Unravelling novel and pleiotropic genes for cannon bone circumference and bone mineral density in Yorkshire pigs

Leg weakness is a prevalent health condition in pig farms. The augmentation of cannon bone circumference and bone mineral density can effectively improve limb strength in pigs and alleviate leg weakness. This study measured forelimb cannon bone circumference (fCBC) and rear limb cannon bone circumference (rCBC) using an inelastic tapeline and rear limb metatarsal area bone mineral density (raBMD) using a dual-energy X-ray absorptiometry bone density scanner. The samples of Yorkshire castrated boars were genotyped using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the level of whole-genome sequencing data (iWGS). This study used iWGS data to perform genome-wide association studies and identified novel significant SNPs associated with fCBC on SSC6, SSC12, and SSC13, rCBC on SSC12 and SSC14, and raBMD on SSC7. Based on the high phenotypic and genetic correlations between CBC and raBMD, multi-trait meta-analysis was performed to identify pleiotropic SNPs. A significant potential pleiotropic quantitative trait locus (QTL) regulating both CBC and raBMD was identified on SSC15. Bayes fine mapping was used to establish the confidence intervals for these novel QTLs with the most refined confidence interval narrowed down to 56 kb (15.11 to 15.17 Mb on SSC12 for fCBC). Furthermore, the confidence interval for the potential pleiotropic QTL on SSC15 in the meta-analysis was narrowed down to 7.45 kb (137.55 to137.56 Mb on SSC15). Based on the biological functions of genes, the following genes were identified as novel regulatory candidates for different phenotypes: DDX42, MYSM1, FTSJ3, and MECOM for fCBC; SMURF2, and STC1 for rCBC; RGMA for raBMD. Additionally, RAMP1, which was determined to be located 23.68 kb upstream of the confidence interval of the QTL on SSC15 in the meta-analysis, was identified as a potential pleiotropic candidate gene regulating both CBC and raBMD. These findings offered valuable insights for identifying pathogenic genes and elucidating the genetic mechanisms underlying CBC and BMD. This study aimed to identify novel and pleiotropic genes regulating cannon bone circumference (CBC) and metatarsal area bone mineral density (raBMD) using genome-wide association studies, and demonstrated that RAMP1 was the potential pleiotropic candidate gene regulating CBC and raBMD, providing valuable insights for elucidating the genetic mechanisms underlying limb growth and bone mineral accumulation. Leg weakness, a highly prevalent health condition in pig breeding farms, adversely affects the lifespan of breeding pigs. The augmentation of cannon bone circumference (CBC) and bone mineral density (BMD), which are objective measures of limb strength in pigs, can effectively alleviate leg weakness. To identify candidate genes regulating CBC and BMD in pigs, this study performed single-trait genome-wide association studies and multi-trait meta-analysis on all individuals with phenotype data. Additionally, the confidence intervals of quantitative trait locus (QTL) were determined using Bayesian methods. Four CBC-associated QTLs and one BMD-associated QTL were identified. Additionally, one potential pleiotropic QTL associated with both CBC and rear limb metatarsal area BMD (raBMD) was identified. This study demonstrated that DDX42, MYSM1, FTSJ3, and MECOM were candidate genes regulating forelimb CBC, while SMURF2 and STC1 were candidate genes regulating rear limb CBC. Additionally, RGMA was demonstrated to regulate raBMD, while RAMP1 was identified as a potential pleiotropic gene regulating both CBC and raBMD. The findings of this study provide valuable insights into the genetic mechanisms underlying limb growth and bone mineral accumulation.