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Sugita H.,Tohoku University | Ardiyanti A.,Tohoku University | Yokota S.,Tohoku University | Yonekura S.,Shinshu University | And 6 more authors.
Livestock Science | Year: 2014

Previous studies demonstrated that single nucleotide polymorphisms (SNPs) in exon 5 of the bovine growth hormone (GH) gene affected live weight and carcass traits in Japanese Black cattle. The aims of the present study were to identify SNPs in the promoter region of the GH gene and to analyze their effects on carcass traits and intramuscular (i.m.) fatty acid compositions in Japanese Black cattle (511 steers and 252 heifers; 30.5±0.1 months old). SNPs in the promoter region of the GH gene were detected at g.253, g.303, and g.502 and classified into 4 haplotypes, i.e. haplotype P (T-C-C), Q (C-C-C), R (C-C-T), and S (T-T-C). Among genotypes at g.253, genotype TT had the highest carcass weight (CW), rib thickness (RT), and C14:0 and C16:1 contents, but the lowest C18:0 content. The rib eye area (REA) in genotype TT was higher compared with that in genotype CC. Genotype CC had the lowest C16:0 content and higher C18:1 and MUFA contents compared with those in genotype TT. Among genotypes at g.303, genotype CC had the highest C14:0, C16:0, and C16:1 contents, but the lowest C18:1 content. Genotype TT had the lowest CW and RT, but the highest C18:0 content. At both locations, the heterozygous animals showed intermediate values for most traits. Regarding GH promoter diplotypes, diplotype PP had higher CW, C16:0, and C16:1 than diplotype SS and tended to have the lowest C18:0 compared with diplotype QQ and SS. In conclusion, SNPs at g.253 and g.303 in the GH promoter region affects carcass traits in Japanese Black cattle. © 2014 Elsevier B.V.

Yokota S.,Tohoku University | Sugita H.,Tohoku University | Ardiyanti A.,Tohoku University | Shoji N.,Yamagata Prefectural Animal Industrial Institute | And 6 more authors.
Animal Genetics | Year: 2012

The fatty acid synthase (FASN) and stearoyl-CoA desaturase (delta-9-desaturase) (SCD) genes affect fatty acid composition. This study evaluated the contributions of polymorphisms of these genes on fatty acid composition in muscle in two different populations: 1189 and 1058 Japanese Black cattle from the Miyagi and the Yamagata populations respectively. We sampled intramuscular fat from the longissimus thoracis muscle in the Miyagi population and from the trapezius muscle in the Yamagata population. The collective contributions of FASN and SCD polymorphisms to total additive genetic variance for oleic acid were 13.46% in the Miyagi population and 16.29% in the Yamagata population and to phenotypic variance were 5.45% and 6.54% respectively. Although the individual effects of FASN and SCD polymorphisms on fatty acid composition were small, overall gene substitution may effectively improve fatty acid composition. In addition, we found that gene polymorphism contributions of fatty acids varied by population even in the same breed. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Uemoto Y.,National Livestock Breeding Center | Sasago N.,National Livestock Breeding Center | Abe T.,National Livestock Breeding Center | Okada H.,G and G science Inc | And 7 more authors.
Animal Science Journal | Year: 2012

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. © 2012 The Authors. Animal Science Journal © 2012 Japanese Society of Animal Science.

Henderson G.,Agresearch Ltd. | Cox F.,Agresearch Ltd. | Ganesh S.,Agresearch Ltd. | Jonker A.,Agresearch Ltd. | And 151 more authors.
Scientific Reports | Year: 2015

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific. © 2015 Macmillan Publishers Limited.

Uemoto Y.,National Livestock Breeding Center | Abe T.,National Livestock Breeding Center | Tameoka N.,National Livestock Breeding Center | Hasebe H.,National Livestock Breeding Center | And 5 more authors.
Animal Genetics | Year: 2011

Fatty acid composition, especially oleic acid (C18:1), plays an important role in the eating quality of meat in Japanese Black cattle. Therefore, the objective of this study was to identify loci associated with C18:1 in the intramuscular fat of the trapezius muscles in Japanese Black cattle using the Illumina BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. We also evaluated the relationship between C18:1 and three fatty acid synthesis genes, fatty acid synthase (FASN), stearoyl-CoA desaturase and sterol regulatory element-binding protein-1. In this experiment, we applied a mixed model and Genomic Control approach using selective genotyping to perform a genome-wide association study. A total of 160 animals (80 animals with higher values and 80 animals with lower values), selected from 3356 animals based on corrected phenotype, were genotyped using the Illumina BovineSNP50 BeadChip and three fatty acid synthesis genes, and the quality of these SNPs was assessed. In this study, a total of 38 955 SNPs, which included SNPs in the three fatty acid synthesis genes, were used, and the estimated inflation factor was 1.06. In the studied population, a total of 32 SNPs, including the FASN gene, had significant effects, and in particular 30 SNPs of all significant SNPs were located between 49 and 55 Mbp on chromosome 19. This study is one of the first genome-wide association studies for fatty acid composition in a cattle population using the recently released Illumina BovineSNP50 BeadChip. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics,.

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