2.4. Genome Scanning for Selective Signal Analysis

The whole genome selection signals were determined by comparing individuals with 15 NTV to those with 16 NTV. A selective scanning analysis was performed using VCFtools 0.1.16 software [18] and setting a 100 KB sliding window with a step size of 10 KB. The genetic differentiation value (F_ST) between the two groups was calculated, with the empirical top 1% as the threshold (F_STtop0.01 = 0.18). Genes partially or completely overlapping with selection signal regions were selected based on the Sus scrofa 11.1 genome assembly using the BioMart data management (http://www.biomart.org/, accessed on 1 January 2023). Furthermore, these selection signal regions were also compared with pig QTL from the animal QTL database (https://www.animalgenome.org/cgi-bin/QTLdb/, accessed on 1 January 2023).