Abstract: To systematically evaluate the genetic status of indigenous pig resources in Guangdong province and evaluate the extent of gene introgression from commercial breeds, we analyzed genome-wide SNP data from five Guangdong indigenous breeds (Yuedong black, Meihua, Yuezhong large black-white, Lantang, and Liangguang small-ear spotted pigs; n = 48), three commercial breeds (Duroc, Landrace, and Large White; n = 43), and seven Visayan warty pigs (Sus cebifrons) used as out group. Principal component analysis (PCA), ancestry component estimation (ADMIXTURE), and neighbor-joining (NJ) phylogenetic reconstruction analysis consistently demonstrated clear genetic differentiation between Guangdong indigenous pigs and commercial breeds, with the indigenous pigs forming a distinct genetic cluster. Notably, Yuedong black pigs exhibited substantial within-breed genetic heterogeneity, with individuals showing mixed ancestral contributions from Liangguang small spotted pigs, Duroc, and other sources. Genetic diversity assessment showed that Guangdong indigenous pigs possessed higher nucleotide diversity (π = 0.002 229～0.002 885) than commercial breeds (π = 0.001 693～0.001 973). Among them, Yuedong black pigs displayed the highest 仔 value (0.002 885), indicating the retention of abundant genetic variation. Mean inbreeding coefficients estimated from runs of homozygosity (FROH) ranged from 0.131 to 0.273 in Guangdong indigenous pigs, significantly lower than those observed in commercial breeds (0.357 ～0.449). In addition, linkage disequilibrium (LD) decayed more rapidly in indigenous pigs, reflecting weaker artificial selection intensity and greater genetic diversity. To minimize reference genome bias, we performed Dsuite D-statistic analysis using out group based allele repolarization. Under the unbiased topology (Large White×Landrace, indigenous pig, out group), a significant signal of Large White introgression was detected in Yuezhong large black-white pigs (D = 0.019 6, adjusted P = 5.41 × 10-3). Introgression trends were also observed for Liangguang small spotted and Lantang pigs but did not reach significance after multiple-testing correction, while no significant introgression was detected in Yuedong black or Meihua pigs. Collectively, our results indicated that Guangdong indigenous breeds retain distinct genetic backgrounds and substantial genetic diversity. However, certain breeds have experienced varying levels of genetic introgression from commercial breeds. We recommend implementing tiered conservation strategies based on breed-specific genetic characteristics: for Yuedong black pigs, priority should be placed on maintaining its internal subpopulation diversity; for breeds such as Yuezhong large black-white pigs with detected introgression signals, vigilance is needed against the erosion of genetic distinctiveness caused by exotic introgression, and genomics-assisted conservation should be implemented in a timely manner.

Key words: Guangdong indigenous pigs, conservation genomics, genetic diversity, introgression, whole-genome SNP