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SNP discovery and genotyping using restriction-site-associated DNA sequencing in chickens

文献类型： 外文期刊

作者： Zhai, Zhengxiao 1 ; Zhao, Wenjing 1 ; He, Chuan 1 ; Yang, Kaixuan 3 ; Tang, Linlin 3 ; Liu, Shuyun 1 ; Zhang, Yan 4 ; Hua 1 ;

作者机构： 1.Shanghai Jiao Tong Univ, Sch Agr & Biol, Dept Anim Sci, Shanghai Key Lab Vet Biotechnol, Shanghai 200240, Peoples R China

2.Shanghai Personal Biotechnol Ltd Co, Shanghai 200336, Peoples R China

3.Shanghai Acad Agr Sci, Anim Husb & Vet Res Inst, Shanghai 201106, Peoples R China

4.Virginia Tech, Virginia Bioinformat Inst, Blacksburg, VA 24061 USA

关键词： breed;marker discovery;next-generation sequencing;reduced-representation sequencing;whole-genome selection

期刊名称：ANIMAL GENETICS （ 影响因子：3.169； 五年影响因子：3.058 ）

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收录情况： SCI

摘要： Single nucleotide polymorphisms (SNPs) are essential to the understanding of population genetic variation and diversity. Here, we performed restriction-site-associated DNA sequencing (RAD-seq) on 72 individuals from 13 Chinese indigenous and three introduced chicken breeds. A total of 620 million reads were obtained using an Illumina Hiseq2000 sequencer. An average of 75587 SNPs were identified from each individual. Further filtering strictly validated 28895 SNPs candidates for all populations. When compared with the NCBI dbSNP (chicken_9031), 15404 SNPs were new discoveries. In this study, RAD-seq was performed for the first time on chickens, implicating the remarkable effectiveness and potential applications on genetic analysis and breeding technique for whole-genome selection in chicken and other agricultural animals.

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