Publishing type：Research paper (scientific journal)   Publisher：Japan Society of Equine Science  

DOI： 10.1294/jes.31.35

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BIOMED CENTRAL LTD  

Background: Conception is a fundamental trait for successful cattle reproduction. However, conception rates in Japanese Black cattle have been gradually declining over the last two decades. Although conception failures are mainly caused by embryonic mortality, the role of maternal genetic factors in the process remains unknown. Copy number variation (CNV), defined as large-scale genomic structural variants, contributes to several genetic disorders. To identify CNV associated with embryonic mortality in Japanese Black cattle, we evaluated embryonic mortality as a categorical trait with a threshold model and conducted a genome-wide CNV association study for embryonic mortality using 791 animals.Results: We identified a deleted-type CNV ranging from 378,127 to 412,061 bp on bovine chromosome 8, which was associated with embryonic mortality at 30-60 days after artificial insemination (AI). The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). Analysis of sequence traces from the CNV identified that 63 bp reads bridging the breakpoint were present on both sides of the CNV, indicating that the CNV was generated by non-allelic homologous recombination using the 63 bp homologous sequences. Western blot analysis showed that the CNV results in a null allele of ANXA10. This association was replicated using a sample population size of 2552 animals. To elucidate the function of ANXA10 in vivo, we generated Anxa10 null mice using the CRISPR/Cas9 system. Crossbreeding experiments showed that litter size from crosses of both Anxa10(-/-) and Anxa10(+/-) females had fewer pups than did Anxa10(+/+) females, and embryos of Anxa10(-/-) females died between implantation stages E4.5 and E12.5. These results indicate that loss of maternal Anxa10 causes embryonic mortality.Conclusions: This study identified a deleted-type CNV encompassing ANXA10 in cows that was associated with embryonic mortality at 30-60 days after AI. Using a mouse model, we confirmed that litter sizes were smaller in crosses of both Anxa10(-/-) and Anxa10(+/-) females relative to those of wild females. These results indicate that ANXA10 is a maternal factor that is critical for embryo development.

DOI： 10.1186/s12864-016-3312-z

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY  

Marker-assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits.

DOI： 10.1111/asj.12453

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Days open (DO), which is the interval from calving to conception, is an important trait related to reproductive performance in cattle. To identify quantitative trait loci for DO in Japanese Black cattle, we conducted a genome-wide association study with 33303 single nucleotide polymorphisms (SNPs) using 459 animals with extreme DO values selected from a larger group of 15488 animals. We identified a SNP on bovine chromosome 2 (BTA2) that was associated with DO. After imputation using phased haplotype data inferred from 586812 SNPs of 1041 Japanese Black cattle, six SNPs associated with DO were located in an 8.5-kb region of high linkage disequilibrium on BTA2. These SNPs were located on the telomeric side at a distance of 177kb from the parathyroid hormone 2 receptor (PTH2R) gene. The association was replicated in a sample of 1778 animals. In the replicated population, the frequency of the reduced-DO allele (Q) was 0.63, and it accounted for 1.72% of the total genetic variance. The effect of a Q-to-q allele substitution on DO was a decrease of 3.74days. The results suggest that the Q allele could serve as a marker in Japanese Black cattle to select animals with superior DO performance.

DOI： 10.1111/age.12360

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BMC  

Background: Female fertility, a fundamental trait required for animal reproduction, has gradually declined in the last 2 decades in Japanese Black cattle. To identify associated genetic variants in Japanese Black cattle, we evaluated female fertility as a metric to describe the average inverse of the number of artificial inseminations required for conception from the first through the fourth parity (ANAI(4)) and conducted a genome-wide association study (GWAS) using 430 animals with extreme ANAI(4) values from 10,399 animals.Results: We found that 2 variants, namely a single-nucleotide polymorphisms (SNP; g.48476925C > T) and a 3-bp indel (g.48476943_48476946insGGC), in the upstream region of the activin receptor IIA gene (ACVR2A) were associated with ANAI(4). ACVR2A transcripts from Japanese Black cattle of the Q haplotype, defined by the SNP and the 3-bp indel, with increased ANAI(4) were 1.29-1.32-fold more abundant than q-derived transcripts. In agreement, reporter assay results revealed that the activity of the ACVR2A promoter was higher in reporter constructs with the Q haplotype than in those with the q haplotype by approximately 1.2 fold. Expression of exogenous ACVR2A induced dose-dependent increases of reporter activity from the follicle-stimulating hormone, beta polypeptide (FSHB) promoter in response to activin A in a pituitary gonadotrophic cell line. The findings suggested that sequence variations in the upstream region of ACVR2A with the Q haplotype increased ACVR2A transcription, which in turn induced FSHB expression. This association was replicated using a sample population size of 1,433 animals; the frequency of the Q haplotype was 0.39, and Q-to-q haplotype substitution resulted in an increase of 0.02 in terms of ANAI(4).Conclusions: This GWAS identified variants in the upstream region of ACVR2A, which were associated with female fertility in Japanese Black cattle. The variants affected the level of ACVR2A mRNA expression, which could lead to an allelic imbalance. This association was replicated with a sample population of 1,433 animals. Thus, the results suggest that the Q haplotype could serve as a useful marker to select Japanese Black cattle with superior female fertility.

