• Genomics & Informatics
• /
• v.9 no.2
• /
• pp.69-73
• /
• 2011

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 $0.19{\pm}0.16$ and $0.22{\pm}0.16$ 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.

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

• Asian-Australasian Journal of Animal Sciences
• /
• v.32 no.4
• /
• pp.485-493
• /
• 2019

Objective: This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information. Methods: A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity ($H_E$), polymorphism information content, F-statistics ($F_{ST}$), linkage disequilibrium (LD) and effective population size ($N_e$). Results: The chromosome-wise distribution of $F_{ST}$ in BS, LR, and YS populations were within the range of 0-0.36, and the average $F_{ST}$ value was estimated to be $0.07{\pm}0.06$. This result indicated some level of genetic segregation. An average LD ($r^2$) for the BS, LR, and YS breeds was estimated to be approximately 0.41. This study also found an average $N_e$ of 19.9 (BS), 31.4 (LR), and 34.1 (YS) over the last 5th generations. The effective population size for the BS, LR, and YS breeds decreased at a consistent rate from 50th to 10th generations ago. With a relatively faster $N_e$ decline rate in the past 10th generations, there exists possible evidence for intensive selection practices in pigs in the recent past. Conclusion: To develop customized chips for the genomic selection of various breeds, it is important to select and utilize SNP based on the genetic characteristics of each breed. Since the improvement efficiency of breed pigs increases sharply by the population size, it is important to increase test units for the improvement and it is desirable to establish the pig improvement network system to expand the unit of breed pig improvement through the genetic connection among breed pig farms.

• Journal of Animal Science and Technology
• /
• v.64 no.6
• /
• pp.1215-1225
• /
• 2022

The epidemiology of parasite infection in local and imported breeds is quite an essential topic in the meat industry and human health. This study aims to determine the prevalence of Dicrocoelium dendriticum in local sheep breeds (Naemi, Najdi, and Harri) and imported breeds from Romania (Romani breed) and the epidemiology of the infection in Saudi Arabia. Morphological description, the relationship between dicrocoeliasis and sex, age, and histological changes were also presented. A total of 6845 slaughtered sheep at Riyadh Automated slaughterhouse were investigated and followed up for 4 months between 2020-2021. It included 4,680 local breeds and 2,165 imported Romanian breeds. Fecal samples and livers and gallbladders from slaughtered animals were examined for apparent pathological lesions. The results indicated that the infection rate in slaughtered animals was 10.6% in imported Romani sheep and 0.9% in the local Naeimi breed. After identifying the parasite morphologically, negative results were obtained from examining feces, gallbladders, and livers of Najdi and Harry sheep breeds. The mean number of eggs per 20 µL/gallbladder was low (72.78 ± 17.8: 76.11 ± 5.07), medium (334.59 ± 90.6: 292.91 ± 26.63), and high (1113.2 ± 22.3: 1004 ± 143.4) in imported and Naeime sheep, respectively. Significant differences were found between gender and age (males and females were 3.67% and 6.31%; > 2 years 4.39%, 1-2 years 4.22%, and 1 year 3.53%) respectively. Histopathological lesions in the liver were more pronounced. Our survey confirmed the presence of D. dendriticum in imported Romani and local Naeimi sheep, and the potential role of imported sheep in the epidemiology of dicrocoeliasis in Saudi Arabia.

• Journal of Animal Science and Technology
• /
• v.64 no.6
• /
• pp.1226-1236
• /
• 2022

Mongolian horses are one of the oldest horse breeds, and are very important livestock in Mongolia as they are used in various fields such as transportation, food (milk, meat), and horse racing. In addition, research and preservation on pure Mongolian breeds are being promoted under the implementation of the new Genetics of Livestock Resources' act in Mongolia. However, despite the implementation of this act, genetic research on Mongolian horses using microsatellites (MS) has not progressed enough. Therefore, this study was conducted to analyze the genetic polymorphism of five breeds (Gobi shankh, Tes, Gal shar, Darkhad, and Undurshil) using 14 MS markers recommended by International Society for Animal Genetics (ISAG). The mean number of alleles (MNA) was 8.29, expected heterozygosity frequency (H_Exp) was 0.767, observed heterozygosity frequency (H_Obs) was 0.752, and polymorphism information content (PIC) was 0.729. The Nei's genetic distance analysis showed that the genetic distance between Gobi shankh and Darkhad horses was the farthest, and the other three breeds, Tes, Gal shar, and Undurshil were found to be close to each other. Similarly, the principal coordinate analysis (PCoA) and factorial correspondence analysis (FCA) showed that the Gobi shankh and Darkhad horses were genetically distinct from other breeds. On the other hand, it appears that Tes, Gal shar, and Undurshil horses, which are genetically similar, most likely interbred with each other. Therefore, it is expected that these results will help the conservation of genetic resources in Mongolia and the establishment of policies related to Mongolian horses.

