• Animal Bioscience
• /
• v.34 no.12
• /
• pp.1895-1902
• /
• 2021

Objective: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods: In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results: In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (F_ROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion: This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.7
• /
• pp.938-943
• /
• 2017

Objective: Qingyu pig, a Chinese indigenous pig breed, exhibits two types of coat colour phenotypes, including pure black and white with black spotting respectively. Melanocortin receptor 1 (MC1R) and agouti signaling protein (ASIP) are two widely reported pivotal genes that significantly affect the regulation of coat colour. The objectives of this study were to investigate whether the polymorphisms of these two genes are associated with coat colour and analyze the molecular mechanism of the coat colour separation in Qingyu pig. Methods: We studied the phenotype segregation and used polymerase chain reaction amplification and Sanger sequencing to investigate the polymorphism of MC1R and ASIP in 121 Qingyu pigs, consisting of 115 black and 6 white with black spotted pigs. Results: Coat colour of Qingyu pig is associated with the polymorphisms of MC1R but not ASIP. We only found 2 haplotypes, $E^{QY}$ and $E^{qy}$, based on the 13 observed mutations from MC1R gene. Among which, $E^{qy}$ presented a recessive inheritance mode in black spotted Qingyu pigs. Further analysis revealed a g.462-463CC insertion that caused a frameshift mutation and a premature stop codon, thus changed the first transmembrane domain completely and lost the remaining six transmembrane domains. Altogether, our results strongly support that the variety of Qingyu pig's coat colour is related to MC1R. Conclusion: Our findings indicated that black coat colour in Qingyu pig was dominant to white with black spotted phenotype and MC1R gene polymorphism was associated with coat colour separation in Qingyu pig.

• Asian-Australasian Journal of Animal Sciences
• /
• v.29 no.3
• /
• pp.321-326
• /
• 2016

The porcine major histocompatibility complex (MHC) is called swine leukocyte antigen (SLA), which controls immune responses and transplantation reactions. The SLA is mapped on pig chromosome 7 (SSC7) near the centromere. In this study, 3 class I (SLA-1, SLA-3, and SLA-2) and 3 class II (DRB1, DQB1, and DQA) genes were used for investigation of SLA haplotypes in Yucatan miniature pigs in Korea. This pig breed is a well-known model organism for biomedical research worldwide. The current study indicated that Korean Yucatan pig population had 3 Class I haplotypes (Lr-4.0, Lr-6.0, and Lr-25.0) and 3 class II haplotypes (Lr-0.5, Lr-0.7, and Lr-0.25). The combinations of SLA class I and II haplotype together, 2 homozygous (Lr-4.5/4.5 and Lr-6.7/6.7) and 3 heterozygous (Lr-4.5/6.7, Lr-4.5/25.25, and Lr-6.7/25.25) haplotypes were identified, including previously unidentified new heterozygous haplotypes (Lr-4.5/4.7). In addition, a new SLA allele typing method using Agilent 2100 bioanalyzer was developed that permitted more rapid identification of SLA haplotypes. These results will facilitate the breeding of SLA homozygous Yucatan pigs and will expedite the possible use of these pigs for the biomedical research, especially xenotransplantation research.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.5
• /
• pp.669-676
• /
• 2007

