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Yamada T.,Niigata University | Sasaki S.,Maebashi Institute of Animal Science | Sukegawa S.,Tsukuba Center Inc. | Takahagi Y.,Tsukuba Center Inc. | And 4 more authors.
Journal of Animal and Veterinary Advances | Year: 2011

Growth performance as well as marbling is the main breeding objectives in Japanese Black cattle, the major beef breed in Japan. The researchers have recently reported that a Single Nucleotide Polymorphism (SNP), referred to asg.231054C>T in promoter region of the Titin (TTN) gene was associated with marbling in Japanese Black beef cattle with the T allele being associated with a high level of marbling. The TTN is known to be involved in myofibrillogenesis and has been previously shown to be located within genomic region of a quantitative trait locus for rib eye area. Thus, the TTN was considered as a positional functional candidate for the gene responsible for growth performance. In this study, the researchers analyzed the effect of the TTN g.231054C>T SNP genotypes on the growth-related carcass traits in Japanese Black beef cattle. The SNP was marginally associated with rib eye area in two experiments using 101 sires (p = 0.067) and 820 paternal half-sib progeny steers from 3 sires homozygous for C allele at the g.231054C>T (p = 0.090) in Japanese Black beef cattle. These findings suggest possible effect of the g.231054C>T on the growth-related trait in Japanese Black beef cattle. The TTN SNP polymorphism may be useful for effective marker-assisted selection to increase the beef productivity in Japanese Black beef cattle. © Medwell Journals, 2011. Source


Watanabe N.,Oita Prefectural Institute of Animal Industry | Satoh Y.,Animal Industry Research Institute | Fujita T.,Oita Prefectural Institute of Animal Industry | Ohta T.,Niigata University | And 4 more authors.
BMC Research Notes | Year: 2011

Background: Marbling defined by the amount and distribution of intramuscular fat, so-called Shimofuri, is an economically important trait of beef cattle in Japan. Our previous study detected 3 single nucleotide polymorphisms (SNPs), g.231054C > T, g.3109537C > T and c.*188G > A, respectively, in the 5' flanking region of the titin (TTN), the 5' flanking region of the ribosomal protein L27a (RPL27A) and the 3' untranslated region of the akirin 2 genes (AKIRIN2), which have been considered as positional functional candidates for the genes responsible for marbling, and showed association of these SNPs with marbling in Japanese Black beef cattle. In the present study, we investigated the allele frequency distribution of the 3 SNPs among the 5 cattle breeds, Japanese Black, Japanese Brown, Japanese Shorthorn, Holstein and Brown Swiss breeds. Findings. We genotyped the TTN g.231054C > T, RPL27A g.3109537C > T and AKIRIN2 c.*188G > A SNPs by polymerase chain reaction-restriction fragment length polymorphism method, using 101 sires and 1,705 paternal half sib progeny steers from 8 sires for Japanese Black, 86 sires and 27 paternal half sib progeny steers from 3 sires for Japanese Brown, 79 sires and 264 paternal half sib progeny steers from 14 sires for Japanese Shorthorn, 119 unrelated cows for Holstein, and 118 unrelated cows for Brown Swiss breeds. As compared to the frequencies of the g.231054C > T T, g.3109537C > T T and c.*188G > A A alleles, associated with high marbling, in Japanese Black breed that has been subjected to a strong selection for high marbling, those in the breeds, Japanese Shorthorn, Holstein and Brown Swiss breeds, that have not been selected for high marbling were null or lower. The Japanese Brown breed selected slightly for high marbling showed lower frequency than Japanese Black breed in the g.3109537C > T T allele, whereas no differences were detected between the 2 breeds in the frequencies of the g.231054C > T T and c.*188G > A A alleles. Conclusions: Based on this finding, we hypothesized that the pressure of the strong selection for high marbling in Japanese Black breed has increased the frequencies of the T, T and A alleles at the TTN g.231054C > T, RPL27A g.3109537C > T and AKIRIN2 c.*188G > A SNPs, respectively. This study, together with the previous association studies, suggested that the 3 SNPs may be useful for effective marker-assisted selection to increase the levels of marbling. © 2011 Yamada et al; licensee BioMed Central Ltd. Source


Nishimura S.,Shirakawa Institute of Animal Genetics | Watanabe T.,Shirakawa Institute of Animal Genetics | Watanabe T.,National Livestock Breeding Center | Mizoshita K.,Cattle Breeding Development Institute of Kagoshima Prefecture | And 6 more authors.
BMC Genetics | Year: 2012

Background: Significant quantitative trait loci (QTL) for carcass weight were previously mapped on several chromosomes in Japanese Black half-sib families. Two QTL, CW-1 and CW-2, were narrowed down to 1.1-Mb and 591-kb regions, respectively. Recent advances in genomic tools allowed us to perform a genome-wide association study (GWAS) in cattle to detect associations in a general population and estimate their effect size. Here, we performed a GWAS for carcass weight using 1156 Japanese Black steers.Results: Bonferroni-corrected genome-wide significant associations were detected in three chromosomal regions on bovine chromosomes (BTA) 6, 8, and 14. The associated single nucleotide polymorphisms (SNP) on BTA 6 were in linkage disequilibrium with the SNP encoding NCAPG Ile442Met, which was previously identified as a candidate quantitative trait nucleotide for CW-2. In contrast, the most highly associated SNP on BTA 14 was located 2.3-Mb centromeric from the previously identified CW-1 region. Linkage disequilibrium mapping led to a revision of the CW-1 region within a 0.9-Mb interval around the associated SNP, and targeted resequencing followed by association analysis highlighted the quantitative trait nucleotides for bovine stature in the PLAG1-CHCHD7 intergenic region. The association on BTA 8 was accounted for by two SNP on the BovineSNP50 BeadChip and corresponded to CW-3, which was simultaneously detected by linkage analyses using half-sib families. The allele substitution effects of CW-1, CW-2, and CW-3 were 28.4, 35.3, and 35.0 kg per allele, respectively.Conclusion: The GWAS revealed the genetic architecture underlying carcass weight variation in Japanese Black cattle in which three major QTL accounted for approximately one-third of the genetic variance. © 2012 Nishimura et al.; licensee BioMed Central Ltd. Source


Watanabe N.,Oita Prefectural Institute of Animal Industry | Yamada T.,Kyoto University | Yoshioka S.,Beef Information and Genetics Institute Inc | Itoh M.,Oita Prefectural Institute of Animal Industry | And 6 more authors.
Animal Science Journal | Year: 2010

Our previous study detected a single nucleotide polymorphism (SNP), g.1471620G>. T, in the 5′ flanking region of the endothelial differentiation sphingolipid G-protein-coupled receptor 1 (EDG1) gene, which has been considered as a positional functional candidate for the gene responsible for marbling, and showed association of the g.1471620G>. T SNP with marbling in Japanese Black beef cattle. In the present study, we investigated the allele frequency distribution of the g.1471620G>. T SNP among the 5 cattle breeds, Japanese Black, Japanese Brown, Japanese Short Horn, Holstein, and Brown Swiss breeds. The T allele at the g.1471620G>. T SNP associated with high marbling was found at high frequency in Japanese Black breed that has been subjected to a strong selection for high marbling, while the allele was absent or at very low frequencies in the other breeds that have not been strongly selected for high marbling. Based on this finding, we hypothesized that the pressure of the strong selection for high marbling in Japanese Black breed has increased the frequency of the T allele at the g.1471620G>. T SNP in the EDG1. © 2009 The Authors. Journal compilation © 2009 Japanese Society of Animal Science. Source

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