Genomic Conservation and Application of Pigs in the Taihu Region of China

The Chinese indigenous pigs in Taihu region are an invaluable component of the world's pig genetic resources, which are the most prolific breeds of swine in the world. In this study,252 pigs from all the six indigenous breeds in Taihu region were sequenced using by genome reducing and sequencing (GGRS) approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. 105,550 SNPs and 122,632 Indels were identified across genome. Among them, about 35%SNPs and 38% Indels were mapped to gene regions, and 24% SNP and 25% Indels fell into QTL regions related to economically important traits. The KEGG pathway and GO enrichment analysis revealed that genes assumed to be large-effect mutations were significantly overrepresented in 22and 56gene sets, respectively. A total of 343 breed-specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to further investigate their genetic diversity and population structure, positive selection signals, molecular evolutionary history at the genome level and provide valuable references for improvement of their breeding and cultivation.