DOI： 10.1186/s12863-015-0282-0

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Postnatal mortality (PM) of calves is an economically important trait, because a high mortality rate of calves decreases farm income and significantly increases production costs. In spite of the economic importance of PM, genetic studies on PM have been scarce for Japanese Black cattle. The objectives of this study were to estimate the direct and maternal heritability for PM using a Bayesian threshold model with Gibbs sampling in Japanese Black cattle. The original data consisted of 43723 records of animals born from January 2005 to June 2006. Four binary traits of mortality were considered: D1-14, D15-60, D61-180 and D1-180 with numbers indicating the period of risk in days after birth. Direct heritabilities for PM ranged from 0.12 to 0.31 and maternal heritabilities for PM were lower than the direct heritabilities and ranged from 0.02 to 0.16. Direct genetic correlations between D1-14 and D15-60, between D15-60 and D61-180, and between D1-14 and D61-180 were 0.501, 0.689 and 0.062, respectively. Direct genetic correlations of birth weight with D1-14, D15-60, D61-180 and D1-180 were 0.089, 0.482, 0.434 and 0.394, respectively. These results indicated that different genes were responsible for early and late PM and early PM (D1-14) can be genetically reduced without influencing birth weight.

DOI： 10.1111/asj.12233

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Age at first calving (AFC) is an important trait for achieving earlier reproductive performance in cattle. To identify quantitative trait loci for AFC in Japanese Black cattle, we conducted a genome-wide association study using 866 animals with extreme AFC values selected from a larger group of 52009 animals. We identified single nucleotide polymorphisms (SNPs) on bovine chromosome 2 that were associated with AFC. These SNPs were located within 112.8-kbp intronic region of delta/notch-like EGF repeat containing (DNER) and proved to be in a state of high linkage disequilibrium. The association was replicated in an independent sample of 2963 animals. In the replicated population, the frequency of the reduced AFC allele (Q) was 0.463, and the allele accounts for 8% of the total genetic variance. The effect of allele substitution on AFC was a decrease of 11.54days. The results suggest that the Q allele could serve as a useful marker in Japanese Black cattle to select animals with superior AFC performance.

DOI： 10.1111/age.12109

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DOI： 10.1111/asj.12108

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Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise F-ST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.

DOI： 10.1111/asj.12045

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Background: Calving efficiency can be described as the measure of a cow's ability to produce viable offspring within a specific period of time. This trait is crucial in beef cattle because calves are necessary both for the production of beef and for heifer replacements. Recently, the number of calves produced at 4 years of age (NCP4) has been used to evaluate the calving efficiency of Japanese Black cattle. To identify variants associated with calving efficiency in Japanese Black cattle, we conducted a genome-wide association study (GWAS) using 688 animals with extreme NCP4 values selected from 15,225 animals.Results: We identified genetic variants on bovine chromosome 12 (BTA12) that were associated with NCP4. The General Transcription Factor IIF, polypeptide 2 (GTF2F2), located in the 132 kbp-associated region, proved to be in strong linkage disequilibrium. We found 15 associated variants in the promoter and the 3' UTR regions. Consistent with this finding, transcripts of GTF2F2 derived from the haplotype (Q) with the increased number of calves were 1.33-fold more abundant than q-derived transcripts. Furthermore, luciferase assays revealed that the activity of the 3' UTR, a region that includes nine SNPs, was higher in constructs with the Q haplotype than in those with the q haplotype by approximately 1.35-fold. In contrast, the activity of the promoter region did not differ between haplotypes. The association was replicated in an independent sample of 827 animals that were randomly selected from the remainder of the cohort from the same farms used in the GWAS. In the replicated population, the frequency of the Q haplotype is 0.313, and this haplotype accounts for 2.69% of the total phenotypic variance. The effect of the Q to q haplotype substitution on NCP4 was 0.054 calves. These findings suggest that variants in the 3' UTR of GTF2F2 affect the level of GTF2F2 mRNA, which is associated with calving efficiency.Conclusions: This GWAS has identified variants in the 3' UTR of GTF2F2 that were associated with the NCP4 of Japanese Black cattle, and this association was validated in an independent sample. The Q haplotype will be immediately useful in improving the calving efficiency of Japanese Black cattle.

