Association of a single nucleotide polymorphism in akirin 2 gene with marbling in Japanese Black beef cattle.

BACKGROUND: Marbling defined by the amount and distribution of intramuscular fat, so-called Shimofuri, is an economically important trait of beef cattle in Japan. The c17-25 expressed sequence tag (EST) has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus, the akirin 2 (AKIRIN2) gene containing the c17-25 EST sequence was considered as a positional functional candidate for the gene responsible for marbling. In this study, we explored single nucleotide polymorphism (SNP) in the AKIRIN2 and analyzed association of the SNP with marbling. FINDINGS: A SNP in the 3' untranslated region of the AKIRIN2, referred to as c.*188G>A, was the only difference detected between high- and low-marbled steer groups. The SNP was associated with marbling in 3 experiments using 100 sires (P = 0.041), 753 paternal half-sib progeny steers from 4 sires heterozygous for the c.*188G>A (P = 0.005), and 730 paternal half-sib progeny steers from 3 sires homozygous for the A allele at the c.*188G>A (P = 0.047), in Japanese Black beef cattle. The effect of genotypes of the SNP on subcutaneous fat thickness was not statistically significant (P > 0.05). CONCLUSION: These findings suggest that the AKIRIN2 SNP polymorphism is associated with marbling and may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle.

Association of a single nucleotide polymorphism in titin gene with marbling in Japanese Black beef cattle.

BACKGROUND: Marbling defined by the amount and distribution of intramuscular fat is an economically important trait of beef cattle in Japan. We have recently reported that single nucleotide polymorphisms (SNPs) in the endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 (EDG1) gene were associated with marbling in Japanese Black beef cattle. As well as EDG1, the titin (TTN) gene, involved in myofibrillogenesis, has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus TTN was considered as a positional functional candidate for the gene responsible for marbling. In this study, we explored SNP in TTN and analyzed association of the SNP with marbling. FINDINGS: A SNP in the promoter region of TTN, referred to as g.231054C>T, was the only difference detected between high- and low-marbled steer groups. The SNP was associated with marbling in 3 experiments using 101 sires (P = 0.004), 848 paternal half-sib progeny steers from 5 sires heterozygous for the g.231054C>T (P = 0.046), and 820 paternal half-sib progeny steers from 3 sires homozygous for C allele at the g.231054C>T (P = 0.051), in Japanese Black beef cattle. The effect of genotypes of the SNP on subcutaneous fat thickness was not statistically significant (P > 0.05). CONCLUSION: These findings suggest that in addition to the EDG1 SNPs, the TTN SNP polymorphism is associated with marbling and may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle. Further replicate studies will be needed to confirm the allelic association observed here, and to expand the results to evaluate all possible genotypic combinations of alleles.

Novel SNP in 5' flanking region of EDG1 associated with marbling in Japanese Black beef cattle.

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 (EDG1) gene has been considered as a positional functional candidate for the gene responsible for marbling. We have recently reported that 2 single nucleotide polymorphisms (SNPs), c.-312A>G in the 5' untranslated region (UTR) and c.*446G>A in the 3' UTR in EDG1 were associated with marbling in Japanese Black beef cattle, but this was not functional and a causal mutation for marbling. In the present study, we detected 2 novel SNPs, referred to as g.1475435G>A and g.1471620G>T, in the 5' flanking region of the EDG1 between low-marbled and high-marbled steer groups, which were previously shown to have EDG1 expression differences in musculus longissimus muscle. The g.1475435G>A SNP seemed not to segregate in Japanese Black beef cattle. The g.1471620G>T SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. Based on these findings, we hypothesized that the g.1471620G>T SNP might have an impact on EDG1 expression and also marbling.

Association of a single nucleotide polymorphism in ribosomal protein L27a gene with marbling in Japanese Black beef cattle.

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The c2-11#2 expressed sequence tag (EST) has been previously shown to possess expression difference in musculus longissimus muscle between low-marbled and high-marbled steer groups, and to be located within genomic region of a quantitative trait locus for marbling. Thus, the ribosomal protein L27a (RPL27A) gene containing the c2-11#2 EST sequence was considered as a positional candidate for the gene responsible for marbling. In the present study, a single nucleotide polymorphism (SNP) in the promoter region of the RPL27A, referred to as g.3109537C>T, was detected between the 2 steer groups. The SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. The effect of genotypes of the SNP on the predicted breeding value for subcutaneous fat thickness was not statistically significant. These findings suggest that the RPL27A SNP may be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle.

Polymorphisms for 7 expressed sequence tags showing marbling-associated expression changes.

We have recently showed that the 7 expressed sequence tags (ESTs), c2-11#2, c3-3, c20-29, c22-3, c26-18#1, c26-42, and g5-10, possess expression differences in musculus longissimus muscle between low-marbled and high-marbled steer groups. In the present study, we detected single nucleotide polymorphisms (SNPs) in the 5' flanking regions of the 7 EST sequences between the 2 steer groups. A SNP for the c2-11#2 EST exhibited significantly different allelic distribution between animals with extremely high predicted breeding value for marbling and with extremely low one. The SNP in the ribosomal protein L27a (RPL27A) gene containing the c2-11#2 EST sequence may be related to changes in gene expression and/or marbling.

Polymorphisms in promoter regions of PDHB, SORBS1, and EDG1 genes showing marbling-associated expression changes.

We have recently showed that the pyruvate dehydrogenase (lipoamide) beta (PDHB) gene involved in fatty acid oxidation, the sorbin and SH3 domain containing 1 (SORBS1) gene involved in insulin-stimulated glucose uptake, and the endothelial differentiation, sphingolipid G-protein-coupled receptor, 1 (EDG1) gene involved in blood vessel formation possess expression differences in musculus longissimus muscle between low-marbled and high-marbled steer groups. In the present study, we detected single nucleotide polymorphisms (SNPs) in the promoter regions of the 3 genes between the 2 steer groups. A SNP in the EDG1 exhibited significantly different allelic distribution between animals with extremely high predicted breeding value for marbling and with extremely low one. The EDG1 SNP may be related to changes in gene expression and/or marbling.