Abstract：To gain a better understanding for the relationship between the genome structure and the reproduction mechanism of Xiang pig, the genome sequence of Xiang pig (Sus scrofa) was detected using next-generation sequencing method. Plenty of structural variations (SVs) were detected from chromosome X (chrX) of two Xiang pig groups with high (XH) or low (XL) litter size using several bioinformatics programs. There were 3 246 SVs being screened out from chrX of Xiang pig, in which 311 SVs were unique in XH group and 138 SVs in XL group with 449 SVs in total. It was notified that a SV hotspot locating at 61~109 Mb of chrX group was found out from samples of group XH. There were 138 SVs in the SV hotspot region, with 65 of them in deletion genotype. In addition, about 47 proteins might be disturbed by 80 of specific SVs in genes of Xiang pig. Out of 31 in the 47 genes contained QTL which was related with reproduction traits such as genes of NLGN4X, GPR143, ZDHHC15, ATRX, NXF2, AMOT, GRIA3, THOC2. These genes were significantly enriched in the adrenal gland development, regulation of intracellular steroid hormone receptor signaling pathway, RIG-I-like receptor signaling pathway and lipoprotein metabolic process base on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. 10/47 SVs in populations of Xiang pig were genotyped by PCR methods. The frequency of SV_GPR143 genotypes was significantly different between XH and XL groups (P＜0.05). And the SV_GPR143 locus showed a correlation ship with the litter sizes (ρ=0.217) of Xiang pig with 1.96 piglets in DD genotype lower than that in NN genotype (P＜0.05). It indicated that much more amount of SVs presented in group XH and might contribute to the high reproduction trait of Xiang pig.
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