• 한국축산식품학회지
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• 제30권6호
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• pp.918-922
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• 2010

Due to the large amount of beef imported from the USA to Korea, Korean consumers have become increasingly interested in the country of origin since it can affect market prices. Previously, Bos indicus and Bos taurus-specific markers were developed for the purpose of cattle breed identification, specifically discrimination of Australian beef. In this study, six SNP markers derived from Illumina 50K bovine SNP chip data were used for the discrimination between Korean cattle (Hanwoo) and imported beef from USA. PCR-RFLP genotyping methods were also developed, which indicates that these markers can be applied relatively easily compared to other markers. Taking into account a discrimination rate of 55% based on MC1R marker between Hanwoo and imported beef from USA, two additional markers, SNPs 23803 and 34776, were ideal and resulted in probability of identification of 0.942 and probability of misjudgment of 0.03. Therefore, the markers developed in this study can greatly contribute to the correct discrimination between beef from USA and Hanwoo beef.

• Journal of Animal Science and Technology
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• 제60권12호
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• pp.31.1-31.10
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• 2018

Background: Research on loci influencing milk production traits of dairy cattle is one of the main topics of investigation in livestock. Many genomic regions and polymorphisms associated with dairy production have been reported worldwide. In this context, the purpose of this study was to identify candidate loci associated with milk yield in Argentinean dairy cattle. A database of candidate genes and single nucleotide polymorphisms (SNPs) for milk production and composition was developed. Thirty-nine SNPs belonging to 22 candidate genes were genotyped on 1643 animals (Holstein and Holstein x Jersey). The genotypes obtained were subjected to association studies considering the whole population and discriminating the population by Holstein breed percentage. Phenotypic data consisted of milk production values recorded during the first lactation of 1156 Holstein and 462 Holstein ${\times}$ Jersey cows from 18 dairy farms located in the central dairy area of Argentina. From these records, 305-day cumulative milk production values were predicted. Results: Eight SNPs (rs43375517, rs29004488, rs132812135, rs137651874, rs109191047, rs135164815, rs43706485, and rs41255693), located on six Bos taurus autosomes (BTA4, BTA6, BTA19, BTA20, BTA22, and BTA26), showed suggestive associations with 305-day cumulative milk production (under Benjamini-Hochberg procedure with a false discovery rate of 0.1). Two of those SNPs (rs43375517 and rs135164815) were significantly associated with milk production (Bonferroni adjusted p-values < 0.05) when considering the Holstein population. Conclusions: The results obtained are consistent with previously reported associations in other Holstein populations. Furthermore, the SNPs found to influence bovine milk production in this study may be used as possible candidate SNPs for marker-assisted selection programs in Argentinean dairy cattle.

• Animal Bioscience
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• 제34권4호
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• pp.499-505
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• 2021

Objective: The objective of this study was to evaluate the genetic behavior of a population of Holstein cattle in response to the variation of environmental temperature by analyzing the effects of genotype by environment interaction (GEI) through reaction norms for the somatic cell score (SCS). Methods: Data was collected for 67,206 primiparous cows from the database of the Paraná Holstein Breeders Association in Brazil, with the aim of evaluating the temperature effect, considered as an environmental variable, distinguished under six gradients, with the variation range found being 17℃ to 19.5℃, over the region. A reaction norm model was adopted utilizing the fourth order under the Legendre polynomials, using the mixed models of analysis by the restricted maximum likelihood method by the WOMBAT software. Additionally, the genetic behavior of the 15 most representative bulls was assessed, in response to the changes in the temperature gradient. Results: A mean score of 2.66 and a heritability variation from 0.17 to 0.23 was found in the regional temperature increase. The correlation between the environmental gradients proved to be higher than 0.80. Distinctive genetic behaviors were observed according to the increase in regional temperature, with an observed increase of up to 0.258 in the breeding values of some animals, as well as a reduction in the breeding of up to 0.793, with occasional reclassifications being observed as the temperature increased. Conclusion: Non-relevant GEI for SCS were observed in Holstein cattle herds of southern Brazil. Thus, the inclusion of the temperature effect in the model of genetic evaluation of SCS for the southern Brazilian Holstein breed is not required.

