title: An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing.
abstract: 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.
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Rongrong
authors: R
authors: Liao
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Zhen
authors: Z
authors: Wang
authors: Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China.
authors: Qiang
authors: Q
authors: Chen
authors: National Poultry Engineering Research Center, Animal Husbandry and Veterinary Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors: Yingying
authors: Y
authors: Tu
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Zhenliang
authors: Z
authors: Chen
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
authors: Qishan
authors: Q
authors: Wang
authors: National Poultry Engineering Research Center, Animal Husbandry and Veterinary Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
authors: Changsuo
authors: C
authors: Yang
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
authors: Xiangzhe
authors: X
authors: Zhang
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
authors: Yuchun
authors: Y
authors: Pan
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D003362:Cost-Benefit Analysis; D023281:Genomics; D060005:Genotyping Techniques / Q000191:economics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D017422:Sequence Analysis, DNA