DOI： 10.1186/1471-2156-14-41

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Estimates of genetic parameters were obtained for body measurement traits of 648 animals at 4 months of age, of 545 at 8 months and carcass traits of 14972 animals with the use of an animal model by the restricted maximum likelihood procedure. The estimated heritabilities for carcass traits were high (0.41 to 0.54). At 4 months the estimated direct heritabilities for body measurement traits were moderate to high (0.28 to 0.64), except for chest width (0.19); at 8 months they were also moderate to high (0.23 to 0.49), except for chest depth and chest width (0.18 and 0.06, respectively). Maternal heritabilities for all body measurement traits were low at both ages. The results indicate that because of their moderate direct genetic correlations with body measurement traits, carcass weight, rib thickness and subcutaneous fat thickness can be improved; however, rib eye area and beef marbling standard show little such possibility considering their correlation with body measurement traits.

DOI： 10.1111/asj.12005

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This study was conducted to evaluate the importance of maternal effect on body measurement traits at an early stage of growth, and to estimate the genetic relationships between direct and maternal effects and among body measurement traits at 0 month (0-mo) and 4 months (4-mo) of age in a population of Japanese Black calves. Body measurements and body weight of 889 Japanese Black calves were estimated with the use of an animal model by the Residual Maximum Likelihood procedure. Direct heritabilities were low to moderate, ranging between 0.17 +/- 0.09 and 0.48 +/- 0.13 at 0-mo, and slightly lower, ranging between 0.15 +/- 0.07 and 0.33 +/- 0.13 at 4-mo. Estimated maternal heritabilities were low to moderate, ranging between 0.08 +/- 0.07 and 0.33 +/- 0.07 at 0-mo and 0.13 +/- 0.06 to 0.33 +/- 0.06 at 4-mo. The direct genetic correlations between 0-mo and 4-mo were moderate to highly positive, ranging from 0.53 +/- 0.23 to 0.96 +/- 0.09. The estimated direct genetic correlation of chest width with other width traits was low and positive at both ages, whereas with hip width it was high and positive (0.80 +/- 0.09) at 0-mo, suggesting that simultaneous improvement of body width of the front and back parts is possible. Maternal genetic effects were relatively independent of direct genetic effects for body measurement traits and can be considered in genetic evaluation.

DOI： 10.1111/j.1740-0929.2011.00936.x

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Language：English   Publisher：Cambridge University Press  

The objective of the present study was to determine the optimal culling strategy in relation to biological and economic efficiency (BE and EE, respectively) and annualized net revenue (AN) in the Japanese Black cow–calf production system with special reference to the beef quality of culled cows. The herd model focused on two ways of mating: one-mating trial system (ONE) and continuous-mating trial system (CON). ONE assumed that heifers that fail to conceive are culled and cows that fail to conceive are culled at weaning of their calves, while CON assumed that mating continues until all females theoretically conceive. Least square means of carcass data of Japanese Black cows collected from a cooperative farm in Japan were used to estimate the carcass price of a cow by parity and Beef Marbling Standard (BMS) number. The simulation, assuming the current production situation in Japan, indicated that sales of culled cows accounted for 0·10–0·20 of total sales and was an important element in total production. Comparisons between ONE and CON showed that production efficiency in the current situation is higher in CON. The BE, EE and AN were higher in CON than in ONE. The two economic indicators were less sensitive to changes in annual discount rate but highly sensitive to changes in female calf price and BMS number of cows, indicating the importance of considering fluctuations in calf price and potential quality of culled cows' carcasses when estimating the economically optimal parity of culling. The three indicators derived different optimal solutions even in the same mating trial systems, stressing the importance of choice of production indicators when determining the culling strategy and evaluating animal production.

DOI： 10.1017/S0021859611000347

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DOI： 10.2527/jas.2008-0948

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Heterogeneity of variance among subclasses of an effect is a potential source of bias in genetic evaluation. Degrees of the heterogeneity of variance among farm-market-year-sex (FMYS) subclasses for carcass weight, beef marbling standard number, rib-eye area, rib thickness and subcutaneous fat thickness were investigated in Japanese Black cattle. Consequences of adjusting for the heterogeneity on the predicted breeding values (PBVs) or on the genetic indexes derived from the PBVs of the five carcass traits were assessed. A total of 57 461 records were collected between 1997 and 2002 from steers and heifers fattened at farms across Japan. These records were grouped into 1591 FMYS subclasses. Bartlett's test showed that the degree of the heterogeneity of variance among the FMYS subclasses was sizeable in all traits (P < 0.0001). By applying a two-step adjustment procedure it was possible to reduce the standard deviation, the coefficient of variation and the Gini coefficient of the phenotypic variances by 67.5% to 75.0% in the different traits. The applied adjustment caused a substantial re-ranking of elite dams in the PBV for each trait as well as in the genetic index. This study provided evidence that the applied adjustment reduces the bias in the PBVs due to heterogeneous variances and increases the accuracy of bull-dam selection.

