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Sasazaki S, Kondo H, Moriishi Y, Kawaguchi F, Oyama K, Mannen H. Comprehensive genotyping analysis of single nucleotide polymorphisms responsible for beef marbling in Japanese Black cattle. BMC Genom Data 2024; 25:17. [PMID: 38336623 PMCID: PMC10854043 DOI: 10.1186/s12863-024-01199-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
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_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.
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Affiliation(s)
- Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
| | - Hina Kondo
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yurika Moriishi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kenji Oyama
- Food Resources Education & Research Center, Kobe University, Kasai, Japan
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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Sasazaki S, Yamamoto R, Toyomoto S, Kondo H, Akiyama T, Kohama N, Yoshida E, Kawaguchi F, Oyama K, Mannen H. Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations. Genes (Basel) 2022; 13:genes13071190. [PMID: 35885973 PMCID: PMC9320647 DOI: 10.3390/genes13071190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 01/25/2023] Open
Abstract
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_ALDH7A1; p = 3.46 × 10−5) in Hyogo cattle and a missense polymorphism of intercellular adhesion molecule-1 (ICAM1) (SNP37_ICAM1; p = 3.33 × 10−4) in Miyazaki cattle. Interestingly, SNP93_ALDH7A1 was not significant (p = 0.459) in Miyazaki cattle, and SNP37_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_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_ICAM1 was identified as a promising candidate QTN for beef marbling. Further research on the effect of SNP37_ICAM1 on adipocyte differentiation is expected to provide insights into the mechanism underlying beef marbling formation.
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Affiliation(s)
- Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (R.Y.); (S.T.); (H.K.); (F.K.); (H.M.)
- Correspondence:
| | - Raito Yamamoto
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (R.Y.); (S.T.); (H.K.); (F.K.); (H.M.)
| | - Shintaro Toyomoto
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (R.Y.); (S.T.); (H.K.); (F.K.); (H.M.)
| | - Hina Kondo
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (R.Y.); (S.T.); (H.K.); (F.K.); (H.M.)
| | - Takayuki Akiyama
- Hokubu Agricultural Technology Institute, Hyogo Prefectural Technology Center for Agriculture, Forestry & Fisheries, Asago 669-5254, Japan; (T.A.); (N.K.)
| | - Namiko Kohama
- Hokubu Agricultural Technology Institute, Hyogo Prefectural Technology Center for Agriculture, Forestry & Fisheries, Asago 669-5254, Japan; (T.A.); (N.K.)
| | - Emi Yoshida
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, Kasai 679-0198, Japan;
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (R.Y.); (S.T.); (H.K.); (F.K.); (H.M.)
| | - Kenji Oyama
- Food Resources Education & Research Center, Kobe University, Kasai 675-2103, Japan;
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (R.Y.); (S.T.); (H.K.); (F.K.); (H.M.)
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Sasazaki S. Development of DNA markers for improvement of meat quality in a Japanese Black cattle population in Hyogo Prefecture. Anim Sci J 2021; 92:e13663. [PMID: 34882912 DOI: 10.1111/asj.13663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/28/2023]
Abstract
The polymorphisms associated with economic traits in livestock animals provide useful information as genetic indicators for breeding improvement. Over the last two decades, several DNA markers have been developed in Japanese Black cattle; however, the effect of these markers differs across populations due to differences in their genetic structures and backgrounds. As such, there is a need to verify the effectiveness of these markers in each population. This review summarizes the effectiveness of previously reported markers on carcass traits and the development of novel DNA markers in a Japanese Black cattle population in Hyogo Prefecture. As result of genome wide association studies and resequencing analyses, two novel significant markers associated with meat quality-related traits (beef marbling and fatty acid composition) were developed. These findings will lead to the identification of responsible genes and polymorphisms and contribute to the development of novel DNA markers for numerous traits in various cattle populations.
