• Journal of Life Science
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• v.21 no.3
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• pp.341-348
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• 2011

In an effort to gain greater understanding of the maternal lineages of the Jeju native pig (JNP), we analyzed the mitochondrial DNA (mtDNA) CYTB gene and compared it with those of other pig breeds. PCR-RFLP analysis was conducted with six pig breeds including JNP, and then the RFLP patterns allowed for the separation of the pig breeds into two distinct haplotypes (mtCYTB1 and mtCYTB2). The JNP CYTB sequences were detected in both the European and Asian breed clusters on the phylogenetic tree. The J2 group was sorted with the indigenous cluster of Asian pig lineages and was related closely to Chinese native pig breeds, but a second group, J1, was sorted with the European pig lineages and appeared to be related to Spanish Iberian native pigs, rather than to Asian breeds. These results indicate that the JNP currently raised on Jeju Island have two major maternal origins estimated in Asian and European pigs. We concluded that the JNP that share a common lineage with indigenous Asian pigs were domesticated in the distant past, originating from pigs that were already being raised elsewhere at that time, and that the European pig breeds introduced in the twentieth century have also contributed to the formation of this pig population.

• Journal of Animal Science and Technology
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• v.56 no.7
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• pp.23.1-23.7
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• 2014

Background: Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome-wide scan in pig populations in order to identify loci/candidate genes underlie phenotypic variation in pig breeds and facilitate genetic improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers. To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the $F_{ST}$ approach. Results: In the comparison of Berkshire and KNP breeds using the FDIST approach, a total of 1108 outlier loci (3.48%) were significantly different from zero at 99% confidence level with 870 of the outlier SNPs displaying high level of genetic differentiation ($F_{ST}{\geq}0.490$). The identified candidate genes were involved in a wide array of biological processes and molecular functions. Results revealed that 19 candidate genes were enriched in phosphate metabolism (GO: 0006796; ADCK1, ACYP1, CAMK2D, CDK13, CDK13, ERN1, GALK2, INPP1; MAK, MAP2K5, MAP3K1, MAPK14, P14KB, PIK3C3, PRKC1, PTPRK, RNASEL, THBS1, BRAF, VRK1). We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and immune response (HCST and RYR1). Conclusions: Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.

• Molecules and Cells
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• v.43 no.8
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• pp.728-738
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• 2020

Time and cost-effective production of next-generation sequencing data has enabled the performance of population-scale comparative and evolutionary studies for various species, which are essential for obtaining the comprehensive insight into molecular mechanisms underlying species- or breed-specific traits. In this study, the evolutionary and functional analysis of Korean native pig (KNP) was performed using single nucleotide polymorphism (SNP) data by comparative and population genomic approaches with six different mammalian species and five pig breeds. We examined the evolutionary history of KNP SNPs, and the specific genes of KNP based on the uniqueness of non-synonymous SNPs among the used species and pig breeds. We discovered the evolutionary trajectory of KNP SNPs within the used mammalian species as well as pig breeds. We also found olfaction-associated functions that have been characterized and diversified during evolution, and quantitative trait loci associated with the unique traits of KNP. Our study provides new insight into the evolution of KNP and serves as a good example for a better understanding of domestic animals in terms of evolution and domestication using the combined approaches of comparative and population genomics.

• Journal of Embryo Transfer
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• v.30 no.2
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• pp.91-97
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• 2015

Amphiregulin (AREG), a glycoprotein that is a member of the epidermal growth factor (EGF) family, is expressed by the porcine conceptus and endometrium. AREG genotypes were determined based on an SNP in the intron 3 of the gene. Contradictory effects of AREG genotypes on reproductive traits in different pig breeds were reported previously. G allele had undesirable effect on reproductive trait in Meishan breed, while it had favorable effects in Polish Landrace and Large White. We determined AREG genotypes of 179 pigs including the Duroc, Landrace, Yorkshire, Korean native pig (KNP), and Meishan breeds. Two new SNPs were identified near the previously reported SNP in the intron 3 of AREG. Frequencies of AREG alleles among the Duroc, Landrace, Yorkshire, and KNP sows were significantly different (p<0.001), indicating association between AREG genotypes and pig breeds. The first parity litter size was significantly affected by the breeds (p=0.014), but not by AREG genotypes (p=0.148). However, there were breed and AREG genotype associated trends in the first parity litter size. The first parity litter size appeared to be higher in Duroc and KNP sows with G allele, while it appeared to be lower in Landrace sows with G allele. Significant variability of AREG alleles among pig breeds, for the first time in Duroc and KNP sows, was identified. AREG genotypes may influence reproductive traits differentially for each breed and thus, AREG genotypes may need to be considered when sows are bred to increase litter size.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.10
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• pp.1490-1495
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• 2007

Insulin-like growth factor binding protein-4 (IGFBP-4) is a member of the IGF super family, and regulates the action of IGFs. The polymorphism of porcine IGFBP-4 gene in 17 pig breeds (total n = 570) was detected by PCR-SSCP, and alleles A and B were detected. In these pig breeds, it was found that exotic pig breeds carried high frequencies of allele A, while Chinese native pig breeds carried high frequencies of allele B. The role of porcine IGFBP-4 was investigated in 172 F2 offspring of a $Lantang{\times}Lantang $ population. Forty eight growth traits were recorded for analyzing the association between IGFBP-4 gene polymorphism and quantitative performance traits. In this resource family, pigs with AA genotype had higher fore-body weight, bone weight of mid-body, bone weight of rear-body, fore-leg weight and rear-leg weight than those pigs with BB genotype (p<0.05); while pigs which carried BB genotype had higher back-fat thickness at C point and lard weight than those pigs with AA genotype (p<0.05); pigs with AA genotype had higher body weight than those with BB genotype; for meat quality traits, pigs with AA genotype had higher meat color than those of BB genotype (p<0.01), and pigs with BB genotype had higher marbling than those of AA and AB genotypes (p<0.01 and p<0.05, respectively).Based on these results, it is necessary to do more studies on IGFBP-4 before using the IGFBP-4 locus for the application of marker-assisted selection programs.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.616-627
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• 2014