DOI： 10.1111/j.1740-0929.2008.00576.x

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The objectives of this study were to estimate genetic parameters for gestation length (GL), including estimation of maternal effects, and to investigate the genetic relationships of GL with birth weight and carcass traits in a Japanese Black cattle population. The original data comprised 34 775 records of animals born from October 1999 to August 2003. Two different models were used to analyze the data for GL. The first model (M1) included direct genetic effect of the calf and maternal genetic effect as random effects. The second model (M2) treated GL as a trait of the dam and included direct genetic effects only. M1 was used in bi-variate analysis. The direct and maternal heritabilities for GL estimated from M1 were 0.53 and 0.14, respectively. This result shows that GL is moderately inherited and can be controlled genetically. The direct x maternal genetic correlation for GL was -0.73. Direct genetic correlations of GL with carcass traits were close to zero. However, genetic correlation of maternal GL with carcass weight was moderate (0.25).

DOI： 10.1111/j.1740-0929.2008.00530.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Society of Animal Science  

DOI： 10.2527/jas.2007-0063

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The objectives of this study were 1) to investigate the effect of changes in carcass market prices due to bovine spongiform encephalopathy (BSE) occurrences on estimates of genetic parameters and economic weights for carcass traits
and 2) to compare direct and indirect approaches for prediction of genetic merit of Japanese Black cattle for profitability of their progeny. The direct approach utilized estimated breeding values of carcass prices, whereas in the indirect approach, selection indices were constructed as products of economic weights and breeding values of component traits. Data were composed of 80,191 carcass records divided into 5 periods based on changes in carcass prices as a result of occurrences of BSE in Japan and the United States. The periods ranged from a period before occurrence of BSE in Japan to a period of beef import restrictions and a rise in prices. Carcass traits analyzed included HCW, LM area, rib thickness, subcutaneous fat thickness, and marbling score (MS). Price traits included carcass unit price and carcass sale price. Estimates of heritability for price traits were moderate (0.32 to 0.46) and slightly sensitive to changes in carcass market prices. Genetic correlations of HCW and LM area with price traits increased and that between MS and carcass sale price decreased with period, whereas estimates of genetic correlation between MS and carcass unit price were high in all periods (0.96 to 0.98). Economic weights for carcass traits varied with periods because carcass prices were highly sensitive to economic importance of traits. Nevertheless, correlations between within-period breeding values for price traits estimated using direct and indirect approaches were high (0.92 to 0.99). This result indicates that selection realized by direct and indirect approaches will provide very similar results. A comparison among within-approach breeding values estimated in different periods showed that the largest differences in breeding values of sires for price traits were between the periods after occurrences of BSE in Japan and in the United States. Economic effects of BSE occurrences influenced the importance of carcass traits and economic merits of price traits through a change of carcass prices from period to period, irrespective of the approach taken in determining the genetic merit of breeding animals for profitability of their progeny. ©2006 American Society of Animal Science. All rights reserved.

DOI： 10.2527/jas.2005-610

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The importance of genotype × environment (region or management system) interactions for carcass traits in Japanese Black cattle was investigated using both univariate and multivariate animal models. The univariate approach was used mainly to test the significance of interaction effects. The multivariate approach was used to estimate genetic correlations, which indicated the magnitude of genotype × environment (GE) interactions. The more a genetic correlation deviates from 1, the larger the interaction. From the univariate approach, the addition of genotype × environment (region or management system) interaction (co)variance components resulted in an improved fit of the model for all traits in both cases (P &lt
0.001). However, estimates of genetic correlation between regions obtained from the multivariate approach for hot carcass weight, LM area, rib thickness, s.c. fat thickness, and marbling score were 0.97, 0.95, 0.93, 0.97, and 0.93, respectively. The corresponding estimates between management systems were 0.84, 0.92, 0.84, 0.90, and 0.97, respectively. These results indicate that GE interaction effects on carcass traits of Japanese Black cattle may be biologically unimportant. Therefore, breeding values obtained using the multivariate method would rank sires similarly in all environments. Consequently, carcass traits measured in these two different regions or management systems can be treated as the same traits. ©2005 American Society of Animal Science. All rights reserved.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BLACKWELL WISSENSCHAFTS-VERLAG GMBH  

The population structure of the Japanese Brown in Kumamoto Prefecture was investigated with pedigree analysis. Two hundred heifers were randomly sampled, in 1960, 1970, 1980, and 1990. Population genetic parameters, i.e. F-statistics, index of subdivision, generation interval, effective population size, and effective number of sires, were estimated. The effective number of sires decreased, most dramatically, from 1970 to 1980. The average inbreeding coefficient (F-IT) increased, from 0.64% in 1960 to 5.43% in 1990. F-ST increased in parallel with F-IT, while F-IS remained low. From 1960 to 1980, the index of diversity showed a decreasing trend, but this improved a little, with the index at 1.1 in 1990. The generation interval tended to be longer year by year, and was 5.52 during 1980-90. On the other hand, N-c decreased, from 724.6 before 1960 to 40.1 at the present The population structure of the Japanese Brown is not problematical at present, when considering F-IT, but the irreversible inbreeding coefficient (F-ST) increases constantly.

