Number of vertebrae is associated with body size and meat productivity in pigs. The aim of this study was to identify QTL and associated positional candidate genes affecting the number of thoracic vertebrae (THO). A genomewide association study was conducted in a large resource population derived from an F intercross between Landrace and Korean native pigs using the Porcine SNP 60K BeadChip and the genomewide complex trait analysis (GCTA) program based on a linear mixed-effects model. A total of 38,385 SNP markers from 1,105 F progeny were analyzed for the THO trait after filtering for quality control. A total of 90 genomewide significant SNP markers (P < 1.30 x 10(-6)) on SSC 7 covering a 20-Mb region were identified for THO in this study. Several previous studies also mapped QTL for vertebral numbers in this region. The strongest association signals were detected at ASGA0035500 (P-value = 4.46 x 10(-40); 103,574,383 bp) and DIAS0000795 (P-value = 4.46 x 10(-40); 103,594,753 bp). The QTL region on SSC 7 for THO encompasses VRTN and LTBP2, which are previously described candidate genes for vertebral number variation. To refine the QTL region, a haplotype-based linkage and linkage disequilibrium (LALD) analysis using the DualPHASE program was applied because subsequent conditional association and haplotype block analyses could not resolve the region that contains the 2 loci. The LALD analysis refined the critical region to a 533.9-kb region including LTBP2; VRTN was located outside the critical region. The LTBP2 gene encoding latent transforming growth factor beta binding protein 2 is involved in bone metabolisms. Based on these data, we propose LTBP2 as a positional candidate gene for THO in pigs. After further functional studies and verification of the association in other independent populations, these results could be useful for optimizing breeding programs that improve THO and other economically important traits in pigs.