• Asian-Australasian Journal of Animal Sciences
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• 제29권9호
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• pp.1353-1362
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• 2016

Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.

• Asian-Australasian Journal of Animal Sciences
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• 제14권5호
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• pp.597-602
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• 2001

This study was conducted to examine the relationships between the methods used to determine the number of transferable embryos collected per flush and the estimated cumulative genetic improvements in the Japanese Holstein MOET breeding population. Cumulative genetic improvements were predicted by Monte Carlo simulation using three different determination methods (MODEL 1, MODEL 2, and MODEL 3), for calculating the number of embryos collected per flush. Moreover EBVs were estimated including or ignoring coefficients of inbreeding in MME. Inbreeding coefficients were also predicted. The number of transferable embryos was determined using normal, gamma, and Poisson distributions in MODEL 1, gamma and Poisson distributions in MODEL 2, and only the Poisson distribution in MODEL 3. The fitness of MODEL 2 in relation to field data from Hokkaido Japan was the best, and the results for MODEL3 indicated that this model is unsuitable for determining the number of transferable embryos. The largest cumulative genetic improvement (3.11) in the 10th generation was predicted by MODEL 3 and the smallest (2.83) by MODEL 2. Mean coefficients of correlation between the true and estimated breeding values were 0.738, 0.729, and 0.773 in MODELS 1, 2, and 3, respectively. It is suggested that the smallest genetic improvement in MODEL 2 resulted from the smallest correlation coefficient between the true and estimated breeding values. The differences in milk, fat, and protein yields between MODELS 2 and 3 were 182.0, 7.0, and 5.6 kg, respectively, in real units when each trait was independently selected. The inbreeding coefficient was the highest (0.374) in MODEL 2 and the lowest (0.357) in MODEL 3. The effects of different methods for determining the number of transferable embryos per flush on genetic improvements and inbreeding coefficients of the simulated populations were remarkable. The effects of including coefficients of inbreeding in MME, however, were unclear.

• Asian-Australasian Journal of Animal Sciences
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• 제32권3호
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• pp.320-333
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• 2019

Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction. Methods: In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA). Results: The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle. Conclusion: Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.

• Asian-Australasian Journal of Animal Sciences
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• 제23권1호
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• pp.1-6
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• 2010

The objectives of this study were to i) investigate genetic performance for linear type traits of individual Holstein dairy cows, especially focusing on comparative traits, and to estimate genetic variances for these traits using actual data, and ii) compare genetic performance and improvement of progeny by birth country of the cows. Linear type traits defined with five comparative traits on this study were general stature composite (GSC), dairy capacity composite (DCC), body size composite (BSC), foot and leg composite (FLC), and udder composite (UDC). These traits were scored from 1 to 6 with 1 = poor, 2 = fair, 3 = good, 4 = good plus, 5 = very good and 6 = excellent. Final scores (FS) were also included in this study. Data used was collected from the years 2000 to 2004 by the Korea Animal Improvement Association (KAIA). Only data of more than five tested cows by herd appraisal date and by sires having more than ten daughters were included to increase the reliability of the data analyses. A total of 30,204 records of the selected traits, which was collected from 26,701 individuals having pedigree information were used. Herd appraisal date, year of age, lactation stage (grouped by month), and time lagged for milking (in hours) were assumed as fixed effects on the model. Animal additive genetic effects considering pedigree relationship and residual errors were assumed with random effects. Year of age at appraisal date was classified from one to nine years of age, assigning the value of nine years of age for animals that were greater than or equal to nine years of age. From our results, the estimate for heritability was 0.463, 0.346, 0.473, 0.290, and 0.430 on GSC, DCC, BSC, FLC and UDC, respectively. The estimate for FS heritability was 0.539. The greatest breeding values for GSC were estimated for Canada, with the breeding values for American lines increasing for 10 years starting in 1989 but tending to decrease after that until 2004. For DCC, the breeding values for American and Canadian lines showed similar patterns until 1999, after which the breeding values for the American lines declined sharply. For BSC, data from Korea, Canada and the USA followed similar trends overall except when the breeding values of the American lines decreased starting in 1999. Overall, the methods used to evaluate genetic performance in this study were acceptable and allowed for the discovery of differences by country of genetic origin, likely due in part to the American use of selection indexes based primarily on milk yield traits until methods for evaluating other traits began to emerge.

• Asian-Australasian Journal of Animal Sciences
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• 제18권9호
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• pp.1348-1352
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• 2005

Most breeds of sheep in Iran are adapted to their agro ecological niches where it is likely that they were also artificially selected by their owners. In general, most of sheep breeds are multipurpose producing lambs, wool and milk. To compare the physical and chemical composition of the carcasses of ten Iranian native fat-tailed sheep breeds, 243 male lambs (6-7 months of age) of ten fattailed, Iranian breeds of sheep, Sanjabi (S), Ghezel (G), Afshari (A), Mehrabani (M), Lori (L), Lori Bakhtiari (LB), Kordi Khorasan (K), Sangesari (Sa), Baluchi (B) and Chal (C) were studied. Lamb breed group had a significant (p<0.05) effect on all the carcass traits measured. The LB and C lambs showed the same live weight which was significantly (p<0.05) higher than the other breeds. Carcass dressing- out percentage in S lambs was lowest (p<0.05), but not different from G lambs. K and Sa breeds showed the highest (p<0.05) carcass dressing-out percentage. The S lambs had the highest (p<0.05) lean meat percent. Lean meat percentage was not significantly (p>0.05) different in the G, A, M and C breeds. The Sa and K breeds showed the lowest lean meat percent. The S lambs showed the lowest (p<0.05) fat percent in their carcass, while K and Sa showed the highest (p<0.05). Subcutaneous fat in K, Sa and B was higher (p<0.05) than the other breeds. Lambs of S, G, A and M breeds had the lowest subcutaneous fat in their carcasses (p>0.05). Intramascular fat was significantly (p<0.05) lower in M, S and C despite the fact that this values were highest in B and K lambs. The K and Sa breeds had highest fat-tail percentage (p<0.05) in their carcass, whereas S and G showed lowest. Lambs of G, S and A breeds had higher bone percent than other breeds (p<0.05). Lowest bone percent (p<0.05) was seen in K and Sa lambs. The carcass moisture percent was not significantly (p>0.05) different in S, G, A, M, L and C breeds. M lambs showed the lowest crude protein percentage and S breed the highest (p<0.05). There were no significant (p>0.05) differences among other lamb breeds for this trait. Chemical fat percentage was the same in S, G, A, C and M breeds, but significantly (p<0.05) lower from LB, K, Sa and B. Ash percent in S, G and A had no significant (p>0.05) difference. According to higher lean meat and lower fat percentages in the carcass, the ranking of breeds would be S, G, A, M and C.