The COL9A1 gene is associated with longissimus dorsi muscle area in the pig.

Genotyping and association analyses: The genotyping of SNPs c.290-106A>C and c.2357T>G (p.Ser786Ala) (dbSNP acc. no. ss86352089, ss86352090) was implemented in two populations using a MassARRAY system (Sequenom Inc.). Population A consisted of 2066 sows from Newsham Choice Genetics. The 10th-rib LMA and backfat were measured using real-time ultrasonic imaging with a Pie Medical 200 (Classic Medical Supply Inc.). The association analyses used the mixed procedure (SAS9.0) including genetic line, measurement date and genotype as fixed effects, sire as a random effect and body weight as a covariate. Population B was the ISU Berkshire · Yorkshire (B · Y) pig family, comprising 515 F2 animals, and the association analyses were performed as described by Grapes et al. Both COL9A1 SNPs were highly polymorphic (MAF > 0.05) and in strong linkage disequilibrium (D¢ = 1.0, r = 0.911) with each other. The SNPs were very highly significantly (P < 0.001) associated with LMA (Table 1) and were suggestively significant (P < 0.1) with 10th-rib backfat in population A. In the B · Y family, the SNPs were highly significantly associated (P < 0.01) with LMA but were not associated with any of backfat traits (data not shown). The F-value peak for LMA dropped from 9.29 to 7.07 around S0008 after p.Ser786Ala genotypes were included as a fixed effect in the model for QTL analyses (Fig. S1). Comments: The COL9A1 gene encodes an a1-chain of Type IX collagen that acts as a bridge connecting type II collagen with other cartilage molecules. The role of COL9A1 on muscle development and growth has not been reported. The serine residue (p.786) is the last amino acid residue of the COL9A1 non-helical region 2 (NC2) that directs and drives the association of collagen IX a-chains. The COL19A1gene involved in the initial stages of skeletal muscle-cell differentiation is adjacent to COL9A1 on human chromosome 6q. The possible linkage disequilibrium between these collagen genes could promote the association of COL9A1 with LMA. In addition, the magnitude of the effect of p.Ser786Ala was around 2% and 7% of the mean value for the trait in our two populations respectively, which might limit the utilization of this SNP. Functional studies of p.Ser786Ala and association analyses of COL19A1 with LMA are needed.