The development and characterization of a 60K SNP chip for chicken.
The development and characterization of a 60K SNP chip for chicken.
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DOI：
10.1186/1471-2164-12-274
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发表时间：
2011-05-31
期刊：
影响因子：
4.4
通讯作者：
Cheng HH
中科院分区：
文献类型：
--
作者：
Groenen MA;Megens HJ;Zare Y;Warren WC;Hillier LW;Crooijmans RP;Vereijken A;Okimoto R;Muir WM;Cheng HH
在家畜物种如鸡中，高通量单核苷酸多态性（SNP）基因分型测定越来越多地用于全基因组关联研究，并作为育种（称为基因组选择）的工具。为了在各种各样的品种和群体中具有价值，SNP基因分型测定的成功率、SNP在基因组中的分布和所用SNP的次要等位基因频率（MAF）是极其重要的。我们描述了一种中等密度（60 k）Illumina SNP BeadChip在鸡中的设计，该芯片由已知在两种主要类型的商业鸡（肉鸡和蛋鸡）中以高至中等次要等位基因频率（MAF）分离的SNP组成。这是通过使用Illumina测序在简化代表文库上鉴定2只肉鸡和2个蛋鸡品系中具有中度至高度MAF的352，303个SNP来实现的。为了进一步提高芯片的实用性，我们还鉴定了鸡基因组组装（Gallus_gallus-2.1）目前未覆盖的序列上的SNP。这是通过在12倍深度下对鸡基因组进行454测序并鉴定当前鸡基因组组装未覆盖的454衍生的重叠群上的SNP来实现的。我们总共添加了790个SNP，这些SNP映射到454个衍生的重叠群以及421个SNP，这些SNP在当前组装的Chr_random上具有位置。SNP芯片包含57，636个SNP，其中54，293个可以进行基因分型，并显示在鸡群中分离。我们的SNP鉴定程序似乎是高度可靠的，芯片上SNP的总体验证率为94%。我们能够从鸡基因组上的454个序列重叠群中定位328个SNP。这些SNP中的大多数映射到已经在基因组构建Gallus_gallus-2.1.0中表示的染色体。使用28个SNP构建两个新的连锁群，最有可能代表当前基因组组装未覆盖的两个微染色体。Illumina chicken 60 K Beadchip上SNP的高成功率强调了下一代测序（NGS）技术用于SNP鉴定和选择步骤的能力。来自NGS测序的序列重叠群的SNP的鉴定导致鸡基因组的覆盖率提高，并且最可能代表两个鸡微染色体的两个新的连锁群的构建。
In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success rate of the SNP genotyping assay, the distribution of the SNP across the genome and the minor allele frequencies (MAF) of the SNPs used are extremely important. We describe the design of a moderate density (60k) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at high to medium minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two micro-chromosomes not covered by the current genome assembly. The high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence (NGS) technology for the SNP identification and selection step. The identification of SNPs from sequence contigs derived from NGS sequencing resulted in improved coverage of the chicken genome and the construction of two new linkage groups most likely representing two chicken micro-chromosomes.
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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：
2.9
作者：
Megens HJ;Crooijmans RP;Bastiaansen JW;Kerstens HH;Coster A;Jalving R;Vereijken A;Silva P;Muir WM;Cheng HH;Hanotte O;Groenen MA
通讯作者：
Groenen MA
影响因子：
64.8
作者：
Rubin, Carl-Johan;Zody, Michael C.;Andersson, Leif
通讯作者：
Andersson, Leif
影响因子：
7
作者：
Li, Heng;Ruan, Jue;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
4.4
作者：
Wahlberg P;Carlborg O;Foglio M;Tordoir X;Syvänen AC;Lathrop M;Gut IG;Siegel PB;Andersson L
通讯作者：
Andersson L