Search

Background: Beef marbling is considered a desirable trait in the meat industry. Therefore, understanding the genetic factors that cause marbling is important. Previously, we performed a genome-wide association study to examine genetic factors associated with beef marbling in Japanese Black cattle and identified a candidate region between 10-30 Mbp on chromosome 7. We verified the effect of the SNPs in this region on beef marbling using linkage disequilibrium block analysis. We narrowed down the candidate region to a range of 15.8-16.1 Mbp. In this study, we comprehensively detected all of the SNPs in this region and verified their effects on beef marbling., Results: Genome resequencing using four animals exhibiting high beef marbling standard (BMS) and four with low BMS revealed a total of 1,846 polymorphisms within the candidate region. Based on the annotation, we selected 13 SNPs exhibiting a moderate impact, as no high-impact SNPs were detected. All of the SNPs represented missense polymorphisms and were located in the following seven genes: RDH8, ANGPTL6, DNMT1, MRPL4, ICAM1, ICAM3, and ICAM5. Finally, we determined the effects of these SNPs on the BMS of a Japanese Black cattle population (n = 529). Analysis of variance revealed that the five SNPs were located in genes encoding the intercellular adhesion molecules (ICAM1, ICAM3, and ICAM5), and showed a highly significant association compared with the remainder (p < 0.01). The lowest p-value was observed for ICAM3&#95;c.739G > A (p = 1.18E-04). Previous studies have suggested that intercellular adhesion molecules (ICAM) may be an upstream factor that regulates adipocyte differentiation. Therefore, considering the polymorphism and putative gene function, we suggest that ICAM1 is potentially responsible for beef marbling. c.470C > G and/or c.994G > A on ICAM1 may be responsible for this quantitative trait locus., Conclusions: Promising SNP candidates responsible for beef marbling were identified using extensive polymorphism verification in a previously reported QTL region. We aim to elucidate the mechanism of beef marbling in future studies by investigating how these polymorphisms alter protein structure and function., (© 2024. The Author(s).)

In our previous study, we used genome resequencing to detect all candidate polymorphisms within a quantitative trait loci (QTL) region for beef marbling reported previously at 10-30 Mbp on bovine chromosome 7, and we selected 6044 polymorphisms as candidate quantitative trait nucleotides (QTNs). In the present study, we aimed to identify quantitative trait genes (QTGs) and QTNs in this QTL region by verifying the effect of SNPs on beef marbling in two Japanese Black cattle populations using a Dynamic Array integrated fluidic circuit. In total, 96 selected SNPs were genotyped in 441 and 529 animals in Hyogo and Miyazaki cattle populations, respectively. The most significant p -values were detected in a SNP in a splice region of ALDH7A1 (SNP93&#95; ALDH7A1 ; p = 3.46 × 10 -5 ) in Hyogo cattle and a missense polymorphism of intercellular adhesion molecule-1 ( ICAM1 ) (SNP37&#95; ICAM1 ; p = 3.33 × 10 -4 ) in Miyazaki cattle. Interestingly, SNP93&#95; ALDH7A1 was not significant ( p = 0.459) in Miyazaki cattle, and SNP37&#95; ICAM1 showed a weakly significant association ( p = 0.043) in Hyogo cattle. Thus, each population would likely have different QTGs and QTNs for beef marbling in the QTL region. In the Hyogo population, it was not possible to determine the accurate range of the linkage disequilibrium (LD) block in LD block analysis because of a strong LD structure throughout the assessed region. In Miyazaki cattle, however, an LD block containing SNP37&#95; ICAM1 had a range of 15.8-16.1 Mbp, suggesting that QTNs would be located within this region. The functions of 19 genes in the LD block were investigated. ICAM1 is known to play an important role in adipocyte differentiation; given this function and the effect of amino acid substitution, SNP37&#95; ICAM1 was identified as a promising candidate QTN for beef marbling. Further research on the effect of SNP37&#95; ICAM1 on adipocyte differentiation is expected to provide insights into the mechanism underlying beef marbling formation.

In our previous study, we performed genome-wide association study (GWAS) to identify the genomic region associated with Fat area ratio to rib eye area (FAR) and detected a candidate in BTA7 at 10-30 Mbp. The present study aims to comprehensively detect all polymorphisms in the candidate region using whole-genome resequencing data. Based on whole-genome resequencing of eight animals, we detected 127,090 polymorphisms within the region. Of these, 31,945 were located within the genes. We further narrowed the polymorphisms to 6,044 with more than five allele differences between the high and low FAR groups that were located within 179 genes. We subsequently investigated the functions of these genes and selected 170 polymorphisms in eight genes as possible candidate polymorphisms. We focused on SLC27A6 K81M as a putative candidate polymorphism. We genotyped the SNP in a Japanese Black population (n = 904) to investigate the effect on FAR. Analysis of variance revealed that SLC27A6 K81M had a lower p-value (p = .0009) than the most significant SNP in GWAS (p = .0049). Although only SLC27A6 K81M was verified in the present study, subsequent verification of the remaining candidate genes and polymorphisms could lead to the identification of genes and polymorphisms responsible for FAR., (© 2020 Japanese Society of Animal Science.)

