Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations
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...
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MDPI AG
2022-07-01
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| author | Shinji Sasazaki Raito Yamamoto Shintaro Toyomoto Hina Kondo Takayuki Akiyama Namiko Kohama Emi Yoshida Fuki Kawaguchi Kenji Oyama Hideyuki Mannen |
| author_facet | Shinji Sasazaki Raito Yamamoto Shintaro Toyomoto Hina Kondo Takayuki Akiyama Namiko Kohama Emi Yoshida Fuki Kawaguchi Kenji Oyama Hideyuki Mannen |
| author_sort | Shinji Sasazaki |
| collection | DOAJ |
| description | 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 <i>p</i>-values were detected in a SNP in a splice region of <i>ALDH7A1</i> (SNP93_<i>ALDH7A1</i>; <i>p</i> = 3.46 × 10<sup>−5</sup>) in Hyogo cattle and a missense polymorphism of intercellular adhesion molecule-1 (<i>ICAM1</i>) (SNP37_<i>ICAM1</i>; <i>p</i> = 3.33 × 10<sup>−4</sup>) in Miyazaki cattle. Interestingly, SNP93_<i>ALDH7A1</i> was not significant (<i>p</i> = 0.459) in Miyazaki cattle, and SNP37_<i>ICAM1</i> showed a weakly significant association (<i>p</i> = 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_<i>ICAM1</i> 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. <i>ICAM1</i> is known to play an important role in adipocyte differentiation; given this function and the effect of amino acid substitution, SNP37_<i>ICAM1</i> was identified as a promising candidate QTN for beef marbling. Further research on the effect of SNP37_<i>ICAM1</i> on adipocyte differentiation is expected to provide insights into the mechanism underlying beef marbling formation. |
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| spelling | doaj.art-46fb278979c3472894dcaf7f4e327bb72023-11-30T23:14:20ZengMDPI AGGenes2073-44252022-07-01137119010.3390/genes13071190Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle PopulationsShinji Sasazaki0Raito Yamamoto1Shintaro Toyomoto2Hina Kondo3Takayuki Akiyama4Namiko Kohama5Emi Yoshida6Fuki Kawaguchi7Kenji Oyama8Hideyuki Mannen9Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, JapanLaboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, JapanLaboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, JapanLaboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, JapanHokubu Agricultural Technology Institute, Hyogo Prefectural Technology Center for Agriculture, Forestry & Fisheries, Asago 669-5254, JapanHokubu Agricultural Technology Institute, Hyogo Prefectural Technology Center for Agriculture, Forestry & Fisheries, Asago 669-5254, JapanHyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, Kasai 679-0198, JapanLaboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, JapanFood Resources Education & Research Center, Kobe University, Kasai 675-2103, JapanLaboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, JapanIn 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 <i>p</i>-values were detected in a SNP in a splice region of <i>ALDH7A1</i> (SNP93_<i>ALDH7A1</i>; <i>p</i> = 3.46 × 10<sup>−5</sup>) in Hyogo cattle and a missense polymorphism of intercellular adhesion molecule-1 (<i>ICAM1</i>) (SNP37_<i>ICAM1</i>; <i>p</i> = 3.33 × 10<sup>−4</sup>) in Miyazaki cattle. Interestingly, SNP93_<i>ALDH7A1</i> was not significant (<i>p</i> = 0.459) in Miyazaki cattle, and SNP37_<i>ICAM1</i> showed a weakly significant association (<i>p</i> = 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_<i>ICAM1</i> 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. <i>ICAM1</i> is known to play an important role in adipocyte differentiation; given this function and the effect of amino acid substitution, SNP37_<i>ICAM1</i> was identified as a promising candidate QTN for beef marbling. Further research on the effect of SNP37_<i>ICAM1</i> on adipocyte differentiation is expected to provide insights into the mechanism underlying beef marbling formation.https://www.mdpi.com/2073-4425/13/7/1190GWASbeef marblingJapanese Black cattlemeat quality<i>ICAM1</i> |
| spellingShingle | Shinji Sasazaki Raito Yamamoto Shintaro Toyomoto Hina Kondo Takayuki Akiyama Namiko Kohama Emi Yoshida Fuki Kawaguchi Kenji Oyama Hideyuki Mannen Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations Genes GWAS beef marbling Japanese Black cattle meat quality <i>ICAM1</i> |
| title | Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations |
| title_full | Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations |
| title_fullStr | Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations |
| title_full_unstemmed | Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations |
| title_short | Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations |
| title_sort | verification of candidate snp effects reveals two qtls on bta7 for beef marbling in two japanese black cattle populations |
| topic | GWAS beef marbling Japanese Black cattle meat quality <i>ICAM1</i> |
| url | https://www.mdpi.com/2073-4425/13/7/1190 |
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