Effect of Expressions and SNPs of Candidate Genes on Intramuscular Fat Content in Qinchuan Cattle
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. DNA Samples and Phenotypes
2.2. SNP Genotyping by iPLEX MassARRAY
2.3. Real-Time PCR
2.4. Statistical Analyses
3. Results and Discussion
3.1. Associations between Four SNPs in Candidate Genes and IMF Content in Qinchuan Cattle
3.2. Effects of Expression Levels of Four Genes on IMF Content in Longissimus Muscle
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Boylston, T.D.; Morgan, S.A.; Johnson, K.A.; Busboom, J.R.; Wright, R.W.; Reeves, J.J. Lipid content and composition of wagyu and domestic breeds of beef. J. Agr. Food Chem. 1995, 43, 1202–1207. [Google Scholar] [CrossRef]
- Busboom, J.R.; Jeremiah, L.E.; Gibson, L.L.; Johnson, K.A.; Gaskins, C.T.; Reeves, J.J.; Wright, R.W. Effects of biological source on cooking and palatability attributes of beef produced for the Japanese market. Meat Sci. 1993, 35, 241–258. [Google Scholar] [CrossRef]
- Matsuishi, M.; Fujimori, M.; Okitani, K.A. Wagyu beef aroma in wagyu (Japanese black cattle) beef preferred by the Japanese over imported beef. Anim. Sci. J. 2001, 72, 498–504. [Google Scholar] [CrossRef]
- Takasuga, A.; Watanabe, T.; Mizoguchi, Y.; Hirano, T.; Ihara, N.; Takano, A.; Yokouchi, K.; Fujikawa, A.; Chiba, K.; Kobayashi, N.; et al. Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-by-descent mapping. Mamm. Genome 2007, 18, 125–136. [Google Scholar] [CrossRef]
- McClure, M.C.; Morsci, N.S.; Schnabel, R.D.; Kim, J.W.; Yao, P.; Rolf, M.M.; McKay, S.D.; Gregg, S.J.; Chapple, R.H.; Northcutt, S.L.; et al. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim. Genet. 2010, 41, 597–607. [Google Scholar] [CrossRef]
- Kim, H.; Lee, S.K.; Hong, M.W.; Park, S.R.; Lee, Y.S.; Kim, J.W.; Lee, H.K.; Jeong, D.K.; Song, Y.H.; Lee, S.J. Association of a single nucleotide polymorphism in the akirin 2 gene with economically important traits in Korean native cattle. Anim. Genet. 2013, 44, 750–753. [Google Scholar] [CrossRef]
- Casas, E.; Stone, R.T.; Keele, J.W.; Shackelford, S.D.; Kappes, S.M.; Koohmaraie, M. A comprehensive search for quantitative trait loci affecting growth and carcass composition of cattle segregating alternative forms of the myostatin gene. J. Anim. Sci. 2001, 79, 854–860. [Google Scholar] [CrossRef] [Green Version]
- Tong, B.; Sasaki, S.; Muramatsu, Y.; Ohta, T.; Kose, H.; Yamashiro, H.; Fujita, T.; Yamada, T. Association of a single-nucleotide polymorphism inmyosin-binding protein C, slow-type (MYBPC1) gene with marbling in Japanese Black beef cattle. Anim. Genet. 2014, 45, 611–612. [Google Scholar] [CrossRef]
- Peters, S.O.; Kizilkaya, K.; Garrick, D.J.; Fernando, R.L.; Reecy, J.M.; Weaber, R.L.; Silver, G.A.; Thomas, M.G. Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers. J. Anim. Sci. 2012, 90, 3398–3409. [Google Scholar] [CrossRef]
- Sasaki, S.; Yamada, T.; Sukegawa, S.; Miyake, T.; Fujita, T.; Morita, M.; Ohta, T.; Takahagi, Y.; Murakami, H.; Morimatsu, F.; et al. Association of a single nucleotide polymorphism in akirin 2 gene with marbling in Japanese Black beef cattle. BMC Res. Notes 2009, 2, 131. [Google Scholar] [CrossRef] [Green Version]
- Yamada, T.; Sasaki, S.; Sukegawa, S.; Yoshioka, S.; Takahagi, Y.; Morita, M.; Murakami, H.; Morimatsu, F.; Fujita, T.; Miyake, T.; et al. Association of a single nucleotide polymorphism in titin gene with marbling in Japanese Black beef cattle. BMC Res. Notes 2009, 2, 78. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yamada, T.; Sasaki, S.; Sukegawa, S.; Miyake, T.; Fujita, T.; Kose, H.; Morita, M.; Takahagi, Y.; Murakami, H.; Morimatsu, F.; et al. Novel SNP in 5′ flanking region of EDG1 associated with marbling in Japanese Black beef cattle. Anim. Sci. J. 2009, 80, 486–489. [Google Scholar] [CrossRef] [PubMed]
