• Animal Bioscience
• /
• v.36 no.10
• /
• pp.1508-1516
• /
• 2023

Objective: To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population. Methods: We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual. Results: Firstly, the results of genetic diversity analysis showed that the effective population size (N_e) of this population was 3.2, proportion of polymorphic markers (P_N) was 0.515, desired heterozygosity (H_e) and observed heterozygosity (H_o) were 0.315 and 0.335. H_o was higher than H_e, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09. Conclusion: Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.

• Animal Bioscience
• /
• v.36 no.6
• /
• pp.861-868
• /
• 2023

Objective: Loin muscle area (LMA) is an important target trait of pig breeding. This study aimed to identify single nucleotide polymorphisms (SNPs) and genes associated with LMA in the Duroc×(Landrace×Yorkshire) crossbred pigs (DLY). Methods: A genome-wide association study was performed using the Illumina 50K chip to map the genetic marker and genes associated with LMA in 511 DLY pigs (255 boars and 256 sows). Results: After quality control, we detected 35,426 SNPs, including six SNPs significantly associated with LMA in pigs, with MARC0094338 and ASGA0072817 being the two key SNPs responsible for 1.77% and 2.48% of the phenotypic variance of LMA, respectively. Based on previous research, we determined two candidate genes (growth hormone receptor [GHR] and 3-oxoacid Co A-transferase 1 [OXCT1]) that are associated with fat deposition and muscle growth and found further additional genes (MYOCD, ARHGAP44, ELAC2, MAP2K4, FBXO4, FBLL1, RARS1, SLIT3, and RANK3) that are presumed to have an effect on LMA. Conclusion: This study contributes to the identification of the mutation that underlies quantitative trait loci associated with LMA and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in LMA regulation.

• Asian-Australasian Journal of Animal Sciences
• /
• v.32 no.10
• /
• pp.1483-1490
• /
• 2019

Objective: To explore the molecular mechanisms of fat metabolism and deposition in pigs, an experiment was conducted to identify hepatic mRNAs and miRNAs expression and determine the potential interaction of them in two phenotypically extreme pig breeds. Methods: mRNA and miRNA profiling of liver from 70-day Jinhua (JH) and Landrace (LD) pigs were performed using RNA sequencing. Blood samples were taken to detect results of serum biochemistry. Bioinformatics analysis were applied to construct differentially expressed miRNA-mRNA network. Results: Serum total triiodothyronine and total thyroxine were significantly lower in Jinhua pigs, but the content of serum total cholesterol (TCH) and low-density lipoprotein cholesterol were strikingly higher. A total of 467 differentially expressed genes (DEGs) and 35 differentially expressed miRNAs (DE miRNAs) were identified between JH and LD groups. Gene ontology analysis suggested that DEGs were involved in oxidation-reduction, lipid biosynthetic and lipid metabolism process. Interaction network of DEGs and DE miRNAs were constructed, according to target prediction results. Conclusion: We generated transcriptome and miRNAome profiles of liver from JH and LD pig breeds which represent distinguishing phenotypes of growth and metabolism. The potential miRNA-mRNA interaction networks may provide a comprehensive understanding in the mechanism of lipid metabolism. These results serve as a basis for further investigation on biological functions of miRNAs in the porcine liver.

• Animal Bioscience
• /
• v.34 no.7
• /
• pp.1123-1133
• /
• 2021

Objective: Shandong indigenous pig breeds are important Chinese pig resources. Their progressive population decline in recent decades has attracted attention towards their conservation. Conservation genetics of these indigenous breeds are essential for developing a conservation and utilization scheme. Methods: A high-density single nucleotide polymorphism (HD-SNP) chip-based comparative analysis of genetic characteristics was performed for seven Shandong indigenous pig breeds in the context of five Western commercial breeds. Results: The results showed that Shandong indigenous pig breeds varied greatly in genetic diversity, effective population size, inbreeding level, and genetic distance with the Western commercial breeds. Specifically, Laiwu and Dapulian displayed low genetic diversity, and had a genetically distant relationship with the Western commercial breeds (average F statistics [F_ST] value of 0.3226 and 0.2666, respectively). Contrastingly, the other five breeds (Yantai, Licha, Yimeng, Wulain, and Heigai) displayed high genetic diversity within breed and had some extent of mixture pattern with the Western commercial breeds, especially Duroc and Landrace (F_ST values from 0.1043 to 0.2536). Furthermore, intensive gene flow was discovered among the seven Shandong indigenous breeds, particularly Wulian, Licha, and Heigai, as indicated by the large cluster formed in the principal component analysis scatterplot and small population differentiation (average of 0.1253) among them. Conclusion: Our study advances the understanding of genetic characteristics of Shandong indigenous breeds and provides essential information for developing an appropriate conservation and utilization scheme for these breeds.

