Genome-Wide Association Study of Rib Number and Total Thoracolumbar Vertebrae Number in a Jishen Black Pig Population

The Jishen Black pig is a synthetic breed incorporating the genetic backgrounds of Chinese indigenous pigs and Western lean-type pigs. The objective of this study was to characterize phenotypic variation, estimate genetic parameters, and identify genomic loci associated with rib number (NR) and the total number of thoracolumbar vertebrae (NTLV) in Jishen Black pigs. NR, NTLV, and lumbar vertebra number (NLV) were measured in 389 pigs, and genotyping was performed using a 70K SNP chip. Genetic parameters were estimated using HIBLUP, and genome-wide association studies (GWAS) were conducted using the MLM and BLINK models in GAPIT v3.0. The mean values of NR, NTLV, and NLV were 14.88, 20.94, and 6.05, respectively, and their heritability estimates were 0.568, 0.493, and 0.140, respectively. GWAS identified a shared major association peak for NR and NTLV on SSC7 at 91.19–98.15 Mb, centered on VRTN and the adjacent ABCD4-LTBP2-AREL1-PGF linkage region, among which the loci at 96.12 Mb, 96.56 Mb and 97.79 Mb are NR-specific loci. Additional signals included MIB1 on SSC6 and MMRN2 on SSC14 for NTLV, together with NR-specific loci on SSC7 at 111.59 Mb and on SSC8. Database annotation indicated that several significant SNPs overlapped with records for rib number, carcass length, loin muscle area, backfat thickness, or teat number. This study identifies major genomic regions associated with vertebral-number traits in Jishen Black pigs and expands current knowledge of their genetic basis.