• Korean Journal of Veterinary Service
• /
• v.45 no.4
• /
• pp.269-275
• /
• 2022

Blood type in dogs is based on the antigen present on the red blood cell surface. Dog erythrocyte antigen 1 is a crucial red blood cell antigen in dogs, whereas the dog erythrocyte antigen 7 has been studied in limited dog breeds worldwide. To assess the prevalence of dog erythrocyte antigens 1 and 7 in 11 breeds in the Republic of Korea, 624 dog blood samples were examined for antigen detection. Overall, 520 dogs (83.3%) showed dog erythrocyte antigen 1 expression. The distribution varied from 50.0~100.0% according to the breed. Dog erythrocyte antigen 1-positive blood type was the highest in Chihuahua (100%), followed by Jindo dog (98.5%), and Sapsaree (95.3%). Dog erythrocyte antigen 7 was positive in 125 dogs (20.0%), and the positivity varied from 5.0~42.9% according to the breed. Dog erythrocyte antigen 7-positive blood type was the highest in Beagle (42.9%), followed by Chihuahua (37.5%), and Jindo dog (27.8%). The high prevalence of dog erythrocyte antigen 1 is because of the high proportion of Jindo dog and Sapsaree breeds that were mostly positive for the antigen. The high abundance of these breeds could be due to inbreeding and local breeding in the Republic of Korea. To our best knowledge, this study is the first to report on the prevalence of dog erythrocyte antigens 1 and 7 among various canine breeds in the Republic of Korea. The prevalence data obtained from this study may contribute to baseline information on veterinary transfusion medicine in small animal practice.

• Asian-Australasian Journal of Animal Sciences
• /
• v.17 no.9
• /
• pp.1204-1209
• /
• 2004

Random amplification of polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) analysis was carried out using DNA samples of 30 animals of Rathi cattle and 42 animals of Tharparkar cattle. Genomic DNA was isolated as per standard protocol and evaluated for its quality, purity and concentration. Twenty three random primers were screened out of which 15 primers yielded satisfactory amplifications and were used for further analysis. Average numbers of polymorphic fragments per primer were 7.07${\pm}$0.86 in Rathi and 6.80${\pm}$0.61 in Tharparkar cattle. The percentage of polymorphic bands in these two cattle breeds were 86 and 87%, respectively. Within breed genetic similarities for pooled over primers in the animals of Rathi and Tharparkar breeds were .577${\pm}$0.30 and 0.531${\pm}$0.02, respectively on the basis of band frequency (BF) and 0.645${\pm}$0.04 and 0.534${\pm}$0.04, respectively on the basis of band sharing (BS). Averages of between breed genetic similarities for pooled over primers were 0.97 and 0.92 according to BF and BS, respectively, which reflect higher degree of genetic similarity between Rathi and Tharparkar cattle breeds. Index of genetic distance based on BF and BS for pooled over primers was 0.030${\pm}$0.011 and 0.088${\pm}$0.031, respectively. Percentage of polymorphic bands and within-breed genetic similarities on the basis of band frequency (BF) and band sharing (BS) for pooled over primers revealed higher genetic similarity in Rathi than Tharparkar cattle population. High estimates of between breed genetic similarities for pooled over primers indicated that either Rathi is having decent from Tharparkar or both the cattle breeds are having common descent. Low value of Index of genetic distances between these two cattle breeds may be due to the fact that Rathi and Tharparkar cattle breeds are the native of Thar Desert in Northwest India. The results of between breed genetic distances also confirm the existence of high degree of genetic similarity between these two breeds of cattle.

• Journal of Animal Science and Technology
• /
• v.47 no.3
• /
• pp.341-354
• /
• 2005

For the genetic assessment of the cattle breeds including Hanwoo, eleven microsatellite markers on ten bovine autosomes were genetically characterized for 618 individuals of nineteen cattle breeds; North Eastern Asian breeds (Korean cattle, Korean Black cattle, Japanese Black cattle, Japanese Brown cattle, Yanbian cattle), Chinese yellow cattle (Luxi cattle, Nanyang cattle), European Bas taurus (Angus, Hereford, Charolais, Holstein, Limousin), African Bas taurus (N'Dama, Baoule), African Bas indicus (Kavirondo Zebu, White Fulani), Asian Bas indicus (Sahiwal, Nelore) and one Bali cattle, Bas banteng as an outbreed-reference population. Allele frequencies derived from the genotyping data were used in estimating heterozygosities, gene diversities and genetic distances. The microsatellite loci were highly polymorphic, with a total of 162 different alleles observed across all loci. Variability in allele numbers and frequencies was observed among the breeds. The average expected heterozygosity of North Eastern Asian breeds was higher than those of European and African taurines, but lower than those of Asian and African indicines. Genetic distances were estimated using Nei's DA genetic distance and the resultant DA matrix was used in the construction of the phylogenetic trees. The genetic distances between North Eastern Asian cattle breeds and Bas indicus were similar with those between European Bas taurus and Bas indicus, and African Bas taurus and Bas indicus, respectively. The clusters were clearly classified into North Eastern Asian, European and African taurines groups as well as different cluster with Chinese mainland breeds, firstly out-grouping with Bas indicus. These results suggest that Korean cattle, Hanwoo, had not been originated from a crossbred between Bas primigenius in Europe and Bas indicus in India and North Eastern Asian Bas taurus may be have separate domestication from European and African Bas taurus.

