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10.3390/genes13071190
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Article

Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations

by
Shinji Sasazaki
1,*,
Raito Yamamoto
1,
Shintaro Toyomoto
1,
Hina Kondo
1,
Takayuki Akiyama
2,
Namiko Kohama
2,
Emi Yoshida
3,
Fuki Kawaguchi
1,
Kenji Oyama
4 and
Hideyuki Mannen
1
1
Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
2
Hokubu Agricultural Technology Institute, Hyogo Prefectural Technology Center for Agriculture, Forestry & Fisheries, Asago 669-5254, Japan
3
Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, Kasai 679-0198, Japan
4
Food Resources Education & Research Center, Kobe University, Kasai 675-2103, Japan
*
Author to whom correspondence should be addressed.
Genes 2022, 13(7), 1190; https://doi.org/10.3390/genes13071190
Submission received: 8 June 2022 / Revised: 28 June 2022 / Accepted: 30 June 2022 / Published: 1 July 2022
(This article belongs to the Special Issue From QTL Mapping to QTG and QTN Identification)
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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.
Keywords: GWAS; beef marbling; Japanese Black cattle; meat quality; ICAM1 GWAS; beef marbling; Japanese Black cattle; meat quality; ICAM1

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MDPI and ACS Style

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 2022, 13, 1190. https://doi.org/10.3390/genes13071190

AMA Style

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. 2022; 13(7):1190. https://doi.org/10.3390/genes13071190

Chicago/Turabian Style

Sasazaki, Shinji, Raito Yamamoto, Shintaro Toyomoto, Hina Kondo, Takayuki Akiyama, Namiko Kohama, Emi Yoshida, Fuki Kawaguchi, Kenji Oyama, and Hideyuki Mannen. 2022. "Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations" Genes 13, no. 7: 1190. https://doi.org/10.3390/genes13071190

APA Style

Sasazaki, S., Yamamoto, R., Toyomoto, S., Kondo, H., Akiyama, T., Kohama, N., Yoshida, E., Kawaguchi, F., Oyama, K., & Mannen, H. (2022). Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations. Genes, 13(7), 1190. https://doi.org/10.3390/genes13071190

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