Indigenous Okinawa Agu pigs were once widely raised in Okinawa, Japan. Numbers of this breed reached 104,321 in 1899 (Touma, Arakawa, & Oikawa, 2020), but with the introduction of European pig breeds in the early 1900s, Agu pigs were gradually replaced by foreign breeds, and even faced imminent extinction in the 1980s. Due to a conservation program that was started in 1981, populations of Agu pigs have recovered and the pork from this breed (Agu pork) is known for its good taste. In our assessments of meat quality, Agu pigs had high intramuscular fat contents (IMF), high juiciness, and high monounsaturated fatty acid (MUFA) and low polyunsaturated fatty acid (PUFA) levels (Touma, Onaga, Toubaru, & Oikawa, 2017). Recently, demand for Agu pork has increased with the growing desire among consumers and pork producers for specialty and value-added pork. As shown for other indigenous breeds, Agu pigs growth performances and lean meat productivity are low (Touma et al., 2017). Moreover, Agu pigs have poor fertility, with small litter sizes (total number born, 4.8) (Touma & Oikawa, 2017) and low conception rates (Yamauchi et al., 2009), likely reflecting inbreeding (Touma et al., 2020). Thus, it is difficult to secure a stable supply of Agu pork. Generally, indigenous breeds have low growth and meat production, but have good meat qualities (

Objective: Agu pigs are indigenous to the Okinawa prefecture, which is the southernmost region of Japan. Agu pigs were exposed to a genetic bottleneck during the 20th century, due to the introduction of European pig breeds. The objective of this study was to elucidate the genetic structure of Agu pigs and to determine their relationships with those of five European breeds, two Chinese breeds and Ryukyu wild boar using microsatellite markers. Methods: A total of 203 DNA samples from 8 pig breeds were used in this study. Genotyping was performed using 21 microsatellite markers distributed across 17 chromosomes. Results: Numbers of effective alleles in Agu pigs were fewer than in European breeds and Ryukyu wild boar. Among domestic pigs, Agu pigs had the lowest heterozygosity (0.423) and highest inbreeding coefficient (F IS = 0.202), indicating a severe loss of heterozygosity in Agu pigs possibly due to inbreeding. Neighbor-joining tree analysis was performed based on Reynolds' genetic distances, which clustered Agu pigs with Duroc pigs. However, principal component analysis revealed a unique genetic position of the Agu pig, and the second principal component separated Agu pigs from all other breeds. Structure analysis with the optimal assumption of seven groups (K = 7) indicated that Agu pigs form an independent cluster from the other breeds. In addition, high and significant F ST values (0.235 to 0.413) were identified between Agu pigs and the other breeds. Conclusion: This study revealed a substantial loss of genetic diversity among Agu pigs due to inbreeding. Our data also suggest that Agu pigs have a distinctive genetic structure, although gene flows from European breeds were observed.

: Agu, a relatively small-bodied pig with a black coat, is indigenous to Okinawa, the southernmost island in Japan. The objective of this study was to evaluate growth, carcass and meat quality traits of Agu pigs and to elucidate breed characteristics. A total of 16 Agu pigs and 18 LWD three-way cross pigs (Duroc sires×F1 dams ; Landrace×Large White) were fed a commercial diet ad libitum at 70 kg and slaughtered at 110 kg. Daily gain, dressing percentage and the area of the Longissimus dorsi muscle (LM) were significantly lower in Agu than in LWD pigs at the same body weight. Agu pigs had much thicker backfat than the LWD pigs at the same finishing body weight. The content of intramuscular fat (IMF) was significantly higher in Agu than in LWD pigs. Though raw Agu meat had lower water holding capacity, cooked meat had lower cooking loss and higher pressed juice percentage than LWD meat. Moreover, the inner layer of Agu backfat contained a higher proportion of monounsaturated fatty acids (MUFA), a lower proportion of polyunsaturated fatty acids (PUFA) and had a lower melting point. The results revealed that Agu pigs had meat characteristics different from those of LWD pigs that are a common crossbred in commercial production.Jpn. J. Swine Science, 54, 3 : 121-129

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.

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