title: Genotyping by genome reducing and sequencing for outbred animals.
abstract: Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample.
authors.affiliation: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Chen
authors.forename: Yufang
authors.initials: Y
authors.lastname: Ma
authors.forename: Yumei
authors.initials: Y
authors.lastname: Yang
authors.forename: Zhenliang
authors.initials: Z
authors.lastname: Chen
authors.forename: Rongrong
authors.initials: R
authors.lastname: Liao
authors.forename: Xiaoxian
authors.initials: X
authors.lastname: Xie
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.forename: Pengfei
authors.initials: P
authors.lastname: He
authors.forename: Yingying
authors.initials: Y
authors.lastname: Tu
authors.forename: Xiangzhe
authors.initials: X
authors.lastname: Zhang
authors.forename: Changsuo
authors.initials: C
authors.lastname: Yang
authors.forename: Hongjie
authors.initials: H
authors.lastname: Yang
authors.forename: Fuqing
authors.initials: F
authors.lastname: Yu
authors.forename: Youmin
authors.initials: Y
authors.lastname: Zheng
authors.forename: Zhiwu
authors.initials: Z
authors.lastname: Zhang
authors.forename: Qishan
authors.initials: Q
authors.lastname: Wang
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000818:Animals; D001947:Breeding / Q000379:methods; D015723:Gene Library; D005819:Genetic Markers / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D013552:Swine / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D009841:Oligonucleotides