Application of Whole Genome Resequencing to Detect SNPs for Selection Against Boar Taint in Norwegian Male Pig Breeds

Boar taint, a complex variable trait identified by an objectionable smell/taste in the meat from intact male pigs, is caused primarily by deposition of androstenone and skatole in adipose tissue. Pig industries usually used castration as a tool for preventing boar taint. However, this cause inconvenience to consumers and leads to both reduced growth efficiency and excess deposition of fat. Selective breeding may serve as an alternative to castration which requires the identification of single nucleotide polymorphisms (SNPs) within QTL regions to select for low levels of boar taint without simultaneously affecting levels of sex steroids. We did whole genome re-sequencing of 23 Duroc and 22 Landrace of Norwegian male pigs to an average coverage 10x using the Illumina HiSeq2000 machine and detected SNPs within three QTL regions underlying either androstenone or skatole. This approach not only detects SNPs in multiple samples simultaneously but also intact SNP information about each breed and individual that carries the different genetic variants. Short reads were pre-filtered before mapping to Sus scrofa 10.2 genome using Bowtie2 tool. Mapped reads were called for SNPs within QTL region on SSC5, 7 and 13 using Freebayes tool.  We removed SNPs lying with in repeat regions. In an effort to remove artifacts SNPs, we applied some stringent filtering rules.  Final list of SNPs were annotated thereafter small subset of SNPs genotyped in Norwegian pig populations to done further association studies on either SNPs or their haplotype and finally we will choose significant SNPs for selection purpose.