ABSTRACT
Genetic polymorphisms within immunity-related candidate genes in pigs have been identified to control variations in immune functions and/or disease resistance. It has become necessary to evaluate the effects of other genetic markers of economically important traits prior to introducing them into marker-assisted selection programs. In this study, polymorphisms of porcine genes coding Interferon-induced Gunylate binding protein 1 (GBP1), GBP2, CD163, and CD169 were investigated for their association with growth and meat quality traits in a Korean native pig breed-Yorkshire inter-crossed F2 pig population (KY-F2). KY-F2 animals (n=346) have been successfully used for linkage mapping to identify quantitative loci that control meat quality, growth, and immunity traits. In our results, polymorphisms in genes GBP1 and GBP2 showed association with pig growth rate as well as meat quality traits such as crude fat, drip loss, and meat color (yellowness) in the KY-F2 population. The polymorphism in gene CD163 only showed association with crude fat, as a meat quality trait. CD169 gene was associated with pork tenderness. In conclusion, four immune-related genetic markers were validated for their association with growth and meat quality traits to gauge their potential use in a swine selection program. The results warrant further studies in other commercial pig populations.
Subject(s)
Animals , Carrier Proteins , Chromosome Mapping , Clinical Coding , Disease Resistance , DNA , Genetic Markers , Meat , Polymorphism, Genetic , SwineABSTRACT
One of the major problems in the modern pig industry is infectious disease. Susceptibility to infectious diseases is influenced by both constitutional (e.g. genotype, age, gender, and reproductive status) and environmental factors (e.g. nutrition, management, infections, and other forms of stress). Genetic variations within individual animals or herds can cause differences in the execution of immune functions against infectious agents in domestic pigs. The objectives of the present study were to identify genetic factor(s) responsible for piglet survival and mortality under commercial field conditions with infectious diseases as well as determine QTL regions for immune capacity in a pig reference family. Sex ratio was examined between normal grown and presumed dead groups of F2 animals generated by Korean native pigs (KNP) and Yorkshire (YS) breeds. The ratio of males was significantly higher in the presumed dead group than in the normal grown group. In order to study genetic factors associated with presumed mortality under disease outbreak, allelic frequencies of 239 single nucleotide polymorphisms (SNPs) were compared between normal grown and presumed dead groups. Exactly 22 SNPs showed significant differences in their allelic frequencies between the two groups, and four of them were validated with another commercial population divided by normal and emaciated pigs. Furthermore, the relationships between 239 SNPs and immune-related traits were studied. These results demonstrate that identification of genetic components of animal immune systems and susceptibility to infectious diseases is possible and will be useful to improve disease resistance in individuals as well as in breeding programs.
Subject(s)
Animals , Humans , Male , Breeding , Communicable Diseases , Disease Outbreaks , Disease Resistance , Genetic Variation , Genotype , Immune System , Mortality , Polymorphism, Single Nucleotide , Sex Ratio , Sus scrofa , SwineABSTRACT
Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project, few of these have been validated at large in Bos indicus breeds. We have genotyped 192 animals, representing 5 cattle populations of Ethiopia, with the Illumina Bovine 8K SNP BeadChip. These include 1 Sanga (Danakil), 3 zebu (Borana, Arsi and Ambo), and 1 zebu x Sanga intermediate (Horro) breeds. The Hanwoo (Bos taurus) was included for comparison purposes. Analysis of 7,045 SNP markers revealed that the mean minor allele frequency (MAF) was 0.23, 0.22, 0.21, 0.21, 0.23, and 0.29 for Ambo, Arsi, Borana, Danakil, Horro, and Hanwoo, respectively. Significant differences of MAF were observed between the indigenous Ethiopian cattle populations and Hanwoo breed (p or =0.10 and < or =0.5) accounted for an overall estimated 73.79% of the 7,045 SNPs. The Hanwoo displayed a higher proportion of common variant SNPs (90%). Investigation within Ethiopian cattle populations showed that on average, 16.64% of the markers were monomorphic, but in the Hanwoo breed, only 6% of the markers were monomorphic. Across the sampled Ethiopian cattle populations, the mean observed and expected heterozygosities were 0.314 and 0.313, respectively. The level of SNP variation identified in this particular study highlights that these markers can be potentially used for genetic studies in African cattle breeds.