• Animal Bioscience
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• 제36권1호
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• pp.19-28
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• 2023

Objective: The objective of this study was to perform genome (genome wide association studies [GWAS]) and chromosome (CWAS) wide association analyses to identify single nucleotide polymorphisms (SNPs) associated with growth traits in registered Simmental and Simbrah cattle. Methods: The phenotypes were deregressed BLUP EBVs for birth weight, weaning weight direct, weaning weight maternal, and yearling weight. The genotyping was performed with the GGP Bovine 150k chip. After the quality control analysis, 105,129 autosomal SNP from 967 animals (473 Simmental and 494 Simbrah) were used to carry out genotype association tests. The two association analyses were performed per breed and using combined information of the two breeds. The SNP associated with growth traits were mapped to their corresponding genes at 100 kb on either side. Results: A difference in magnitude of posterior probabilities was found across breeds between genome and chromosome wide association analyses. A total of 110, 143, and 302 SNP were associated with GWAS and CWAS for growth traits in the Simmental-, Simbrah- and joint -data analyses, respectively. It stands out from the enrichment analysis of the pathways for RNA polymerase (POLR2G, POLR3E) and GABAergic synapse (GABRR1, GABRR3) for Simmental cattle and p53 signaling pathway (BID, SERPINB5) for Simbrah cattle. Conclusion: Only 6,265% of the markers associated with growth traits were found using CWAS and GWAS. The associated markers using the CWAS analysis, which were not associated using the GWAS, represents information that due to the model and priors was not associated with the traits.

• Animal Bioscience
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• 제36권3호
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• pp.506-520
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• 2023

Objective: Japanese Brown (JBR) cattle, especially the Kochi (Tosa) pedigree (JBRT), is a local breed of moderately marbled beef. Despite the increasing demand, the interbreed differences in muscle metabolites from the highly marbled Japanese Black (JBL) beef remain poorly understood. We aimed to determine flavor-related metabolites and postmortem metabolisms characteristic to JBRT beef in comparison with JBL beef. Methods: Lean portions of the longissimus thoracis (loin) muscle from four JBRT cattle were collected at 0, 1, and 14 d postmortem. The muscle metabolomic profiles were analyzed using capillary electrophoresis time-of-flight mass spectrometry. The difference in post-mortem metabolisms and aged muscle metabolites were analyzed by statistical and bioinformatic analyses between JBRT (n = 12) and JBL cattle (n = 6). Results: A total of 240 metabolite annotations were obtained from the detected signals of the JBRT muscle samples. Principal component analysis separated the beef samples into three different aging point groups. According to metabolite set enrichment analysis, post-mortem metabolic changes were associated with the metabolism of pyrimidine, nicotinate and nicotinamide, purine, pyruvate, thiamine, amino sugar, and fatty acid; citric acid cycle; and pentose phosphate pathway as well as various amino acids and mitochondrial fatty acid metabolism. The aged JBRT beef showed higher ultimate pH and lower lactate content than aged JBL beef, suggesting the lower glycolytic activity in postmortem JBRT muscle. JBRT beef was distinguished from JBL beef by significantly different compounds, including choline, amino acids, uridine monophosphate, inosine 5'-monophosphate, fructose 1,6-diphosphate, and betaine, suggesting interbreed differences in the accumulation of nucleotide monophosphate, glutathione metabolism, and phospholipid metabolism. Conclusion: Glycolysis, purine metabolism, fatty acid catabolism, and protein degradation were the most common pathways in beef during postmortem aging. The differentially expressed metabolites and the relevant metabolisms in JBRT beef may contribute to the development of a characteristic flavor.

• 농업과학연구
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• 제33권1호
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• pp.1-10
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• 2006

본 연구는 개발된 품종 특이적인 DNA 표지인자를 이용하여 한우와 비한우의 고기를 판별하고자 하였다. 한우와 유럽종 고기소들의 유전적 차이를 Random amplified polymorphic DNA(RAPD) 분석으로 조사한 바, 홀스타인, 헤어포드, 에버딘엥거스, 리모진 및 시멘탈과 같은 한우가 아닌 유럽 종들의 RAPD 패턴들은 동일하였으나, 한우는 이들과 다른 패턴을 보였다. 한우는 유럽종들에서 모두 검출된 특정의 밴드가 발견되지 않았다. 1.4Kbp인 밴드는 한우와 수입소 고기를 판별해 낼 수 있는 유용한 DNA 표지인자로 인정되었다. 실제로, 한우 673 마리, 홀스타인 141 마리의 혈액시료 및 수입육 115의 고기시료를 가지고 시행한 실험에서 그 DNA 표지인자는 비한우에서는 256두 중 245두에서 검출되었으나, 한우에서는 673두 중 644두의 시료에서 검출되지 않아서, 비한우의 검출율은 95%, 한우의 비검출율은 96%를 보였다. 이러한 결과는 그 DNA 표지인자를 이용하여 한우와 비한우 고기를 판별할 수 있음을 시사하였다. 그러나 두 품종 사이의 교잡종은 한우나 비한우의 RAPD 패턴 중에서 한 가지를 무원칙하게 선택하여 나타내고 있으므로, 이러한 DNA 표지인자만으로서는 판별하기가 어려웠다.

