Interpretive Summary: Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep

By: Yingwei Guo, Fengting Bai, Jintao Wang, Shaoyin Fu, Yu Zhang, Xiaoyi Liu, Zhuangbiao Zhang, Junjie Shao, Ran Li, Fei Wang, Lei Zhang, Huiling Zheng, Xihong Wang, Yongbin Liu, Yu Jiang

Large-scale genotyping platforms are valuable tools for animal selection and breeding programs. The bead chip has been widely used in both research and commercial applications for a long time. A highly efficient and economical genotyping platform has been developed recently. In the present study, by combining the advantages of resequencing and bead chips, we developed a high-resolution capture array based on target sequencing with capture-in-solution technology (liquid chip), including updated functional probes according to the latest research. We further evaluated this approach by using 317 individuals and found that 210K single-nucleotide polymorphisms can be accurately genotyped, confirming the ratio of the captured regions compared with the designed rations is around 99.7%. Genome-wide association studies conducted using this chip suggested IRF2BP2 gene may be involved in hair types and ARHGAP21-KIAA1217 locus may be related to teats number. The liquid chip with high accuracy and low cost can be widely used in genome-wide association studies and genome selection, supporting efforts in molecular breeding and genetic improvement of sheep.