• Journal of Animal Science and Technology
• /
• v.55 no.5
• /
• pp.467-473
• /
• 2013

This study compared the pork quality and muscle fiber characteristics between the Jeju black pig (JBP) and domesticated pig breeds, including three-way crossbred (Landrace ${\times}$ Yorkshire ${\times}$ Duroc, LYD), Berkshire (B), Duroc (D), Landrace (L), Meishan (M), and Yorkshire (Y) pigs. JBP had the lowest carcass weight among the pig breeds (p<0.05) and its NPPC marbling score was lower than the other domesticated pig breeds (p<0.05), except for M. M had the highest value for backfat thickness among the pig breeds (p<0.05), whereas its NPPC marbling score was the lowest (p<0.05). The pH values were higher in JBP and B at 45 min and 24 h postmortem, respectively, but LYD and M had the lowest pH values at 45 min and 24 h postmortem, respectively (p<0.05). M had a higher lightness and lower redness than the other breeds (p<0.05). Moreover, M had the highest drip loss among the pig breeds (p<0.05), whereas D had the lowest drip loss and the highest redness (p<0.05). In terms of muscle fiber characteristics, JBP and LYD had the largest type IIB fibers (p<0.05). The fiber number and area composition of type I fibers were higher in JBP than the others (p<0.05) however type IIA fibers were lowest in JBP among the pig breeds (p<0.05). Overall, our results indicate that JBP provided better pork quality compared with M, but the carcass trait and pork quality of JBP were not better than LYD and D, respectively.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.7
• /
• pp.1023-1029
• /
• 2007

Inhibins participate in the regulation of pituitary follicle-stimulating hormone synthesis and secretion, follicular maturation and steroidogenesis in the female. Inhibin ${\beta}_A$ gene (INHBA) was studied as a candidate gene for the prolificacy of sheep. Single nucleotide polymorphisms of the entire coding region and partial 3' untranslated region of INHBA were detected by PCR-SSCP in two high fecundity breeds (Small Tail Han and Hu sheep) and six low fecundity breeds (Dorset, Texel, German Mutton Merino, South African Mutton Merino, Chinese Merino and Corriedale sheep). Only the PCR products amplified by primers 3, 4 and 5 displayed polymorphisms. For primer 3, genotype CC was only detected in Chinese Merino sheep, genotype AA was detected in the other seven sheep breeds. Genotype BB was only detected in Hu sheep. Only Hu sheep displayed polymorphism. Eight or four nucleotide mutations were revealed between BB or CC and AA, respectively, and these mutations did not result in any amino acid change. For primer 4, genotypes EE, EG and GG were detected in Dorset and German Mutton Merino sheep, genotypes EE, EF and FF were detected in Chinese Merino sheep, only genotype EE was detected in the other five sheep breeds. Only Dorset, German Mutton Merino and Chinese Merino sheep displayed polymorphism. Sequencing revealed one nucleotide mutation ($114G{\rightarrow}A$) of exon 2 of INHBA gene between genotype FF and genotype EE, and this mutation did not cause any amino acid change. Another nucleotide change ($143C{\rightarrow}T$) was identified between genotype GG and genotype EE, and this mutation resulted in an amino acid change of $serine{\rightarrow}leucine$. For primer 5, genotypes KK and KL were detected in German Mutton Merino and Corriedale sheep, genotypes KK, LL and KL were detected in the other six sheep breeds. Genotype MM was only detected in Hu sheep. All of these eight sheep breeds displayed polymorphism. Sequencing revealed one nucleotide mutation ($218A{\rightarrow}G$) of exon 2 of the INHBA gene between genotype LL and genotype KK, and nine nucleotide mutations between genotype MM and genotype KK. These mutations did not alter amino acid sequence. The partial sequence (395 bp for exon 1 and 933 bp for exon 2) of the INHBA gene in Small Tail Han sheep (with genotype KK for primer 5) was submitted into GenBank (accession number EF192431). Small Tail Han sheep displayed polymorphisms only in the fragment amplified by primer 5. The Small Tail Han ewes with genotype LL had 0.53 (p<0.05) or 0.63 (p<0.05) more lambs than those with genotype KL or KK, respectively. The Small Tail Han ewes with genotype KL had 0.10 (p>0.05) more lambs than those with genotype KK.