This study was conducted to detect quantitative trait loci (QTL) affecting growth and body composition in an $F_2$ reference population of Korean native pig and Landrace crossbreds. The three-generation mapping population was generated with 411 progeny from 38 $F_2$ full-sib families, and 133 genetic markers were used to produce a sex-average map of the 18 autosomes. The data set was analyzed using least squares Mendelian and parent-of-origin interval-mapping models. Lack-of-fit tests between the models were used to characterize QTL for mode of expressions. A total of 8 (39) QTL were detected at the 5% genome (chromosome)-wise level for the 17 analyzed traits. Of the 47 QTL detected, 21 QTL were classified as Mendelian expressed, 13 QTL as paternally expressed, 6 QTL as maternally expressed, and 7 QTL as partially expressed. Of the detected QTL at 5% genome-wise level, two QTL had Mendelian mode of inheritance on SSC6 and SSC9 for backfat thickness and bone weight, respectively, two QTL were maternally expressed for leather weight and front leg weight on SSC6 and SSC12, respectively, one QTL was paternally expressed for birth weight on SSC4, and three QTL were partially expressed for hot carcass weight and rear leg weight on SSC6, and bone weight on SSC13. Many of the Mendelian QTL had a dominant (complete or overdominant) mode of gene action, and only a few of the QTL were primarily additive, which reflects that heterosis for growth is appreciable in a cross between Korean native pig and Landrace. Our results indicate that alternate breed alleles of growth and body composition QTL are segregating between the two breeds, which could be utilized for genetic improvement of growth via marker-assisted selection.

• Food Science of Animal Resources
• /
• v.31 no.3
• /
• pp.356-365
• /
• 2011

We assessed the effects of single-nucleotide polymorphisms (SNPs) within the porcine fatty acid synthase (FASN) gene regarding meat quality and fatty acid composition in two pig populations: Korean native pigs (KNP) were crossed with Yorkshire (YS) $F_2$, and KNP were crossed with Landrace (LR) $F_2$. Direct DNA sequencing using eight KNP and eight YS pigs revealed two SNPs: c.265C>T (silent) in exon 4 and c.6545A>C (Asn${\rightarrow}$His) in exon 39. The frequency of the two SNPs was analyzed using the polymerase chain reaction-restriction fragment length polymorphism method in seven pig breeds and their association with meat quality traits and fatty acid composition was studied. In the $KNP{\times}YSF_2$ population, both SNPs were significantly associated with the level of monounsaturated fatty acids, including palmitoleic (C16:1) and oleic acid (C18:1) (p<0.005). c.6545A>C was associated with intramuscular fat content in both populations. Our results indicate that variations in c.265C>T and c.6545A>C of the pig FASN can be used to select animals with better fatty acid composition and meat quality. Moreover, KNP was a useful breed for identifying genetic factors affecting meat quality and fatty acid composition and for producing high quality pork.

• Journal of Animal Science and Technology
• /
• v.66 no.2
• /
• pp.366-373
• /
• 2024

This study aims to estimate the connectedness rating (CR) of Korean swine breeding herds. Using 104,380 performance and 83,200 reproduction records from three swine breeds (Yorkshire, Landrace and Duroc), the CR was estimated for two traits: average daily gain (ADG) and number born alive (NBA) in eight breeding herds in the Republic of Korea (hereafter, Korea). The average CR for ADG in the Yorkshire breed ranges from 1.32% to 28.5% depending on the farm. The average CR for NBA in the Yorkshire herd ranges from 0% to 12.79%. A total of 60% of Yorkshire and Duroc herds satisfied the preconditions suggested for genetic evaluation among the herds. The precondition for the genetic evaluation of CR for ADG, as a productive trait, was higher than 3% and that of NBA, as a reproductive trait, was higher than 1.5%. The ADG in the Yorkshire herds showed the highest average CR. However, the average CR of ADG in the Landrace herds was lower than the criterion of the precondition. The prediction error variance of the difference (PEVD) was employed to assess the validation of the CR, as PEVDs exhibit fluctuations that are coupled with the CR across the herds. A certain degree of connectedness is essential to estimate breeding value comparisons between pig herds. This study suggests that it is possible to evaluate the genetic performance together for ADG and NBA in the Yorkshire herds since the preconditions were satisfied for these four herds. It is also possible to perform a joint genetic analysis of the ADG records of all Duroc herds since the preconditions were also satisfied. This study provides new insight into understanding the genetic connectedness of Korean pig breeding herds. CR could be utilized to accelerate the genetic progress of Korean pig breeding herds.

