Tsuyoshi Abe

Novel mutations of the FASN gene and their effect on fatty acid composition in Japanese Black beef.

Eight novel and four known mutations were detected in the coding sequence of the bovine fatty acid synthase (FASN) gene of an F2 population from Japanese Black and Limousin cattle. Two mutations, g.16024A>G and g.16039T>C, detected in exon 34, which determine amino acid substitutions of threonine (T) to alanine (A) and tryptophan (W) to arginine (R), were clearly separated in the parental breeds. The haplotypes (TW and AR) segregated in F2 individuals and had a significant effect on the fatty acid composition of backfat, intermuscular fat, and intramuscular fat. The TW haplotype was associated with increasing C18:0 and C18:1 content and the ratio of monounsaturated to saturated fatty acids, and decreasing C14:0, C14:1, C16:0, and C16:1 content. The two mutations were screened in two commercial Japanese Black half-sibling populations and similarly determined the contribution to the fatty acid composition of intramuscular fat. The frequency of the TW haplotype was markedly higher in Japanese Black (0.67) than in Holstein (0.17), Angus (0.02), and Hereford (0.07). We conclude that these mutations may contribute to the characteristic fatty acid composition of Japanese Black beef.

Genome-wide association study for carcass traits, fatty acid composition, chemical composition, sugar, and the effects of related candidate genes in Japanese Black cattle

We performed a genome-wide association study (GWAS) and candidate gene analysis to: (i) evaluate the effectiveness of the GWAS in our small population by performing GWAS for carcass weight (CW) and fatty acid composition; (ii) detect novel candidate regions affecting non-CW carcass traits, chemical composition and sugar; and (iii) evaluate the association of the candidate genes previously detected in CW and fatty acid composition with other economically important traits. A total of 574 Japanese Black cattle and 40 657 Single nucleotide polymorphisms were used. In addition, candidate gene analyses were performed to evaluate the association of three CW-related genes and two fatty acid-related genes with carcass traits, fatty acid composition, chemical composition and sugar. The significant regions with the candidate genes were detected for CW and fatty acid composition, and these results showed that a significant region would be detectable despite the small sample size. The novel candidate regions were detected on BTA23 for crude protein and on BTA19 for fructose. CW-related genes associated with the rib-eye area and fatty acid composition were identified, and fatty acid-related genes had no relationship with other traits. Moreover, the favorable allele of CW-related genes had an unfavorable effect on fatty acid composition.

Practical capability of a DNA pool‐based genome‐wide association study using BovineSNP50 array in a cattle population

Genome-wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome-wide association studies. However, in DNA pooling design, the additional variance generated by pooling-specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P-values estimated by a genome-wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost-effectiveness of pool-based genome-wide association studies using the BovineSNP50 array in a cattle population.

Effects of Growth Hormone Gene Polymorphism on Lipogenic Gene Expression Levels in Diaphragm Tissues of Japanese Black Heifers

Two SNPs, i.e. L127V and T172M, of bovine growth hormone (GH) causing the presence of GH gene haplotypes A, B, and C was previously shown to alter intramuscular fatty acid (FA) composition in Japanese Black (JB) heifers. To determine the SNP effect on somatotropic hormone concentration and lipogenesis, we measured plasma GH, insulin, and insulin-like growth factor-1 (IGF-1) concentrations. We also measured mRNA levels of fatty acid synthase (FASN), stearoyl-coA desaturase (SCD), and sterol regulatory element binding proteins-1 (SREBP-1) and FA composition in diaphragm tissues. Heifers with genotype CC had the lowest plasma insulin concentration and FASN and SCD mRNA levels among genotypes. FASN mRNA levels in haplotype A tended to positively correlate with saturated FA (SFA) content and negatively correlated with C18:2 and unsaturated FA (USFA) contents. SCD mRNA levels in haplotype A positively correlated with monounsaturated FA (MUFA) contents and negatively correlated with C18:0 content. They also tended to positively correlate with C16:1, C18:1, and USFA contents and USFA/SFA ratio and negatively correlate with SFA content. Taken together, GH gene polymorphism affects the lipogenic genes expression levels and their relationships with fatty acid compositions in diaphragm tissues of JB heifers at 31 months of age.

Cytochrome P450 2D14 (CYP2D14) Gene Deletion Variants in the Japanese Black Cattle and Characterization of their Effects on Metoclopramide Pharmacokinetics

The frequency of cytochrome P450 2D14 (CYP2D14) genetic polymorphisms and their effects on CYP2D14- mediated metabolism have not been reported in cattle. Genetic polymorphisms of the CYP2D14 gene in 57 Japanese Black (JB) cattle were determined by polymerase chain reaction (PCR)-direct sequencing. Two types of CYP2D14 gene deletion variants (GD), GD1 and GD2, were observed in this study. The CYP2D6 deletion reportedly results in delayed metabolism of metoclopramide in human. To investigate the effects of CYP2D14 gene deletion in JB cattle, the GD1, GD2 and wild-type (WT) cattle were administered metoclopramide by an intravenous or oral route. Plasma concentrations of metoclopramide in GD1 cattle were significantly higher 24 hour (h) after intravenous administration (P<0.01) and within 1 h after oral administration of metoclopramide compared to levels in GD2 and WT cattle (P<0.01). The half-life at γ-phase (γHL) of metoclopramide after intravenous administration was significantly higher in GD1 compared to WT cattle (P<0.05). Moreover, the elimination rate constant (K10) of GD1 after oral administration of metoclopramide was significantly higher in GD1 compared to WT animals (P<0.05). These results suggest that the higher plasma concentration of metoclopramide in GD1 cattle is caused by delayed metabolism of metoclopramide, owing to CYP2D14 enzyme deficiency.

Genetic Polymorphisms of Cytochrome P450 2D14 (CYP2D14) Gene in Japanese Black Cattle and Holstein-Friesian Cattle

Two types of cytochrome P450 2D14 (CYP2D14) gene deletions (GD1 and GD2) in Japanese Black cattle has been reported by us. In this study, we determined the frequency of cytochrome P450 2D14 (CYP2D14) genetic polymorphisms in 48 Japanese Black (JB) and 48 Holstein-Friesian (HF) cattle using polymerase chain reaction (PCR)-direct sequencing. Two types of CYP2D14 gene deletion variants, GD1 and GD2, were observed 58% in JB cattle, but only 8% of HF cattle. Genotype frequencies of CYP2D14 gene (105 C>A) also were assessed, but the AA substitution was not detected. The results of CYP2D14 gene variation study in cattle show that CYP2D14 GD allele may be an important mutation relevant to an enzyme defect in JB cattle because of high frequency of gene deletion variants.

Practical capability and cost effectiveness of a DNA pool-based genome-wide association study using BovineSNP50 array in a cattle population.

Genome-wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome-wide association studies. However, in DNA pooling design, the additional variance generated by pooling-specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P-values estimated by a genome-wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost-effectiveness of pool-based genome-wide association studies using the BovineSNP50 array in a cattle population.

Practical capability of a DNA pool-based genome-wide association study using BovineSNP50 array in a cattle population: DNA POOLING DESIGN IN CATTLE POPULATION

Genome-wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome-wide association studies. However, in DNA pooling design, the additional variance generated by pooling-specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P-values estimated by a genome-wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost-effectiveness of pool-based genome-wide association studies using the BovineSNP50 array in a cattle population.