- Wei, D.; Gui, L.; Raza, S.H.A.; Zhang, S.; Khan, R.; Wang, L.; Guo, H.; Zan, L. NRF1 and ZSCAN10 bind to the promoter region of the SIX1 gene and their effects body measurements in Qinchuan cattle. Sci. Rep. 2017, 7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Wei, D.; Raza, S.H.A.; Zhang, J.; Gui, L.; Rahman, S.U.; Khan, R.; Hosseini, S.M.; Kaleri, H.A.; Zan, L. Polymorphism in promoter of SIX4 gene shows association with its transcription and body measurement traits in Qinchuan cattle. Gene 2018, 656, 9–16. [Google Scholar] [CrossRef] [PubMed]
- Gabriel, S.; Ziaugra, L.; Tabbaa, D. SNP genotyping using the sequenom MassARRAY iPLEX platform. Curr. Protoc. Hum. Genet. 2009. [Google Scholar] [CrossRef] [PubMed]
- Tong, B.; Muramatsu, Y.; Ohta, T.; Kose, H.; Yamashiro, H.; Sugiyama, T.; Yamada, T. Association of the expression level of the MYBPC1 gene in skeletal muscle with marbling trait in Japanese black beef cattle. Ann. Anim. Sci. 2015, 15, 349–358. [Google Scholar] [CrossRef] [Green Version]
- Schmittgen, T.D.; Thomas, D.; Livak; Kenneth, J. Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 2008, 3, 1101–1108. [Google Scholar] [CrossRef]
- Sasaki, Y.; Miyake, T.; Gaillard, C.; Oguni, T.; Ohtagaki, S. Comparison of genetic gains per year for carcass traits among breeding programs in the Japanese Brown and the Japanese Black cattle. J. Anim. Sci. 2006, 84, 317–323. [Google Scholar] [CrossRef]
- Tong, B.; Sasaki, S.; Muramatsu, Y.; Ohta, T.; Kose, H.; Fujita, T.; Yamada, T. The G allele at the g.70014208A > G in the MYBPC1 gene associated with high marbling in Japanese Black cattle is at a low frequency in breeds not selected for marbling. J. Genet. 2014, 93, 231–233. [Google Scholar] [CrossRef]
- Sasaki, Y.; Nagai, K.; Nagata, Y.; Doronbekov, K.; Nishimura, S.; Yoshioka, S.; Fujita, T.; Shiga, K.; Miyake, T.; Taniguchi, Y.; et al. Exploration of genes showing intramuscular fat deposition-associated expression changes in musculus longissimus muscle. Anim. Genet. 2006, 37, 40–46. [Google Scholar] [CrossRef]
- Lee, S.H.; Cho, Y.M.; Lee, S.H.; Kim, B.S.; Kim, N.K.; Choy, Y.H.; Hoon, K.; Kim, D.Y.; Im, S.K.; Oh, S.J.; et al. Identification of marbling-related candidate genes in M. Longissimus dorsi of high- and low marbled Hanwoo (Korean Native Cattle) steers. BMB Rep. 2008, 41, 846–851. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, Y.; Wada, R.; Yamashita, T.; Mi, Y.; Deng, C.X.; Hobson, J.P.; Rosenfeldt, H.M.; Nava, V.E.; Chae, S.S.; Lee, M.J.; et al. Edg-1, the G protein-coupled receptor for sphingosine-1-phosphate, is essential for vascular maturation. J. Clin. Invest. 2000, 106, 951–961. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Gene | SNP | Genotype (Number) | IMF Content (%) |
---|---|---|---|
AKIRIN2 | c.*188G>A | GG (212) | 7.57 ± 0.07 |
GA (120) | 7.45 ± 0.07 | ||
AA (18) | 7.44 ± 0.34 | ||
TTN | g.231054C>T | CC (257) | 7.46 ± 0.06 |
CT (87) | 7.55 ± 0.10 | ||
EDG1 | g.42041062G>T | GG (255) | 7.42 ± 0.07 a |
GT (83) | 7.60 ± 0.09 | ||
TT (12) | 8.15 ± 0.03 b | ||
MYBPC1 | g.70014208A>G | GG (291) | 7.48 ± 0.06 |
GA (53) | 7.67 ± 0.09 |
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Li, Y.; Cheng, G.; Yamada, T.; Liu, J.; Zan, L.; Tong, B. Effect of Expressions and SNPs of Candidate Genes on Intramuscular Fat Content in Qinchuan Cattle. Animals 2020, 10, 1370. https://doi.org/10.3390/ani10081370
Li Y, Cheng G, Yamada T, Liu J, Zan L, Tong B. Effect of Expressions and SNPs of Candidate Genes on Intramuscular Fat Content in Qinchuan Cattle. Animals. 2020; 10(8):1370. https://doi.org/10.3390/ani10081370
Chicago/Turabian StyleLi, Yaxing, Gong Cheng, Takahisa Yamada, Jianfeng Liu, Linsen Zan, and Bin Tong. 2020. "Effect of Expressions and SNPs of Candidate Genes on Intramuscular Fat Content in Qinchuan Cattle" Animals 10, no. 8: 1370. https://doi.org/10.3390/ani10081370
APA StyleLi, Y., Cheng, G., Yamada, T., Liu, J., Zan, L., & Tong, B. (2020). Effect of Expressions and SNPs of Candidate Genes on Intramuscular Fat Content in Qinchuan Cattle. Animals, 10(8), 1370. https://doi.org/10.3390/ani10081370