Allele Frequency Distribution of the NCAPG c.1326T>G SNP Associated with Growth-Related Traits in Niigata Population of Japanese Black Beef Cattle

Growth performance as well as marbling is the main breeding objectives in Japanese Black cattle, the major beef breed in Japan. A previous study has identified the c.1326T>G single nucleotide polymorphism (SNP) in the NCAPG (non-SMC condensin I complex, subunit G) gene that leads to the amino acid change p.Ile442Met in the NCAPG protein, which is a candidate causative variation for a bovine carcass weight (CWT) quantitative trait locus (QTL). In this study, we first confirmed the association of the c.1326T>G SNP with the growth-related traits, CWT, rib eye area (REA) and rib thickness (RT), and showed significant effect of the SNP genotypes on the marbling trait, beef marbling score (BMS), in the Japanese Black beef cattle population of the Niigata prefecture, with the G allele being associated with a favorable phenotype of these traits. Thus, we concluded that the c.1326T>G SNP is useful for effective marker-assisted selection to increase meat quality and meat productivity in Japanese Black beef cattle of the Niigata prefecture. Furthermore the frequency of the favorable G allele of the c.1326T>G SNP in the Niigata prefecture population was significantly lower than the frequency of this allele in Japanese Black cattle population of the Kagoshima prefecture. However, no statistically significant difference was detected between the allele frequencies estimated by maternal alleles in the half-sib progeny steers in the Niigata prefecture population and obtained in Japanese Black cattle population of the Kagoshima prefecture.

Allele Frequency Distribution in PNLIP Promoter SNP Is Different between High-Marbled and Low-Marbled Japanese Black Beef Cattle

Marbling defined by the amount and distribution of intramuscular fat is regarded as an economically important trait of beef cattle in Japan. The pancreatic lipase gene (PNLIP) is located within the genomic region of a bovine marbling quantitative trait locus. The rat homologue of PNLIP has been previously shown to be regarded as a possible candidate for the gene responsible for intramuscular fat content. These findings suggested that PNLIP was a positional and functional candidate for the marbling gene. In this study, we detected a single nucleotide polymorphism (SNP), g.37288470A > G, at 1917 bp upstream of the PNLIP transcription initiation site between Holstein steers and somatic nuclear-derived cloned steers from a Japanese Black sire with a very high estimated breeding value for marbling by sequencing analysis. Further, we found statistically significant difference in the allelic distribution of the SNP between 17 Japanese Black unrelated sires with extremely high predicted breeding values for marbling and 17 sires with extremely low ones (P = 0.0332). Our findings suggest that g.37288470A > G SNP in the promoter region of PNLIP might be associated with marbling by altering its gene expression, and be useful for effective marker-assisted selection to increase the levels of marbling in Japanese Black beef cattle.

No replicated association of the c.-312A >G in<i>EDG</i>1 with marbling in Niigata population of Japanese Black beef cattle

Marbling, defined by the amount and the distribution of intramuscular fat and measured as beef marbling score (BMS), is an economically important trait of beef cattle in Japan. We recently reported that a single nucleotide polymorphism (SNP), namely, c.-312A > G, in the endothelial differentiation sphingolipid G-proteincoupled receptor, 1 (EDG1) gene was associated with the BMS level in the Japanese Black beef cattle population of Oita prefecture, with the G allele being associated with a high level of the BMS. Thus, the c.-312A > G SNP seems to be a candidate marker for marker-assisted selection. In this study, we investigated whether this association could be replicated in the Japanese Black beef cattle population of Niigata prefecture and analyzed the effect of the SNP genotypes on the carcass traits other than the BMS. No significant differences in the BMS level were detected among the genotypes of the c.-312A > G SNP in the Niigata Japanese Black beef cattle population. The SNP genotype had no significant effects on the carcass weight, rib eye area and rib thickness of the cattle population. These findings suggested that the association of the c.-312A > G SNP with the BMS level in the Japanese Black beef cattle population was not replicated in the Niigata population, and revealed no effects of the SNP genotype on the beef productivity in the Niigata population. Thus, we concluded that the c.-312A > G SNP is not useful for effective marker-assisted selection to increase meat quality and, additionally, meat productivity in Japanese Black beef cattle of Niigata prefecture.

Replicated association of the single nucleotide polymorphism in PNLIP with marbling in Niigata population of Japanese Black beef cattle

Marbling is regarded as an economically important trait of beef cattle inJapan, and measured as a beef marbling score (BMS). Our previous study reported an association between a single nucleotide polymorphism (SNP), rs4164 8172, in the pancreatic lipase (PNLIP) gene and the BMS level, using the Japanese Black beef cattle population of Oita prefecture. Further, we showed that the T allele at the rs41648172 SNP is associated with a high level of the BMS. Thus, we suggested that the rs41648172 SNP seems to be a candidate marker for marker-assisted selection. Our present study was designed to investigate whether this association could be replicated in other independent Japanese Black cattle population and analyze the effect of the SNP genotypes on the carcass traits other than the BMS. We detected the marginally significant effect of the genotypes of the rs41648172 SNP on the BMS level by using the Japanese Black beef cattle population of Niigata prefecture (P = 0.0919), and obtained the result of the T allele associated with an increase in the BMS level, consistent with our previous data. In addition, we showed no significant association of the SNP with the subcutaneous fat thickness, carcass weight, rib eye area, rib thickness and yield estimate in the Japanese Black beef cattle population ofNiigataprefecture. Thus, we concluded that the rs41648172 SNP was useful for effective marker-assisted selection to increase the BMS level in Japanese Black beef cattle, based on the replicated association of the rs41648172 SNP with the BMS level in the other independent Japanese Black beef cattle population and no effect of the SNP genotypes on the carcass traits other than BMS.