The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index ($F_{ST}$) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values ($F_{IS}$) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity ($H_E$) or $F_{ST}$, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, $F_{ST}$ and D-scores were used. Only 6 to 8 markers ranking $H_E$, $F_{ST}$ or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if discernible levels of co-ancestry exist. In the reference group, optimum assignment accuracy was achievable achieved through a combination of different markers by ranking the heterozygosity, $F_{ST}$ and allelic number of close lineage populations.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.6
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• pp.898-906
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• 2014

The objective of this study was to investigate differences in the faecal microbial composition among Lantang, Bama, Erhualian, Meishan, Xiaomeishan, Duroc, Landrace, and Yorkshire sows and to explore the possible link of the pig breed with the gut microbial community. Among the sows, the Meishan, Landrace, Duroc, and Yorkshire sows were from the same breeding farm with the same feed. Fresh faeces were collected from three sows of each purebred breed for microbiota analysis and volatile fatty acid (VFA) determination. Denaturing gradient gel electrophoresis (DGGE) analysis revealed that samples from Bama, Erhualian, and Xiaomeishan sows, which from different farms, were generally grouped in one cluster, with similarity higher than 67.2%, and those from Duroc, Landrace, and Yorkshire sows were grouped in another cluster. Principal component analysis of the DGGE profile showed that samples from the foreign breeds and the samples from the Chinese indigenous breeds were scattered in two different groups, irrespective of the farm origin. Faecal VFA concentrations were significantly affected by the pig breed. The proportion of acetate was higher in the Bama sows than in the other breeds. The real-time PCR analysis showed that 16S rRNA gene copies of total bacteria, Firmicutes and Bacteroidetes were significantly higher in the Bama sows compared to Xiaomeishan and Duroc sows. Both Meishan and Erhualian sows had higher numbers of total bacteria, Firmicutes, Bacteroidetes and sulphate-reducing bacteria as compared to Duroc sows. The results suggest that the pig breed affects the composition of gut microbiota. The microbial composition is different with different breeds, especially between overseas breeds (lean type) and Chinese breeds (relatively obese type).

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.7
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• pp.931-937
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• 2006

The full-length cDNA of the porcine SMPX gene was obtained by the rapid amplification of cDNA ends (RACE). The nucleotide sequences and the predicted protein sequences share high sequence identity with both human and mouse. The promoter of SMPX was sequenced and then analyzed to find the promoter binding sites. The reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that SMPX has a high level of expression in heart and skeletal muscle, a very low expression in lung and spleen and no expression in liver, kidney, fat and brain. Moreover, SMPX has a differential expression level in skeletal muscle, the expression in 65-day embryos being higher than other stages. The porcine SMPX was mapped to SSCXp24 by using a somatic cell hybrid panel (SCHP) and was found closely linked to SW1903 using the radiation hybrid panel IMpRH. An A/G single nucleotide polymorphism (PCR-RFLP) in the 3'-untranslated region (3'-UTR) was detected in eight breeds. The analysis of allele frequency distribution showed that introduced pig breeds (Duroc and Large White) have a higher frequency of allele A while in the Chinese indigenous pig breeds (Qingping pig, Lantang pig, YushanBlack pig, Large Black-White pig, Small Meishan) have a higher frequencies of allele G. The association analysis using an experimental population (188 pigs), which included two cross-bred groups and three pure-blood groups, suggested that the SNP genotype was associated with intramuscular fat content.

• Animal Bioscience
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• v.34 no.11
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• pp.1757-1765
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• 2021

Objective: The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited. Methods: Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds. Results: In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively. Conclusion: This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.

• Journal of Animal Science and Technology
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• v.48 no.5
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• pp.747-758
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• 2006

A total of 30 pigs (average 60kg) were used to investigate the influence of breeds on meat quality. Pigs were alloted into one of three experimental groups [A (Landrace×Yorkshire×Duroc), B (England Berkshire), and C (Kagoshima Berkshire)]. Pigs were slaughtered at approximately 110kg of live weight for measurement of meat qualities. Crude protein was significantly higher in B than those of other pig breed groups. Shear force value was higher and pH was lower in A than those of other pig breeds. In color, C was significantly higher in a* of meat color and lower in b* of fat color and in brittleness, hardness, springiness, chewiness as compared with other pig breeds. Essential fatty acid were significantly higher in A and lower in B than those of other pig breeds. Aspartic, threonine, serine, glutamic and phenylalanine were higher in C, whereas glycine, alanine, cystine, valine, leucine, tyrosine, histidine, lysine and arginine were significantly higher in A. In sensory evaluation of fresh meat, color was significantly higher in C. However, moisture, crude fat, crude ash and drip loss, marbling score, overall acceptability of fresh meat and all items in sensory evaluation of cooked meat were not significant difference among the pig groups. In conclusions, loin from Kagoshima Berkshire had the lowest shear force and the highest a* value. In the current study few effects of pig breeds were observed. Further studies are needed on the relationship between physico-chemical properties and the pig breeds.