Subject(s)
Animals , Cattle , Ethiopia , Gene Frequency , Polymorphism, Single NucleotideABSTRACT
The use of genomic information in genomic selection programs for dairy and beef cattle breeds has become a reality in recent years. In this investigation, we analyzed single-nucleotide polymorphisms (SNPs) for Hanwoo (n=50) and Holstein (n=50) breeds using the Illumina Bovine SNP50 BeadChip to facilitate genomic selection and utilization of the Hanwoo breed in Korea. Analysis of the entire genomes showed different spectra of SNP frequencies for Hanwoo and Holstein cattle. The study revealed a highly significant (p<0.001) difference between Hanwoo and Holstein cattle in minor allele frequency (MAF). The average MAFs were 0.19+/-0.16 and 0.22+/-0.16 for Hanwoo and Holstein, respectively. From the total of 52,337 SNPs that were successfully identified, about 72% and 79% were polymorphic in Hanwoos and Holsteins, respectively. Polymorphic and fixed SNPs were not distributed uniformly across the chromosomes within breeds or between the two breeds. The number of fixed SNPs on all chromosomes was higher in Hanwoo cattle, reflecting the genetic uniqueness of the Hanwoo breed. In general, the rate of polymorphisms detected in these two breeds suggests that the SNPs can be used for different applications, such as whole-genome association and comparative genetic studies, and are a helpful tool in developing breed identification genetic markers.
Subject(s)
Animals , Cattle , Gene Frequency , Genetic Markers , Genome , Korea , Polymorphism, Single NucleotideABSTRACT
The aim of the study was to investigate pig reference families, generated from Korean native pigs (KNP) that were crossed with Yorkshire (YS) breeds, which were used to evaluate genetic markers to select breeding animals with superior pork quality. A set of five candidate genes (PRKAG3, MC4R, CAST, ESR, and PRLR) was analyzed for association with pork quality traits. PRKAG3 (I199V) SNP genotypes were significantly associated with muscle moisture, protein, and fat contents. The MC4R D298N polymorphism was significantly associated with meat tenderness and color traits. The CAST polymorphism was significantly associated with muscle moisture and crude protein traits. These three genes have been associated with pork quality traits in other pig populations, and some of our results are consistent with earlier studies. In addition, two reproductive candidate genes (ESR and PRLR) did not have significant associations. These results suggest that further study is warranted to investigate and develop more DNA markers associated with pork quality in our KNP-crossed pig families.
Subject(s)
Animals , Humans , Breeding , DNA , Genetic Markers , Genotype , Meat , Muscles , Polymorphism, Single Nucleotide , SwineABSTRACT
PURPOSE: Breast cancer is one of the most frequent malignant tumors in Korea. The major tumor suppressor genes (TSGs) such as p16, Rb, E-cadherin and p53 may play important roles in cell cycle regulation, apoptosis and the regulation of the expression of other genes as well as tumor suppression. Microsatellite alteration such as loss of heterozygosity (LOH) have been reported to be a novel mechanism of carcinogenesis and a useful prognostic factor for many malignant tumors. Also, LOH is also known to be related with allelic loss of various TSGs. This study evaluated LOH of 4 TSGs in invasive ductal carcinomas (IDCs) and we correlated these results with the clinicopathological factors. METHODS: LOH analysis was carried out using a polymerase chain reaction with 12 polymorphic microsatellite markers of 4 TSGs in 50 surgically resected tumors and their non-tumorous counterparts. RESULTS: There was no detectable LOH in the normal tissue. LOH was detected in 86% of the 50 cases of IDCs. LOH was detected on all chromosomes and this showed a statistical difference between benign tumor and malignant tumor. LOH of p16, Rb, E-cadherin and p53 TSGs was detected in 36%, 26%, 54% and 60% of the tumors, respectively. LOH of the p16 and Rb genes was inversely correlated with tumor grade 1. The low rate of detecting LOH on the E-cadherin gene was noted in T1 tumor and stage I disease. LOH of the p53 gene correlated well with the tumor size and stage. The LOH-High results correlate well with the tumor size and stage and the LOH-High results are similar to those of the p53 gene LOH. CONCLUSION: These results suggest that LOH of the 4 major TSGs may contribute to the development and invasion of IDCs. Also, the combined use of various LOH markers may help in deciding the prognosis of IDCs.