The objective of this study was to identify genomic regions associated with fat-related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool-based genome-wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS-BFGL-NGS-35463 and Hapmap23838-BTA-163815) and one SNP on BTA12 (ARS-BFGL-NGS-2915) significantly affected fat percentage (FAR). The significance of ARS-BFGL-NGS-35463 on BTA7 was confirmed by individual genotyping in all pooled samples. Moreover, association analysis between SNP and FAR in 803 Japanese Black cattle revealed a significant effect of SNP on FAR. Thus, further investigation of these regions is required to identify FAR-associated genes and mutations, which can lead to the development of DNA markers for marker-assisted selection for the genetic improvement of beef quality., (© 2018 Japanese Society of Animal Science.)

Previous studies have indicated that some leptin gene polymorphisms were associated with economically important traits in cattle breeds. However, polymorphisms in the leptin gene have not been reported thus far in Japanese Black cattle. Here, we aimed to identify the leptin gene polymorphisms which are associated with carcass traits and fatty acid composition in Japanese Black cattle. We sequenced the full-length coding sequence of leptin gene for eight Japanese Black cattle. Sequence comparison revealed eight single nucleotide polymorphisms (SNPs). Three of these were predicted to cause amino acid substitutions: Y7F, R25C and A80V. Then, we genotyped these SNPs in two populations (JB1 with 560 animals and JB2 with 450 animals) and investigated the effects on the traits. Y7F in JB1 and A80V in JB2 were excluded from statistical analysis because the minor allele frequencies were low (< 0.1). Association analysis revealed that Y7F had a significant effect on the dressed carcass weight in JB2; R25C had a significant effect on C18:0 and C14:1 in JB1 and JB2, respectively; and A80V had a significant effect on C16:0, C16:1, C18:1, monounsaturated fatty acid and saturated fatty acid in JB1. The results suggested that these SNPs could be used as an effective marker for the improvement of Japanese Black cattle., (© 2016 Japanese Society of Animal Science.)

The objective of the current study is to evaluate the association between fatty acid composition and fatty acid synthase gene polymorphisms as responsible mutations. For this purpose, we selected seven previously reported single nucleotide polymorphisms (SNPs) in FASN gene, including one within promoter region (g.841G>C) and six non-synonymous SNPs (g.8805C>T, g.13126C>T, g.15532A>C, g.16024A>G, g.16039C>T, g.17924A>G), and genotyped them in Japanese Black cattle. Genotyping results revealed that g.8805 C>T and g.17924 A>G were monomorphic loci. Genome-wide association analysis including the other five SNPs revealed that only g.841G>C showed significant associations with the percentages of C14:0, C14:1, C16:1 and C18:1 at 5% genome-wide significance level. In order to further evaluate the effect, we genotyped g.841G>C using additional three populations, including two Japanese Black populations and a Holstein cattle population. g.16024A>G was also genotyped and included in the analysis because it has been reported to be associated with fatty acid composition in Japanese Black cattle. In the result of analysis of variance, g.841G>C showed stronger effects on fatty acid percentage than those of g.16024A>G in all populations. These results suggested that g.841G>C would be a responsible mutation for fatty acid composition and contribute to production of high-grade beef as a selection marker in beef cattle., (© 2015 Japanese Society of Animal Science.)

In the current study, a total of 65 single nucleotide polymorphisms (SNPs) within the intron region were developed in goat (Capra hircus) by utilizing genomic information of cattle and sheep due to poor available genomic information on goat. Using these markers, we carried out genetic diversity and structure analyses for 10 Asian goat populations. The phylogenetic tree and principal components analysis showed good correspondence between clustered populations and their geographic locations. The STRUCTURE software analysis illustrated six divergent genetic structures among 10 populations. Myanmar and Cambodia populations showed high admixture patterns with different ancestry, suggesting genetic introgression into native goat populations. We also investigated the correlation between genetic diversity and geographic distance from a domestication center. This result showed a decreasing trend of genetic diversity according to the distance (P = 0.014). This result supported common consensus that western Asia is one of the centers of origin for modern Asian domestic goat., (© 2013 Japanese Society of Animal Science.)

Fatty acid composition is an important economic trait for both dairy and beef cattle and controlled by genetic factors. Candidate genes controlling fatty acid composition may be found in fat synthesis and metabolism pathways. Acetyl-CoA carboxylase is the flux-determining enzyme in the regulation of fatty acid synthesis in animal tissues. One of two isozymes of this enzyme, acetyl-CoA carboxylase-α (ACACA), catalyses the first committed step of fatty acid synthesis in mammalian cytosol, leading to the biosynthesis of long-chain fatty acids. In the current study, the sequence comparison of the coding sequence (CDS) and two promoter regions (PIA and PIII) in bovine ACACA gene was performed between Japanese Black and Holstein cattle to detect nucleotide polymorphisms influencing fatty acid composition in milk and beef. Five single nucleotide polymorphisms (SNPs) were identified in the CDS region, 28 SNPs in the PIA region and three SNPs in the PIII region. Association study revealed that CCT/CCT type of PIII&#95;#1, #2/PIA&#95;#26 indicated a higher percentage of C14:0 in the milk of the Holstein cattle than CCT/GTC type (p = 0.050) and that a difference of the percentage of C16:0 was observed between CCT/CCT and GTC/GTC type (p = 0.023). CDS&#95;#2 T/T type indicated a higher percentage of C18:0 than T/C type (p = 0.008). In addition, the Japanese Black cattle with CC/GT type of PIII&#95;#1, #2 showed a higher percentage of C18:2 in the meat than those with GT/GT type (p = 0.025). Since PIII is the promoter specific to mammary gland during lactation, the altered expression of the ACACA gene owing to the SNPs in the PIII region may influence the fatty acid composition in the milk.

