Genotyping by genome reducing and sequencing for outbred animals

Qiang Chen; Yufang Ma; Yumei Yang; Zhenliang Chen; Rongrong Liao; Xiaoxian Xie; Zhen Wang; Pengfei He; Yingying Tu; Xiangzhe Zhang; Changsuo Yang; Hongjie Yang; Fuqing Yu; Youmin Zheng; Zhiwu Zhang; Qishan Wang; Yuchun Pan

doi:10.1371/journal.pone.0067500

Genotyping by genome reducing and sequencing for outbred animals

PLoS One. 2013 Jul 18;8(7):e67500. doi: 10.1371/journal.pone.0067500. Print 2013.

Authors

Qiang Chen¹, Yufang Ma, Yumei Yang, Zhenliang Chen, Rongrong Liao, Xiaoxian Xie, Zhen Wang, Pengfei He, Yingying Tu, Xiangzhe Zhang, Changsuo Yang, Hongjie Yang, Fuqing Yu, Youmin Zheng, Zhiwu Zhang, Qishan Wang, Yuchun Pan

Affiliation

¹ School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Breeding / methods
Gene Library
Genetic Markers / genetics*
Genotype
High-Throughput Nucleotide Sequencing / economics
High-Throughput Nucleotide Sequencing / methods*
Oligonucleotides / genetics
Polymorphism, Single Nucleotide / genetics*
Swine / genetics*

Substances

Genetic Markers
Oligonucleotides

Grants and funding

This study was supported by the 2011-2012 animal germplasm resources conservation project from Ministry of Agricultrue of China, the National Natural Science Foundation of China (grant no. 31072003, 3100992, 31101706, and 31272414), and the National 948 Project of China (2012-Z26, 2011-G2A).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.