• Animal Bioscience
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• 제37권5호
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• pp.795-806
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• 2024

Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (N_e) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of N_e and LD for the long-term sustainability of these breeds. Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes. Results: The average LD between single nucleotide polymorphisms (SNPs) was r² = 0.13 in the present study. LD decay (r² = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based N_e of KF was determined to be 78, while the N_e estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for N_e estimation), respectively. Conclusion: KF cattle have an N_e exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for long-term sustainable development.

• 한국수정란이식학회지
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• 제23권3호
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• pp.203-209
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• 2008

To estimate the genetic characteristics and cumulative power of discrimination (CPD) existing among Hanwoo (Korean cattle) and exotic foreign population (Angus, Herford, Charolais, Holstein) we used a total of 414 genomic DNAs from five breeds population (Hanwoo, Angus, Hereford, Charolais, Holstein). Genetic characteristics indices including mean allele number among loci, unbiased heterozygosity ($h_i$) within locus and polymorphic information content (PIC) and unbiased average heterozygosity (H) among loci in four breeds were calculated using the generated allele frequencies by each marker. The mean allele numbers for all loci ranged between 5 and 7 while heterozygosity (H) ranged from 0.75 (HW) to 0.64 (HF) among loci and across breeds heterozygosity (H) was 0.69. The generated unbiased average heterozygosity among loci in each breed was integrated to the global formula of CPD resulting in 99.71 % within the populations. The genetic variation of HW (Hanwoo) showed highest estimates among the analyzed breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제9권4호
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• pp.363-370
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• 1996

The effect of breeding length of sire on genetic progress was examined in the Holstein dairy cattle population in Japan. Genetic progress was extimated by gene flow method. Breeding length of sires directly influences the replacement rates of sires and the selection intensity of sires because there are a fixed number of progeny tested young bulls per year. As breeding length of sires increased, rate of gene flow decreased and average proportions of genes deriving from selected animals had lower asymptotic values. When breeding length was short, average proportions of genes required a longer period to converge to asymptotic values. Changes of Rcow-sire's(sire to breed recorded cows) and Ncow-sire's(sire to breed non recorded cows) breeding length influenced not only transmission of their genes but also that of genes derived from all other selected animals. Irrespective of whether the discount rate was assumed to be 0 or 6%, longer term (${\geq}$ 20 years) expected total genetic improvement was maximized by a sire breeding length of five years. For shorter term assessment(10 years), genetic improvement was maximized by a sire breeding length of three years. There was a linear increase in the contribution of the sire to bulls pathway to the total genetic improvement, with increase in the term of assessment.

• Asian-Australasian Journal of Animal Sciences
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• 제19권11호
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• pp.1556-1560
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• 2006

Six breeds of riverine buffalo viz. Murrah, Mehsana, Jaffrabadi, Nagpuri, Nili-Ravi and Bhadawari were characterized using FAO-recommended cattle specific microsatellite markers. Among the total of twenty microsatellite markers screened to explore genomic variability of six buffalo breeds, only ten were polymorphic in nature. Four out of ten polymorphic microsatellite loci were rated as informative. The numbers of alleles detected ranged from 2 to 7, with a mean of $5.5{\pm}0.07$ per microsatellite marker. The most polymorphic marker was BM1818 with a total of 7 alleles present at this locus. One breed specific marker was found in each of Mehsana (BM1818) and Bhadawari (ILSTS030) and four were found in Jaffarabadi (BM1818, ILSTS030, ILSTS054 and ILSTS011). Genetic distance (Ds) between the Mehsana and Bhadawari breed was the maximum (0.29), followed by Murrah and Mehsana (0.27), and Nili-Ravi and Bhadawari (0.26). The lowest Ds was found between the Jaffrabadi and Nagpuri breeds which was only 0.05. The highest divergence time of 1318 years was established between Mehsana and Bhadawari breeds whereas it was found to be lowest (272 years) between the Jaffrabadi and Nagpuri breeds.