DOI： 10.1111/j.1439-0388.1997.tb00490.x

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Kuchinoshima cattle is a breed of the unique feral cattle originated from grazing Japanese native cattle in Kuchinoshima island of Tokara Islands in Kagoshima prefecture during Meiji and Taisho periods. The distribution and frequencies of alleles of the genes associated with economical traits and hereditary disorders have been reported in populations of Japanese Black cattle that is a major beef cattle breed in Japan and Mishima cattle that is another Japanese native cattle breed in Mishima island, but those of Kuchinoshima cattle have not been reported. Therefore, we investigated the allelic distribution and frequencies of the genes associated with economical traits, hereditary disorders, and coat color to reveal genetic characteristic of Kuchinoshima cattle by comparison of the distributions among Kuchinoshima, Japanese Black, and Mishima cattle. By using 32 DNA samples collected from Kuchinoshima cattle, we genotyped &lt;I&gt;NCAPG&lt;/I&gt;, &lt;I&gt;FASN&lt;/I&gt;, &lt;I&gt;SCD&lt;/I&gt;, and &lt;I&gt;SREBP-1&lt;/I&gt; genes associated with economical traits including carcass weight and fatty acid composition, &lt;I&gt;F11&lt;/I&gt; gene responsible for factor XI deficiency, and &lt;I&gt;MC1R&lt;/I&gt; gene involved in coat color determination by PCR or PCR-RFLP assay and compared these results with those of Japanese Black and Mishima cattle. As a result, we found that while both &lt;I&gt;G&lt;/I&gt; and &lt;I&gt;T&lt;/I&gt; alleles of &lt;I&gt;NCAPG&lt;/I&gt; locus were observed in the population of Japanese black cattle, the locus was fixed to &lt;I&gt;T&lt;/I&gt; allele in the populations of Kuchinoshima and Mishima cattle, and that while both &lt;I&gt;TW&lt;/I&gt; and AR alleles of &lt;I&gt;FASN&lt;/I&gt; locus were observed in Japanese black cattle, the locus was fixed to &lt;I&gt;AR&lt;/I&gt; allele in Kuchinoshima cattle and &lt;I&gt;TW&lt;/I&gt; allele in Mishima cattle. For the &lt;I&gt;SCD&lt;/I&gt; and &lt;I&gt;SREBP-1&lt;/I&gt; loci, both &lt;I&gt;A&lt;/I&gt; and &lt;I&gt;V&lt;/I&gt; alleles of &lt;I&gt;SCD&lt;/I&gt; locus were observed in Japanese Black, Kuchinoshima, and Mishima cattle, and both &lt;I&gt;S&lt;/I&gt; and &lt;I&gt;L&lt;/I&gt; alleles &lt;I&gt;SREBP-1&lt;/I&gt; locus were observed in Japanese Black and Mishima cattle but fixed to L allele in Kuchinoshima cattle. Furthermore, while both (+) and (-) alleles of &lt;I&gt;F11&lt;/I&gt; locus were observed in the population of Japanese black cattle, the locus was fixed to (+) allele in the populations of Kuchinoshima and Mishima cattle. Finally, we observed &lt;I&gt;E&lt;/I&gt; &lt;SUP&gt;+&lt;/SUP&gt; and e alleles of &lt;I&gt;MC1R&lt;/I&gt; locus in Kuchinoshima cattle, while &lt;I&gt;E&lt;/I&gt; &lt;SUP&gt;D&lt;/SUP&gt; and &lt;I&gt;E&lt;/I&gt; &lt;SUP&gt;+&lt;/SUP&gt; allele but no e allele in Japanese Black cattle and only &lt;I&gt;E&lt;/I&gt; &lt;SUP&gt;+&lt;/SUP&gt; allele in Mishima cattle were observed. These findings indicate that Kuchinoshima cattle comprises a population of Japanese native cattle possessing unique genetic characteristics different from those of Japanese Black and Mishima cattle, which has been formed under geographically isolated circumstance with relatively small population without influence of foreign breeds.