• Journal of Animal Science and Technology
• /
• v.53 no.1
• /
• pp.35-42
• /
• 2011

The study was conducted to select and optimize microsatellite (MS) markers for evaluation of Korean native pig (KNP) populations in order to provide standard for the classification and breed definition of the indigenous breeds. The study also aimed to characterize and classify each KNP populations. A total of 648 pigs from 17 pig populations including six KNP, four Chinese native pig and four commercial pig populations were analyzed with 26 MS markers. KNP populations formed separate cluster from those of Chinese native pig and introduced pig populations. Expected heterozygosity (He) of KNP populations were 0.48~0.55 except two populations with 0.65. Genetic distances between KNP populations were relatively shorter: 0.12-0.34. Among six KNP populations, three showed high genetic uniformity, two showed lower uniformity and one showed high level of impurity and heterozygosity. The results can be used to evaluate and manage animal genetic resources at national scale.

• Asian-Australasian Journal of Animal Sciences
• /
• v.21 no.2
• /
• pp.245-251
• /
• 2008

The effects of feeding diets containing 20% (L) or 30% (H) neutral detergent fiber (NDF) (DM basis) on performance and carcass traits were studied in three breeds of pig, including pure Mong Cai (MC), crossbred Landrace$\times$Yorkshire (LY) and crossbred MC$\times$Yorkshire (F1). The experiment had a factorial design with two factors, breed and diet. Eighteen piglets of each breed ($60{\pm}3days$) were randomly allocated to three treatments: L-L, low fiber diet in both growing and finishing periods; L-H, low and high fiber diet in the growing and finishing period, respectively; and H-H, high fiber diet in both periods. The diets were iso-energetic and iso-nitrogenous within feeding period. The main fibrous ingredients of the diets were rice bran and cassava residue. There were no effects of fiber level on daily dry matter feed intake (DMI), expressed as g/kg metabolic body weight (BW0.75), in both feeding periods (p>0.05). DMI was highest for MC, followed by F1 and LY (p<0.001). Average daily gain (ADG) in L-L and L-H was higher than in H-H in the growing period (p<0.001) and overall (p<0.05), while feed conversion ratio (FCR) was higher in H-H than in L-L and L-H in the growing period (p<0.05) and overall, but no significant differences between treatments were found in the finishing period. In both periods, Landrace$\times$Yorkshire had the highest ADG and the lowest FCR, followed by F1 and Mong Cai (p<0.001). There were no interactions between breed and diet for performance and carcass traits. Carcass and dressing percentage was lower for L-H and H-H than for L-L (p<0.05). There were no significant differences among treatments in back fat thickness and lean meat percentage, or in crude protein and ether extract contents of lean meat. Carcass, dressing and lean meat percentage was highest for LY, lowest for MC and intermediate for F1 (p<0.001). It can be concluded that feeding a high fiber diet in the growing period reduced pig performance, but there was no effect in the finishing period. Pure Mong Cai pigs are not particularly suitable for meat purposes, although the F1 cross with Large White had reasonably good growth performance and carcass quality.

• Animal Bioscience
• /
• v.34 no.7
• /
• pp.1105-1115
• /
• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Journal of agriculture & life science
• /
• v.44 no.1
• /
• pp.33-42
• /
• 2010

This study was conducted to estimate the effects of breed, sex, Farm-Scale and environment on average daily gain, age at 90kg, backfat thickness, eye muscle area and lean percent of pig. The total number of pig used in this study was 30,525 head consisted of 5,902 Landrace, 18,022 Yorkshire, and 6,601 Duroc on 2004 to 2008. The covariance used in the model to adjust age at the final test. The average daily gain, age at 90kg, and lean percent were significantly superior in medium Farm-Scale. However Backfat thickness and Eye muscle Area were significantly superior in small Farm-Scale. In conclusion this study suggest that breed, sex, test year, test season, Farm-Scale and environment may affect to average daily gain, age at 90kg, backfat thickness, eye muscle area and lean percent. The study about the Farm-Scale has to do continually more than now, and this study will be contributed to development of the pig industry.