Objective To identify single nucleotide polymorphisms (SNPs) in the BMP15 gene associated with ovulation status, teat number, and carcass traits in pigs, providing effective molecular markers and reference information for the breeding and genetic improvement of Liangguang Spotted pigs.

Method A total of 107 Liangguang Spotted pigs were used as experimental animals. The gilts were slaughtered at 365 ± 25 days of age to assess ovulation status, teat number, and carcass traits. SNPs within the BMP15 gene were genotyped using GBTS technology. Association analysis and linkage disequilibrium analysis were performed for ovulation status, teat number, and carcass traits.

Result A total of 64 polymorphic sites were detected in the BMP15 gene of Liangguang Spotted pigs. After excluding SNPs with a mutation frequency lower than 1%, 27 SNPs were retained for association analysis, among which 8 were located in coding regions and 19 were located in non-coding regions. SNP association analysis showed that g.44615220G>C, g.44615222T>A, g.44615224G>C, g.44613316T>C, g.44613600T>G, g.44614611T>C, and g.44615055A>G were significantly associated with ovulation status (P<0.05), while g.44611375C>G, g.44613539A>G, and g.44614651T>C were significantly associated with total teat number (P<0.05). The SNPs g.44615220G>C, g.44615222T>A, and g.44615224G>C were significantly associated with backfat thickness in sows (P<0.05). The SNPs g.44611375C>G, g.44611978T>C, g.44613539A>G, g.44614367A>G, and g.44614651T>C were associated with bone weight, lean meat weight, loin eye area, ham weight, and skin and fat percentage. The SNPs g.44613316T>C, g.44613600T>G, g.44614611T>C, and g.44615055A>G were significantly associated with bone weight, loin eye area, ham weight, and leaf fat weight in sows (P<0.05). Haplotype association analysis revealed strong linkage disequilibrium among g.44615220G>C (H1), g.44615222T>A (H2), and g.44615224G>C (H3) (r² >0.9), and similarly strong linkage disequilibrium among g.44611375C>G (H4), g.44611978T>C (H5), g.44613539A>G (H6), g.44614367A>G (H7), and g.44614651T>C (H8) (r² >0.9). The haplotype combinations H1H2, H1H3, and H2H3 were significantly associated with ovulation status (P<0.05). The haplotype combinations H4H6, H4H8, and H6H8 showed significant associations with teat number (P<0.05). In addition, the haplotype combinations H1H2, H1H3, and H2H3 were significantly associated with backfat thickness (P<0.05), whereas combinations such as H4H5, H7H8, and H4H7 were significantly associated with loin eye area (P<0.05).

Conclusion This study identified 12 SNPs in the BMP15 gene that are significantly associated with ovulation status, teat number, and carcass traits, providing a theoretical basis for future molecular marker–assisted selection in Liangguang Spotted pigs.