DOI： 10.5924/abgri.42.11

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：SOC STUDY REPRODUCTION  

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Japanese Black cattle are the predominant beef breed in Japan. This breed has excellent meat quality, especially degree of (intramuscular) marbling. Degree of marbling was measured at the 6th to 7th rib section and according to the Beef Marbling Standard with scores 1 to 12 (so-called BMS), with number 12 being the best. BMS is used with business deal of beef carcass and has strongly effect on selling price of carcass. On the other hands, more degree of marbling on top round (MTR) is better carcass unit price in same BMS, because of good price of part of thigh. MTR has been focused in recent years. However, MTR is unclear how to evaluate, therefore, collection of records and genetic evaluations are not enough. In this study, records of MTR were collected and then, genetic parameters for BMS and MTR of Japanese Black were estimated. The original data were 11,052 carcass records collected from April in 2008 to June in 2009 at the Agura Farm. Only information from abattoirs having more than 20 records and feedlot farms having more than 10 records were used. This resulted in a total of 10,990 records. In this study, pedigree information was traced back to two generations. An animal model that included all relationships among all animals was used as a statistical model. The fixed effects included sex, farm, abattoir and the combination of slaughter year and month. Slaughter age was fitted as linear covariables. Genetic parameters were estimated using REMLF90 and THRGIBBS1F90 programs. The estimates of heritability were moderately high (0.37 to 0.44) for MTR treated as threshold traits. The estimates of phenotypic and genetic correlations between BMS and MTR were very high (0.87 and 0.98, respectively). These indicate that MTR can be improved genetically and improvement of MTR can treat BMS as indicator.

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DOI： 10.5924/abgri2000.36.29

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DOI： 10.5924/abgri2000.36.29

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DOI： 10.7310/arfe1965.43.51

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Language：Japanese   Publisher：日本動物遺伝育種学会  

DOI： 10.5924/abgri2000.35.25

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Language：Japanese   Publisher：地域農林経済学会  

DOI： 10.7310/arfe1965.43.51

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Publisher：Japanese Society of Animal Breeding and Genetics  

DOI： 10.5924/abgri2000.35.25

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The objective of this study was to investigate effects of attributes and consciousness of farm households on prices and traits of carcass sold from the farms. Questionnaire surveys were conducted to farms under the Agura Co-operative Farm and 91 questionnaires were available for the present analysis. Best linear unbiased estimations (BLUEs) of each farm for carcass prices and traits were estimated using 20,346 carcass records collected from January 2004 to March 2005 at the Agura co-operation Farm. The BLUEs were analyzed by least squares procedures using a model containing attributes and consciousness of farm households obtained from questionnaires as sources of variation. The result showed that farm households who make great account of both income and joy of life in keeping animals can produce carcasses with higher quality. In addition, it was shown that the effect of farm size on carcass unit price was quadratic ; as farm size increased, carcass unit price decreased and increased beyond the size of more than 932 heads.

DOI： 10.2508/chikusan.77.289

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Language：Japanese   Publisher：公益社団法人 日本畜産学会  

Comparisons of breeding stock among the Japanese Black cattle across regions were impeded because breeding programs and genetic evaluations were carried out primarily within regions. A nationwide connectedness was missing. The objective of this study was to investigate the possibility of a national genetic evaluation of breeding stocks based on appropriate mathematical models and suited material. Goodness of fit of the models was measured by the prediction error variance, the Akaike&amp;rsquo;s information criterion and coefficient of determination. The data consisted of field records on carcass traits (beef marbling standard number, BMS No. ; carcass weight, CW ; rib-eye area, REA ; rib thickness, RT ; subcutaneous fat thickness, SFT) of fattened Japanese Black cattle collected from 1997 to 2002 among the nationwide fattening farms of Agura Kyosai Bokujo, Inc. (N=49,810). The pedigree of those animals was surveyed, too. More than 95% of all possible pairs of fattening farms have beef animals with common sires. Further beef animals from different prefectures were dispersed over fattening farms so that comparisons among all prefectures were possible. Six mathematical models were applied, which differed in the way how each of the fixed effects was taken into account. The estimated heritabilities do not vary significantly among the applied mathematical models (h&lt;SUP&gt;2&lt;/SUP&gt; for BMS No. : 0.43 ; CW : 0.45-0.49 ; REA : 0.32-0.33 ; RT : 0.31-0.33 ; SFT : 0.46-0.47). The models with the best goodness of fit are obtained when all the fixed effects are taken into account as a combination effect or when all the fixed effects but the effect of sex are taken into account as a combination of them. We were able to demonstrate that the genetic connectedness among subpopulations is sufficient in the involved fattening farms in order to establish a genetic evaluation on a national scale. A nationwide evaluation of the Japanese Black breeding stocks will enhance the genetic improvement of the breed by a more efficient selection of excellent sires and dams.

