Genotype file of re-sequencing data-set from Meishan and Erhualian pigs

The pig teat number traits have significant economic importance. Meishan and Erhualian pigs in Chinese Taihu Lake region have the highest teat counts worldwide, with an average of 20 teats for Erhualian pig and 17 teats for Meishan pig. To unveil genetic basis of teat number variation in Meishan and Erhualian pigs, this study employed whole-population genome re-sequencing for total 1119 individuals. Subsequently, a genome-wide association study (GWAS), meta-analysis, and Bayesian fine mapping were conducted. Additionally RNA-seq was performed on mammary placodes of 26-day-old Erhualian pig embryos from sows with extremely high and low teat numbers. The GWAS results from two breeds revealed multiple significant QTLs for total teat number (TNT) mainly on SSC1, SSC5, SSC10, and others. Bayesian fine mapping was conducted for the most significant quantitative trait locus (QTL) in both Meishan pig GWAS and meta-analysis resulting in the mapping of SSC1:264293859bp-266080039bp. Similarly, Bayesian fine mapping was performed for the second most significant QTL in meta-analysis, which also was the most significant QTL in Erhualian pig GWAS. This led to the identification of the mapping of SSC5:58093547bp-59198414bp. A total of ninteen protein-coding genes were identified in SSC1:264293859bp-266080039bp and two protein-coding genes were identified in SSC5:58093547bp-59198414bp. In the integration of RNA-seq results from mammary placodes of extreme high and low 26-day-old Erhualian pig embryos, only OLFML2A showed a significant differential expression among these twenty-one candidate genes. OLFML2A was primarily enriched in the extracellular matrix and extracellular matrix organization pathways, which may play a role in the interaction between epithelial and stromal cells of mammary placodes. In addition, the utilization of pig FarmGTEx data for TWAS revealed a significant association between the expression level of OLFML2A in the placenta and TNT in Meishan pig. Furthermore, the results of pheWAS further validate the significant association of OLFML2A with teat number traits in Western commercial pigs. After integrating multiple omics, such as genomics and transcriptomics, we have tentatively identified the OLFML2A gene as a potential causal gene responsible for teat number variation in Meishan and Erhualian pigs. This gene could potentially play a role in the development of mammary placodes in Meishan and Erhualian pigs, consequently influencing the phenotype of teat number.