• Journal of Veterinary Clinics
• /
• v.34 no.2
• /
• pp.126-131
• /
• 2017

This study investigated the incidence rate of umbilical hernia (UH) in pig farms and examined the effect of using them as breeding pigs on reproductive traits. The occurrence of UH ranged from 0.1% to 3.0% in pig farms investigated. UH pigs were found in almost all farms except for a single farm in Jeju Island. Spontaneously occurring UH pigs were selected and used for cross breeding tests. UH-related crosses and their progeny showed significant (P < 0.05) differences in gestation period, the numbers of piglets born and alive, and body weights at birth and $21^{st}$ day comparing to those of the control population. UH-related crosses showed longer gestation period, reduced numbers of piglets, and lighter body weights than those from the control population. Interestingly, reduced number of piglets was about one fourth, suggesting that UH inheritance might play a critical role as a lethal gene during embryogenesis. In addition, UH incidence rate in UH-related crosses was significantly (P < 0.05) higher than that in the control except for UH-cross3. However, in the progeny of control cross, a pig also had UH appearance, indicating that porcine UH might be inherited in recessive inheritance mode. Taken together, the results of this study indicate that UH is one of recessively inherited genetic defect that occurs at ordinary times in pig farms, suggesting that the use of UH animals as sire and/or dam may lead to economic losses due to increased gestation period, reduced numbers of piglets born and alive, and lower growth rates after birth of pigs.

• Asian-Australasian Journal of Animal Sciences
• /
• v.31 no.4
• /
• pp.480-488
• /
• 2018

Objective: Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population. Methods: We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models. Results: After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development. Conclusion: This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.

• Journal of Animal Science and Technology
• /
• v.63 no.4
• /
• pp.892-903
• /
• 2021

The objective of this study is to investigate effect of air cleaner operated during pig breeding period on stress hormones of pigs and their pork quality. The stress hormones (cortisol, epinephrine and norepinephrine) in blood sample of pigs reared in the housing rooms with or without air cleaner have been measured according to a pig's rearing stage: 0 day (farrowing), 21st day (farrowing-weaning), 70th day (weaning-nursery), 140th day (nursery-growing), and 180th day (growing-fattening). The comparison of pork quality according to the application of an air cleaner was performed through the carcass analysis of the pigs shipped from swine house. The levels of cortisol, epinephrine, and norepinephrine in pigs reared in housing rooms with and without air cleaners were found to be within the range of normal reference values. Among pork quality evaluation items, the thickness of intermuscular fat and final carcass grade of pigs raised in housing room with air cleaner was generally superior to those of pigs raised in housing room without air cleaner (p < 0.05). Based on the results obtained from this study, it is concluded that air cleaner does not have a significant effect on reducing pig stress but contributes to improving pork quality in pig breeding.

• Animal Bioscience
• /
• v.37 no.5
• /
• pp.807-816
• /
• 2024

Objective: This study aims to identify the significant regions and candidate genes of growth-related traits (adjusted backfat thickness [ABF], average daily gain [ADG], and days to 90 kg [DAYS90]) in Korean commercial GGP pig (Duroc, Landrace, and Yorkshire) populations. Methods: A genome-wide association study (GWAS) was performed using single-nucleotide polymorphism (SNP) markers for imputation to Illumina PorcineSNP60. The BayesB method was applied to calculate thresholds for the significance of SNP markers. The identified windows were considered significant if they explained ≥1% genetic variance. Results: A total of 28 window regions were related to genetic growth effects. Bayesian GWAS revealed 28 significant genetic regions including 52 informative SNPs associated with growth traits (ABF, ADG, DAYS90) in Duroc, Landrace, and Yorkshire pigs, with genetic variance ranging from 1.00% to 5.46%. Additionally, 14 candidate genes with previous functional validation were identified for these traits. Conclusion: The identified SNPs within these regions hold potential value for future marker-assisted or genomic selection in pig breeding programs. Consequently, they contribute to an improved understanding of genetic architecture and our ability to genetically enhance pigs. SNPs within the identified regions could prove valuable for future marker-assisted or genomic selection in pig breeding programs.

• Asian-Australasian Journal of Animal Sciences
• /
• v.21 no.7
• /
• pp.954-960
• /
• 2008

MiRNAs (microRNAs) are a class of small non-coding RNA molecules of ~21 nucleotides that down- regulate the expression of target genes at post-transcriptional level. In this study, we first accomplished a preliminary scan of miRNA expression using 65 and 90 day fetal pig skeletal muscle samples by microarray hybridization, and 34 miRNAs showed strong positive signals. Five of these miRNAs were selected for further investigation by real-time RT-PCR. The statistical analyses indicated that three miRNAs exhibited significant differential expression (p<0.05) during porcine muscle development from 65 to 90 days of gestation, e.g., miR-24 and miR-424 were down-regulated while miR-133a was up-regulated. Multi-tissue RT-PCR was performed to detect the expression patterns of the five miRNA precursors. The results showed that most of these precursor miRNAs were ubiquitously expressed in different porcine tissues.

• Asian-Australasian Journal of Animal Sciences
• /
• v.15 no.11
• /
• pp.1543-1545
• /
• 2002

A T$\longrightarrow$A mutation in the promoter region of porcine myostatin (MSTN) gene has been identified in our previous work. This study analyzed the associations of the myostatin genotypes (TT, TA) caused by this mutation with birth weigh in Yorkshire pigs. Data from 211 unrelated individuals were collected three times from one breeding farm. Detections of the mutation were carried out by PCR-RFLPs approach. The effects of MSTN genotypes (TT and TA) on birth weight were compared by least square means. The results showed that for birth weight of Yorkshire pigs, individuals with TA genotype were significantly higher than those with TT genotype (p<0.05), and the birth weight for pigs with TA genotype were 1.37 kg in average but only 1.25 kg for pigs with TT genotype, indicating a positive effect of birth weight for A allele.