DOI： 10.2508/chikusan.75.353

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Language：Japanese   Publisher：日本中央競馬会競走馬総合研究所  

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Laryngeal Hemiplegia (LH) leads to a reduction in performance and because of it many promising racehorses have been forced to end their racing career. Therefore it is important for breeding good racehorses to estimate the heritability of LH. In this study, the computer program was developed based on the Bayesian analysis with Gibbs sampling for estimating the heritability of categorical traits assuming liability. A total of 706 records with LH-grade in Thoroughbreds aged 2 to 5 years were assigned for the genetic analysis. LH-grades consisted of five severity classes from 0 to 4. Racehorse breeders are often interested in whether the genetic effect controlling a complex disorder is present in the population. To answer this question, the binary trait analysis would be also useful. The heritability of LH-grade in the Thoroughbred horse was then also estimated as a binary or as a categorical trait. The mode values of the posterior distributions of heritability were 0.23 and 0.20 for the binary and the categorical trait, respectively. The fact that in the Thoroughbred population studied LH is at least partially controlled by genetic factors leads to the suggestion that when applying adequate breeding measures the prevalence of LH will be able to be reduced.

DOI： 10.1294/jes.14.81

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Language：English   Publisher：日本ウマ科学会  

Laryngeal Hemiplegia (LH) leads to a reduction in performance and because of it many promising racehorses have been forced to end their racing career. Therefore it is important for breeding good racehorses to estimate the heritability of LH. In this study, the computer program was developed based on the Bayesian analysis with Gibbs sampling for estimating the heritability of categorical traits assuming liability. A total of 706 records with LH-grade in Thoroughbreds aged 2 to 5 years were assigned for the genetic analysis. LH-grades consisted of five severity classes from 0 to 4. Racehorse breeders are often interested in whether the genetic effect controlling a complex disorder is present in the population. To answer this question, the binary trait analysis would be also useful. The heritability of LH-grade in the Thoroughbred horse was then also estimated as a binary or as a categorical trait. The mode values of the posterior distributions of heritability were 0.23 and 0.20 for the binary and the categorical trait, respectively. The fact that in the Thoroughbred population studied LH is at least partially controlled by genetic factors leads to the suggestion that when applying adequate breeding measures the prevalence of LH will be able to be reduced.

DOI： 10.1294/jes.14.81

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Language：Japanese   Publisher：公益社団法人 日本畜産学会  

In order to elucidate the properties for the breeding of Japanese Black Cattle population in the southern part of Iwate prefecture, genetic parameters, breeding values and genetic trends of carcass traits and daily gain (DG) were estimated using 3,467 field records from the steers and heifers fattened in Maesawa, Iwate prefecture, from 1994 to 1999. Only farmers who shipped more than 30 animals during this period were chosen. It was remarkably noticed that best linear unbiased estimations for beef marbling standard number (BMS) have decreased successively for years. The heritability estimates for carcass traits and DG were as follows : 0.66 for BMS, 0.51 for DG, 0.64 for carcass weight, 0.36 for rib-eye area, 0.25 for rib thickness and 0.33 for subcutaneous fat thickness. The genetic correlation, between BMS and other traits were as follows : 0.1 for DG, 0.18 for the carcass weight, 0.48 for the rib-eye area, 0.37 for the rib thickness and -0.24 for the subcutaneous fat thickness. As far as the genetic trends were concerned, improvements on the BMS and the subcutaneous fat thickness were highly regarded, while the carcass weight was rarely taken into consideration since 1991. On the other hand, the phenotypic average for BMS of animals fattened in Maesawa has tended to decrease since 1991. Based on the present results, factors other than genetic improvement could be considered the cause of the decrease.

DOI： 10.2508/chikusan.74.187

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DOI： 10.5924/abgri2000.30.11

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Language：Japanese   Publisher：公益社団法人 日本畜産学会  

