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

Abstract

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.

Evaluation of genetic richness among Vietnamese native pig breeds using microsatellite markers

“…In general, the He detected in our study was higher than that reported for Spanish pig breeds (Herrero‐Medrano et al, ) but similar to the relatively high levels of genetic diversity obtained for the Iberian pig (Martínez et al, ) and some Brazilian breeds (Sollero et al, ). Compared with Asian breeds, the genetic diversities reported for the VNPs we estimated in this study were similar levels to most Chinese and Korean breeds (Fang et al, ; Kim et al, ; Li et al, ; Thuy et al, ; Zhang et al, ), while several Asian breeds, which have been locally conserved in small population size, showed a quite lower genetic diversity than the VNP breeds (Chang et al, ; Li et al, , ; Touma, Arakawa, & Oikawa, ). These studies indicate that most of the VNP breeds were considered to have no severe bottleneck previously.…”

“…Compared with Asian breeds, the genetic diversities reported for the VNPs we estimated in this study were F I G U R E 4 Heatmap of the fixation indices (F ST ) between Vietnamese native pigs. The higher F ST estimated is in red, the lower F ST estimated is in blue similar levels to most Chinese and Korean breeds (Fang et al, 2005;Kim et al, 2005;Li et al, 2000;Thuy et al, 2006;Zhang et al, 2003), while several Asian breeds, which have been locally conserved in small population size, showed a quite lower genetic diversity than the VNP breeds (Chang et al, 2009;Li et al, 2015Li et al, , 2004Touma, Arakawa, & Oikawa, 2019). These studies indicate that most of the VNP breeds were considered to have no severe bottleneck previously.…”

Comparison of growth performances, carcass characteristics, and meat qualities of Okinawan indigenous Agu pigs and crossbred pigs sired by Agu or Duroc boar

“…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.…”

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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.

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Robust microsatellite markers for hybrid analysis between domesticated pigs and wild boar

“…Validating appropriate microsatellite markers with possible hybridized wild boar and the pigs involved in the hybridization will provide the necessary genetic composition data to develop a cost-efficient monitoring tool to evaluate the introgression of pig genes to the wild boar gene pool. Such cost-efficient analyses have provided monitoring opportunities to estimate abundancy of hybrids (Qi et al, 2010;Matsumoto et al, 2019), population characteristics (Goedbloed et al, 2013a;Sharma et al, 2013) and local genetic structures (Tadano et al, 2016;Touma et al, 2020) in animals.…”