We designed primers using Primer5 (http://www.premierbiosoft.com/primerdesign) for SVs validation (Supplementary Table 2). The DNA templates combined with primers were processed under preheating(93°C, 5 min), amplification (denaturation at 93°C, 40 s, then annealing at 68°C, 30 s, finally elongation at 72°C, 60s, these process executed 33 cycles), and extension(72°C, 7 min) processes. The PCR products from Meishan pig, Tibetan wild boar, and Duroc were separated by size in a 1% agarose gel electrophoresis. SVs were considered successfully validated if their PCR products successfully matched to expected sizes and locations.

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