&lt;i&gt;Claudin-16&lt;/i&gt; (&lt;i&gt;CL-16&lt;/i&gt;) deficiency is an autosomal recessive disease in Japanese black cattle. The association analysis between the deletion mutant allele (&lt;i&gt;d&lt;/i&gt;) of &lt;i&gt;CL-16&lt;/i&gt; deficiency and carcass traits was investigated. Normal allele (&lt;i&gt;D&lt;/i&gt;) and mutant allele (&lt;i&gt;d&lt;/i&gt;) were diagnosed in 464 fattened progeny of three carrier sires (&lt;i&gt;Dd&lt;/i&gt;), and 140 cows of Sire 1 whose common ancestor was revealed as &lt;i&gt;Dd&lt;/i&gt;. The progeny were composed of 230 normal (&lt;i&gt;DD&lt;/i&gt;) and 234 carrier (&lt;i&gt;Dd&lt;/i&gt;). The cows were composed of 60 &lt;i&gt;DD&lt;/i&gt; and 80 &lt;i&gt;Dd&lt;/i&gt;. The association analysis was carried out among the &lt;i&gt;CL-16&lt;/i&gt; genotypes, and carcass traits and predicted breeding value for carcass traits using the 464 progeny and 140 cows, respectively. Analysis of variance was performed considering the &lt;i&gt;CL-16&lt;/i&gt; genotypes, sire, sex, farm and age (linear and quadratic) as the source of variance in order to evaluate factors affecting carcass traits. Significant differences in BMS number, carcass weight, area of rib eye, and rib thickness were observed between the sires. Significant differences in carcass weight were observed in the influence of sex. Significant differences in BMS number, carcass weight, and rib thickness were observed between farms. The regression of any carcass traits on final age (linear and quadratic) was not statistically significant. The significant association of the &lt;i&gt;CL-16&lt;/i&gt; genotypes were not seen in the carcass traits after the effects of environmental factors were eliminated. Moreover, a significant association of the genotypes was not seen (P&gt;0.05) with predicted breeding value for carcass traits in cows of Sire-1. Furthermore, these carcass traits had no significant linkage with the approximately 30 cM region including &lt;i&gt;CL-16&lt;/i&gt; locus in a half-sib family of Sire-1 comprising 136 offspring (P&gt;0.05). Therefore, exclusion of the mutant allele &lt;i&gt;d&lt;/i&gt; from Japanese Black cattle population would not deteriorate the carcass traits.

DOI： 10.2508/chikusan.73.19

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Language：Japanese   Publisher：Japanese Society of Animal Breeding and Genetics  

A reproducibility of experimental data is important for application of differential display method to the comparison of mRNA expression level among many samples. First, we developed the optimum method to evaluate size (BP) and yield (IOD) of PCR products by analyzing an electrophoretic image. BP (A), which is a way to calculate size of each product by using 3 molecular markers loaded in extreme and central lanes of gel as references, was optimal for size evaluation. Further, IOD (A) and IOD (P), respectively, which are way to use a measured absolute value of signal intensity of each product, and to use a relative value of signal intensity of each product as proportion of total sum of all products in an identical lane, as yield, were determined as the suboptimum and optimum evaluation methods. Next, we performed an analysis of variance of intergel, interlane, and interreaction effects, when using the optimum method. We detected statistically significant effects for intergel and interlane, but not for interreaction, when using BP (A) method. As for IOD (A) and IOD (P), significant effects for intergel and interreaction were observed, but not for interlane. Finally, we evaluated the replicate pattern that is suitable for a largescale gene expression profiling, by examining coefficient of variation of combined effects for BP and IOD obtained by 4 different replicate patterns.

DOI： 10.5924/abgri2000.30.11

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Language：Japanese   Publisher：Japanese Society of Animal Science  

Claudin-16 (CL-16) deficiency is an autosomal recessive disease in Japanese black cattle. The association analysis between the deletion mutant allele (d) of CL-16 deficiency and carcass traits was investigated. Normal allele (D) and mutant allele (d) were diagnosed in 464 fattened progeny of three carrier sires (Dd), and 140 cows of Sire 1 whose common ancestor was revealed as Dd. The progeny were composed of 230 normal (DD) and 234 carrier (Dd). The cows were composed of 60 DD and 80 Dd. The association analysis was carried out among the CL-16 genotypes, and carcass traits and predicted breeding value for carcass traits using the 464 progeny and 140 cows, respectively. Analysis of variance was performed considering the CL-16 genotypes, sire, sex, farm and age (linear and quadratic) as the source of variance in order to evaluate factors affecting carcass traits. Significant differences in BMS number, carcass weight, area of rib eye, and rib thickness were observed between the sires. Significant differences in carcass weight were observed in the influence of sex. Significant differences in BMS number, carcass weight, and rib thickness were observed between farms. The regression of any carcass traits on final age (linear and quadratic) was not statistically significant. The significant association of the CL-16 genotypes were not seen in the carcass traits after the effects of environmental factors were eliminated. Moreover, a significant association of the genotypes was not seen (P>0.05) with predicted breeding value for carcass traits in cows of Sire-1. Furthermore, these carcass traits had no significant linkage with the approximately 30 cM region including CL-16 locus in a half-sib family of Sire-1 comprising 136 offspring (P>0.05). Therefore, exclusion of the mutant allele d from Japanese Black cattle population would not deteriorate the carcass traits.

DOI： 10.2508/chikusan.73.19

DOI： 10.1292/jvms.68.319_references_DOI_3Tfx6jEYktXsr2H9WH83lLPf6qK

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Other Link： https://ndlsearch.ndl.go.jp/books/R000000004-I6266493

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