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An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing

文献类型： 外文期刊

作者： Liao, Rongrong 1 ; Wang, Zhen 1 ; Chen, Qiang 2 ; Tu, Yingying 3 ; Chen, Zhenliang 1 ; Wang, Qishan 1 ; Yang, Changsuo 3 ;

作者机构： 1.Shanghai Jiao Tong Univ, Sch Agr & Biol, Shanghai 200030, Peoples R China

2.Kunming Univ Sci & Technol, Fac Life Sci & Technol, Kunming, Yunnan, Peoples R China

3.Shanghai Acad Agr Sci, Natl Poultry Engn Res Ctr, Anim Husb & Vet Res Inst, Shanghai, Peoples R China

4.Shanghai Jiao Tong Univ, Key Lab Vet Biotechnol, Shanghai 200030, Peoples R China

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2015 年 10 卷 8 期

页码：

收录情况： SCI

摘要： Single nucleotide polymorphisms (SNPs) are essential for identifying the genetic mechanisms of complex traits. In the present study, we applied genotyping by genome reducing and sequencing (GGRS) method to construct a 252-plex sequencing library for SNP discovery and genotyping in chicken. The library was successfully sequenced on an Illumina HiSeq 2500 sequencer with a paired-end pattern; approximately 400 million raw reads were generated, and an average of approximately 1.4 million good reads per sample were generated. A total of 91,767 SNPs were identified after strict filtering, and all of the 252 samples and all of the chromosomes were well represented. Compared with the Illumina 60K chicken SNP chip data, approximately 34,131 more SNPs were identified using GGRS, and a higher SNP density was found using GGRS, which could be beneficial for downstream analysis. Using the GGRS method, more than 3528 samples can be sequenced simultaneously, and the cost is reduced to $ 18 per sample. To the best of our knowledge, this study describes the first report of such highly multiplexed sequencing in chicken, indicating potential applications for genome-wide association and genomic selection in chicken.

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