作者：
Ducrot C
BTA 是一种新型试剂，用于将 DNA 附着在玻璃上并有效生成固相扩增 DNA 菌落。
影响因子：
14.9
作者：
Fedurco, M;Romieu, A;Williams, S;Lawrence, I;Turcatti, G
通讯作者：
Turcatti, G
影响因子：
5.3
作者：
COOPER, DN;KRAWCZAK, M
通讯作者：
KRAWCZAK, M
影响因子：
2.4
作者：
Fillon, V.;Vignoles, M.;Vignal, A.
通讯作者：
Vignal, A.