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Affiliation(s)
- Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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Kohama N, Yoshida E, Masaki T, Iwamoto E, Fukushima M, Honda T, Oyama K. Estimation of genetic parameters for carcass grading traits, image analysis traits, and monounsaturated fatty acids in Japanese Black cattle from Hyogo Prefecture. Anim Sci J 2021; 92:e13664. [PMID: 34882915 DOI: 10.1111/asj.13664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 11/27/2022]
Abstract
Genetic parameters for carcass grading traits, image analysis traits, and monounsaturated fatty acid (MUFA) percentages were estimated in 29,942 Japanese Black cattle from Hyogo Prefecture. The analyzed traits included five carcass grading traits, two image analysis traits, fat area ratio and fineness index, and two MUFA traits, one measured in intermuscular fat using near-infrared spectroscopy (NIRS) and the other in intramuscular fat using gas chromatography (GC). The heritability estimates of image analysis traits and MUFA were moderate to high, ranging from 0.395 to 0.740, and it was considered that they could be improved simultaneously with carcass grading traits because no severe genetic antagonism was observed. Although the heritability of the NIRS-based intermuscular MUFA was slightly lower than that of the GC-based intramuscular MUFA, the genetic correlation between the two methods was as high as 0.804. These results indicate that the NIRS method can be used as an alternative evaluation procedure to predict MUFA in intramuscular fat in the longissimus muscle.
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Affiliation(s)
- Namiko Kohama
- Hokubu Agricultural Technology Institute, Hyogo Pref. Technology Center for Agriculture, Forestry and Fisheries, Asago, Hyogo, Japan.,Food Resources Education & Research Center, Kobe University, Kasai, Hyogo, Japan
| | - Emi Yoshida
- Livestock Technology Institute, Hyogo Pref. Technology Center for Agriculture, Forestry, and Fisheries, Kasai, Hyogo, Japan
| | - Tatsunori Masaki
- Livestock Technology Institute, Hyogo Pref. Technology Center for Agriculture, Forestry, and Fisheries, Kasai, Hyogo, Japan
| | - Eiji Iwamoto
- Hokubu Agricultural Technology Institute, Hyogo Pref. Technology Center for Agriculture, Forestry and Fisheries, Asago, Hyogo, Japan
| | | | - Takeshi Honda
- Food Resources Education & Research Center, Kobe University, Kasai, Hyogo, Japan
| | - Kenji Oyama
- Food Resources Education & Research Center, Kobe University, Kasai, Hyogo, Japan
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Bagatoli A, de Melo ALP, Gasparino E, Rodrigues MT, Ferreira L, Garcia OSR, Soares MAM. Association between polymorphisms of APOB, SLC27A6, AGPAT6 and PRLR genes and milk production and quality traits in goats. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ueda S, Hosoda M, Yoshino KI, Yamanoue M, Shirai Y. Gene Expression Analysis Provides New Insights into the Mechanism of Intramuscular Fat Formation in Japanese Black Cattle. Genes (Basel) 2021; 12:genes12081107. [PMID: 34440281 PMCID: PMC8391117 DOI: 10.3390/genes12081107] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
Japanese Black cattle (Japanese Wagyu) have a unique phenotype in which ectopic intramuscular fat accumulates in skeletal muscle, producing finely marbled beef. However, the mechanism of intramuscular fat formation in Japanese Black cattle remains unclear. To investigate the key genes involved in intramuscular fat accumulation, we comprehensively analyzed mRNA levels in subcutaneous and intramuscular fat tissues using RNA sequence (RNA-seq) analysis, which detected 27,606 genes. We identified eight key genes, namely carboxypeptidase E, tenascin C, transgelin, collagen type IV alpha 5 (COL4A5), cysteine and glycine-rich protein 2, PDZ, and LIM domain 3, phosphatase 1 regulatory inhibitor subunit 14A, and regulator of calcineurin 2. These genes were highly and specifically expressed in intramuscular fat tissue. Immunohistochemical analysis revealed a collagen network, including COL4A5, in the basement membrane around the intramuscular fat tissue. Moreover, pathway analysis revealed that, in intramuscular fat tissue, differentially expressed genes are related to cell adhesion, proliferation, and cancer pathways. Furthermore, pathway analysis showed that the transforming growth factor-β (TGF-β) and small GTPases regulators RASGRP3, ARHGEF26, ARHGAP10, ARHGAP24, and DLC were upregulated in intramuscular fat. Our study suggests that these genes are involved in intramuscular fat formation in Japanese Black cattle.
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Affiliation(s)
- Shuji Ueda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (M.H.); (M.Y.); (Y.S.)
- Correspondence: ; Tel.: +81-78-803-5889
| | - Mana Hosoda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (M.H.); (M.Y.); (Y.S.)
| | - Ken-ichi Yoshino
- Biosignal Research Center, Kobe University, Kobe 657-8501, Japan;
| | - Minoru Yamanoue
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (M.H.); (M.Y.); (Y.S.)
| | - Yasuhito Shirai
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan; (M.H.); (M.Y.); (Y.S.)
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