Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region

Abstract

Objective The Agu is the only native pig breed in Japan, which is reared in Okinawa prefecture, the southernmost region in Japan. Its origins are considered to be of Asian lineage; however, the genetic background of the Agu is still unclear. The objective of this study was to elucidate the maternal lineage of the Okinawa indigenous Agu pig with the use of the mitochondrial DNA (mtDNA) control region. Methods The mtDNA control regions of Agu pigs were sequenced and the phylogenetic relationship among Agu, East Asian and European pigs was investigated with the use of 78 Agu individuals. Results Twenty-seven polymorphic sites and five different haplotypes (type 1 to type 5) were identified within the Agu population. Phylogenetic analysis indicated that types 1 and 2 were included in East Asian lineages; however, the remaining types 3, 4, and 5 were of European lineages, which showed a gene flow from European pigs in the 20th century. Sixty-seven out of 78 Agu individuals (85.9%) possessed mtDNA haplotypes 1 and 2 of the East Asian lineage, which were identical to two haplotypes of ancient mtDNA (7,200 to 1,700 years before the present) excavated at archaeological sites in Okinawa. Conclusion This study confirmed that the East Asian lineage is dominant in the maternal genetic background of the Agu population, supporting the hypothesis that the ancestors of the Agu pig were introduced from the Asian continent.

Evaluation of the genetic structure of indigenous Okinawa Agu pigs using microsatellite markers

“…Taken with a previous study of mtDNA [5], our analyses of nuclear DNA suggest that Agu pig populations have maternal Asian origins, but that strong nuclear genetic influences were imposed from European breeds after 1904. Nonetheless, PCA analysis showed that Agu pigs are genetically unique among European and Asian breeds (Figure 3).…”

“…Ryukyu wild boar (Sus scrofa riukiuanus) has inhabited the Okinawa islands since the Pleistocene period [29]. In a previous study of mtDNA control regions, no Ryukyu wild boar haplotypes were found in an Agu pig population [5]. Our nuclear DNA analyses also revealed genetic distinctions between Ryukyu wild boar and Agu pigs ( Table 2; Figures 1-4), suggesting little genetic influence from Ryukyu wild boar.…”

“…It is assumed that Japanese Agu pigs originated from the first introduction of pigs from the Asian continent. A previous study of mtDNA control regions by Touma et al [5] revealed that most Agu individuals have East Asian haplotypes, whereas only 14% of Agu pigs carried European haplotypes. These data are evidence of gene flows from European breeds into Agu pig populations.…”

“…It is generally believed that the ancestors of Agu pigs were introduced from the Asian continent, probably from China, in the latter half of the 14th century when the ancient King-213 Touma et al (2020) Asian-Australas J Anim Sci 33:212-218 dom of Okinawa began to trade with China [2]. In support of this assertion, phylogenetic analyses using mitochondrial DNA (mtDNA) control regions revealed that the haplotypes of Agu pigs were clustered into the Asian clade [3][4][5]. However, mtDNA provide only maternal genetic information and does not reflect the history of inheritance as shown by nuclear genomes, which carry male-mediated gene flows.…”

Mitochondrial DNA variation and phylogeography of native Mongolian goats

“…Mitochondrial DNA (mtDNA) is a critical tool for tracing evolutionary and population genetics of most domesticated animals. Also, mtDNA diversity is vital in assessing the maternal origin, phylogeny, and population structure of all domestic animals [8][9][10][11][12][13]. Previous studies of goat mtDNA (control region) revealed a total of six haplogroups (also known as lineages; A, B, and C by Luikart et al [14]; D by Sultana et al [15]; F by Sardina et al [16]; and G by Naderi et al [6]).…”