Water-holding capacity (WHC) is a meat quality trait that affects economic outcomes caused by the tissue fluid loss and weight loss. The present study indicates that the mutation c.-379T>G in the UBXN1 promoter is associated with promoter activity, UBXN1 mRNA level, and WHC. Therefore, it potentially contributes to WHC improvement by regulating the degradation of myofibrillar proteins. It is a promising marker for selection of pork quality and increases economic benefits of the pork industry.

Litter size is an important economic factor in pig production. This study was conducted to investigate litter-size-related epigenetic markers in uterine tissue from Berkshire pigs. The zona pellucida binding protein (ZPBP) gene was significantly hypomethylated in the larger litter size groups by DNA profiling analysis, and this gene can be used as a valuable epigenetic biomarker for hyperprolific sows.

Using RNA sequencing technology, we identified SNPs in the NAT9 and MAP3K3 genes that are associated with litter size in Berkshire pigs. Our results suggest that selecting Berkshire pigs with the GG genotype of NAT9 and the CT genotype of MAP3K3 can produce more piglets. We suggest that these genetic markers would improve litter size in breeding programs.

We identified a genetic polymorphism in Mucin13 gene affecting E. coli adhesion patterns using (local isolate) diarrhoeagenic E. coli in Indian desi pigs. Five SNPs and one indel previously reported to be associated with an ETEC F4ab/ac adhesion pattern were examined by designing PCR-RFLP protocol. The genotypic frequencies of only one SNP (g.22304A > G) differed significantly (at P < 0.05) in an adhesive, non-adhesive and weakly adhesive population.

Biological processes underlie all livestock traits. Biomarkers are molecular components of the biological processes showing differential expression associated with the phenotype of the trait. Biomarkers enable the monitoring, diagnosis, and prediction of changes in meat quality related to external stimuli and interactions with the genotype. We review the development of biomarkers for meat quality of pigs in diverse pig breeds, environments, and pork production chains.