The mRNA differential display technique was performed to investigate the differences of gene expression in the Longissimus muscle tissues from Meishan and Large White pigs. One novel mRNA that was differentially expressed was identified through semi-quantitative RT-PCR and the cDNA complete sequence was then obtained using the rapid amplification of cDNA ends (RACE) method. Sequence analysis revealed that this mRNA is not homologous to any known porcine gene. Sequence prediction analysis revealed that the this mRNA is not protein-coding mRNA. Polymorphism analyses revealed that there was a A-G mutation on the position of 490bp and PCRTaqI- RFLP analyses revealed that Chinese indigenous pig breeds and European pig breeds displayed obvious genotype and allele frequency differences at this locus. Association analyses revealed that this polymorphic locus was significantly associated with the meat pH of M. longissimus dorsi (LD), M. biceps femoris (BF), M. semispinalis capitis (SC), water holding capacity, drip loss rate, meat colour value M. longissimus dorsi (LD), and estimated lean meat percentage (P<0.05).