Genetic diversity of Ifugao and Kalinga [Philippines] native pigs (Sus scrofa L.) using morphometrics and molecular markers

The conservation of the diversity of the native genetic resources is very important to sustain the global biodiversity. In an effort to study the genetic diversity of the native pigs in the Philippines, a total of 79 samples were collected from two provinces of the Cordillera Administrative Region particularly Ifugao and Kalinga [Philippines] which are known to have an abundance of native pigs. In this study, morphological and 9 microsatellite markers and an mtDNA control region molecular markers were used to determine the extent of genetic diversity of the 79 native pigs (Ifugao, n=41, and Kalinga, n=38) within and among the two populations. Phenotypic characterization showed that the native pigs from the two populations have unique characteristics. Nine SSRs provided information on the genetic variation and differentiation among the populations. High mean numbers of alleles (10.556), mean heterozygosity (0.7128), and mean PIC (0.6803) showed that the nine microsatellite markers were very informative and polymorphic. In addition, data shows that there was a considerable amount of genetic differentiation within population. Particularly, Ifugao native pig breeds had relatively high genetic diversity within breeds compared to that of Kalinga. The very low mean differentiation index (F sub ST) 0.0442 and Nei's genetic distances of 0.1369 between Ifugao and Kalinga populations, however, revealed that genetic differentiation among breeds were low. To determine the lineage and possible origin of the Philippine native pigs, mtDNA control region were analyzed. Interestingly, the native pigs from Ifugao established that there were five haplotypes present in the population compared to the Kalinga which has only two haplotypes. These results supported the data from the SSR study were in Ifugao native pig breeds have relatively higher genetic differentiation compared to the Kalinga native pigs breeds. Furthermore, these haplotypes were grouped together with the Taiwan Type I Lanyu pig separate from the other Asian and European pig breeds. The results inferred that Philippine native pig breeds possess a unique nuclear genetic structure compared to the other Asian and European pig breeds.