Phylogenetic Analysis of Philippine Native Pigs (Sus scrofa L.) from Batanes, Quezon, and Marinduque Based on Mitochondrial DNA D-loop Markers

By analyzing the mitochondrial DNA (mtDNA) displacement loop (D-loop) region, we aimed to assess the genetic diversity of Philippine native pigs from Batanes, Quezon, and Marinduque and to determine the phylogenetic relationship between these subpopulations and other Asian and European pig breeds. Ear tissue samples were collected from the native pigs in Batanes (n = 17), Quezon (n = 37), and Marinduque (n = 40). Genomic DNA was extracted, and the D-loop sequences were amplified by PCR. The D-loop sequences of 94 Philippine samples were initially analyzed using the Kimura 2-parameter model and neighbor-joining method in MEGA7, identifying a total of 17 haplotypes designated as H1–H17. Notably, only eight haplotypes were specific to individuals coming from a particular province, whereas the remaining haplotypes were detected in samples from different provinces. Additional qualitative trait analysis that the majority of Philippine native pigs had black coat color, a plain coat pattern, short cylindrical snouts, straight head profiles, erect and forward-oriented ears, curly tails, and straight backlines. Phylogenetic analysis of the Philippine samples and 16 exotic pig breeds revealed that Philippine native pigs with H1 and H2 haplotypes formed a distinct clade with Taiwanese Type I Lanyu pig, whereas those with H3–H17 haplotypes clustered with other Asian and European pigs. Therefore, our findings suggest a close and unique relationship between Taiwanese Type I Lanyu and Philippine native pigs. The presence of several haplotypes also implies high genetic variation among Philippine native pigs. Specifically, the native pigs from Quezon and Marinduque are the most closely related, whereas those from Quezon and Batanes are the least closely related.