Abstract #M78

# M78
An improved approach for swine SNP genotyping using Genotyping-by-Sequencing.
Cheng Tan*1, Jiangli Ren1, Zhuolin Huang1, Yiqiang Zhao1, Yang Da2, Xiaoxiang Hu1, 1State Key laboratory for Agrobiotechnology, China Agricultural University, Beijing, China, 2Department of Animal Science, University of Minnesota, Saint Paul, MN.

Genotyping-by-sequencing (GBS) technology has a capacity for delivering large numbers of single nucleotide polymorphism (SNP) marker genotypes with potentially lower cost than SNP chips. To achieve stable genotyping results, we selected the EcoRI-MspI enzyme from a large number of candidate enzymes, and used the magnet beads-based purification method to stably and simply recapture GBS tags. Genomic DNA samples from 192 Duroc pigs were digested with EcoRI-MspI enzyme, ligated to adapters containing unique barcode, and sequenced on the Illumina NextSeq 500 system with 75bp single-end sequencing. The results showed that all 192 barcoded DNA samples were represented evenly, and that on average 4 million reads per animal were produced. From these samples, about 450,000 unique sequence tags per sample containing 55,843 SNPs were identified through TASSEL4.0 analysis package requiring a minimum of 10 times that a tag must be present, which covered about 1% of the whole genome. The average call rate per individual was more than 94.6%. By repeating GBS genotyping on 2 different samples with 96 pigs in each sample performed by different technicians, 88.5% of the 55,843 SNPs had the same genomic locations from both samples. The cost of the 55,843 SNPs per sample was under $50 per animal. These results showed that our improved GBS technique is sufficiently high-throughput, economical and provides an acceptable marker density for genomic selection or genome-wide association studies.

Key Words: genotyping-by-sequencing, swine, SNP