The UBX domain containing protein 1-like gene (UBXN1) promotes the protein degradation that affects meat quality, in particular traits related to water holding capacity. The aim of our study was to identify UBXN1 polymorphisms and to analyse their association with meat quality traits. Moreover, the relationship of UBXN1 polymorphisms and its transcript abundance as well as the link between UBXN1 expression and water holding capacity were addressed. Pigs of the breed German landrace (GL) and the commercial crossbreed of Pietrain ì [German large white ì GL] (PiF1) were used for this study. In GL, the novel SNP c.355 C > T showed significant association with conductivity and drip loss (P ? 0.05). Another SNP at nt 674 of the coding sequence [SNP c.674C>T (p.Thr225Ile)] was associated with drip loss (P ? 0.05) and pH1 (P ? 0.1). In PiF1, the SNP UBXN1 c.674C>T was associated with conductivity (P ? 0.01). Moreover, the haplotype combinations showed effects on conductivity within both commercial populations at P ? 0.1. In both populations, high expression of UBXN1 tended to decrease water holding capacity in the early post mortem period. The analysis of triangular relationship of UBXN1 polymorphism, transcript abundance, and water holding capacity evidences the existence of a causal polymorphism in cis-regulatory regions of UBXN1 that influences its expression.