Differences between average allelic frequencies of genes that relate to traits suggest that it would be evidence of artificial selections. Sliding window approach is a useful method to identify genomic regions that have been differently selected between two breeds. The objective of this study was to identify the divergently selected regions between Japanese Black (JB) and Japanese Holstein (JH) cattle based on genotypic information obtained through a high-density single nucleotide polymorphism (SNP) panel. After genotyping of 54 001 SNP markers on 100 animals (50 JB and 50 JH), 40 635 SNPs were suitable for the analysis. For each of these SNPs, the absolute difference between allelic frequencies of JB and JH was calculated. In the current study, 10 consecutive SNPs were defined as components of a window. For each window, the average difference in allelic frequency was calculated. This was termed sliding window average difference (SWAD). Among 40 055 windows, we focused on 39 windows with the largest SWAD. This was equivalent to 0.1% of all windows and the SWAD was more than 0.435. Some of these windows overlapped and were distributed in 11 regions. These regions were in good agreement with reported quantitative trait locus, therefore would be selection signatures and good candidates that harbor the causative mutations., (© 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.)

In the meat industry, correct labeling of beef origins or breed is required to assure quality and safety. This paper describes the development of discrimination markers between Japanese domestic and imported beef from the United States (US) and Australia (AUS) based on a bovine 50K single nucleotide polymorphism (SNP) array using a total of 110 samples: Japanese Black (n = 50), Japanese Holstein (n = 50) and US cattle (n = 10). Genotyping information revealed 1081 SNPs as candidate markers that were polymorphic only in US cattle. The genotyping results by PCR-restriction length polymorphism in Japanese Black (n = 300) and Holstein cattle (n = 146) revealed that 11 SNPs had alleles specific to US cattle. Their allelic frequencies in US cattle (n = 108) ranged from 0.097 to 0.250 with an average of 0.178 and the combined identification probability of US cattle was 0.987. In addition, we also verified the applicability of these US-specific markers to AUS cattle. Their allelic frequencies in AUS cattle (n = 280) ranged from 0.063 to 0.224 with an average of 0.137 and the combined identification probability of AUS cattle was 0.963. In conclusion, a set of these markers could be useful for discriminating between Japanese domestic and imported beef and would contribute to identify origins and prevent falsified labeling of beef., (© 2010 The Authors. Journal compilation © 2010 Japanese Society of Animal Science.)

Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers. The allelic frequencies for each SNP were estimated using additional individuals by PCR-RFLP (restriction fragment length polymorphism). A total of 87 SNP markers added in conjunction with previously developed 27 SNPs were evaluated to assess the utility of the test. The estimated identity power was 2.01 x 10(-34). Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.99999997 and 0.99998010, respectively. This developed SNP panel was quite powerful and could successfully exclude false sires with a probability of >0.9999 even if the dam's genotype information was not obtained. The SNP system would contribute to management of the beef industry in Japan.

In Japan, Japanese Black and Holstein cattle are appreciated as popular sources of meat, and imported beef from Australia and the United States is also in demand in the meat industry. Since the BSE outbreak, the problem of false sales has arisen: imported beef has sometimes been mislabeled as domestic beef due to consumer concerns. A method is needed to correctly discriminate between Japanese and imported cattle for food safety. The objective of this study was to develop breed discrimination markers between Japanese and US cattle using a 50K SNP array. As a result, five US-specific markers (BISNP7, BISNP15, BISNP21, BISNP23, and BISNP26) were developed with allelic frequencies that ranged from 0.102 (BISNP15) to 0.250 (BISNP7) and averaged 0.184. The combined use of the five markers would permit discrimination between Japanese and US cattle with a probability of identification of 0.858. This result indicates the potential of the bovine 50K SNP array as a powerful tool for developing breed identification markers. These markers would contribute to the prevention of falsified beef displays in Japan., (Copyright 2010 Elsevier Ltd. All rights reserved.)

This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers. The allelic frequencies for each marker were estimated by using PCR-RFLP in the Japanese Black population. Based on the frequency data, the estimated identity power of these markers was 2.73 x 10(-12). Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.96929 and 0.99693, respectively. This panel of SNP markers is theoretically sufficient for individual identification, and would also be a powerful tool for a parentage test in Japanese Black cattle. The markers could contribute to the management of the beef industry in Japan.