Characterization of the European type of maternal lineage evident in extant Jeju native pigs

Abstract

Using a partial D-loop sequence of mtDNA, an intensive analysis was conducted of the maternal lineages of Jeju native pigs (JNPs) from Korea. In total, 100 mtDNA sequences were obtained from Asian wild boars (AWBs), European wild boars (EWBs), Asian domestic pigs (ADPs), European domestic pigs (EDPs), and JNPs and were used for phylogeny and network analyses. Two distinct JNP groups — one (JNPA) in the Asian cluster and the other (JNPE) in the European cluster — were identified in the estimated phylogenetic tree and network. The maternal lineage of JNPE was the closest to that of EWB and a clear haplogroup was identified that shared an identical haplotype (hap04) among 15 individuals of JNPE and 2 individuals of EWB. A Landrace and an EWB shared hap03 with a JNPE. EWB, Landrace, Large White, and Duroc formed two clear haplogroups with JNPE in a parsimonious median-joining network analysis, suggesting that an obvious maternal contribution of EDP has occurred in JNPE in recent years. A pair-wise mismatch analysis also indicated that JNPE may have experienced a sudden population expansion, suggesting a more recent establishment compared with the gradual population expansion of JNPA. The JNPE group therefore should be further evaluated in order to decide whether this group should be culled or accepted into further programs for maintenance of the JNP population as a pure breed.