SNP Detection in FREM2 Gene and Its Association with Carcass Quality in Bali Beef
Abstract
The FRAS1-related extracellular matrix protein 2 (FREM2) gene is one of the genes that play a role in controlling marbling scores in beef cattle. This study aimed to identify SNPs in exon 6 of the FREM2 gene and its association with carcass quality in Bali beef using ultrasonography. A total of 93 cattle were used: 55 cattle from Banjarmasin slaughterhouse, South Kalimantan, Indonesia, 28 cattle from Bali Cattle Breeding Centre in Bali Province, and 10 cattle from UPTD Kupang Regency, NTT, Indonesia. SNP of the FREM2 gene was identified by using sequencing techniques and then genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The association of FREM2 gene SNPs with carcass characteristics was analyzed using the General Linear Model (GLM) method using SPSS software version 22. Carcass (longissimus dorsi thickness; back fat thickness) and meat (intramuscular fat; marbling score) characteristics were identified non-invasively using ultrasonography images and then analyzed with Image-J NIH software. SNP at position g.89327G>A was located in exon 6 of the FREM2 gene and did not change the amino acid (prolineproline) sequence in Bali beef. The genotyping results with PCR-RFLP technique SNP g.89327G>A FREM2|BccI gene has high diversity. The alleles of A and G were 0.747 and 0.253, respectively. The diversity of SNP g.89327G>A was significantly associated (p<0.05) with longissimus dorsi thickness (LD), while back fat thickness, intramuscular fat, and marbling score did not significantly different (p>0.05). Thus, SNP at position g.89327G>A in exon 6 of the FREM2 gene might be used as a candidate genetic marker for carcass quality in Bali beef.
References
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Moniruzzaman, M., R. Khatun, & A. A. Mintoo. 2015. Application of marker assisted selection for livestock improvement in Bangladesh. Bangladesh Veterinarian 31:1–11. https://doi.org/10.3329/bvet.v31i1.22837
Nei, M. & S. Kumar. 2000. Molecular Evolution and Phylogenetics. New York: Oxford University. https://doi.org/10.1093/oso/9780195135848.001.0001
Nogalski, Z., P.Pogorzelska-Przybyłek, M. Sobczuk-Szul, A. Nogalska, M. Modzelewska-Kapituła, & C. Purwin. 2018. Carcass characteristics and meat quality of bulls and steers slaughtered at two different ages. Ital. J. Anim. Sci. 17:279–288. https://doi.org/10.1080/1828051X.2017.1383861
Óvilo, C., N. Trakooljul, Y. Núñez, F. Hadlich, E. Murani, M. Ayuso, C. García-Contreras, M. Vázquez-Gómez, A. I. Rey, F. Garcia, J. M. Gracia-Casco, C. Lopez-Bote, B. Isabel, A. Gonzales-Bulnes, K. Wimmers, & M. Munoz. 2022. SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs. Sci. Rep. 12:16361. https://doi.org/10.1038/s41598-022-20817-0
Park, S. J., S. H. Beak, D. J. S. Jung, S. Y. Kim, I. H. Jeong, M. Y. Piao, H. J. Kang, D. M. Fassah, S. W. Na, S. P. Yoo, & M. Baik. 2018. Genetic, management, and nutritional factors affecting intramuscular fat deposition in beef cattle - A review. Asian-Australas. J. Anim. Sci. 31:1043–1061. https://doi.org/10.5713/ajas.18.0310
Putri, R., R. Priyanto, & A. Gunawan. 2015. Association of calpastatin (CAST) gene with growth traits and carcass characteristics in Bali cattle. Med. Pet. 38:145-149. https://doi.org/10.5398/medpet.2015.38.3.145
Raza, S. H. A., L. Gui, R. Khan, N. M. Schreurs, W. Xiaoyu, S. Wu, C. Mei, L.Wang, X. Ma, D. Wei, G. Guo, S. Zhang, X. Wang, H. A. Kaleri, & L. Zan. 2018. Association between FASN gene polymorphisms ultrasound carcass traits and intramuscular fat in Qinchuan cattle. Gene 645:55–59. https://doi.org/10.1016/j.gene.2017.12.034
Salamena, J. F. & B. J. Papilaja. 2010. Characterization and genetic relationships analysis of buffalo Maluku province. J. Indones. Trop. Anim. Agric. 35:75–82. https://doi.org/10.14710/jitaa.35.2.75-82
Singh, U., R. Deb, R. R. Alyethodi, R. Alex, S. Kumar, S. Chakraborty, K. Dhama, & A. Sharma. 2014. Molecular markers and their applications in cattle genetic research: A review. Biomarkers Genomic Medicine 6:49–58. https://doi.org/10.1016/j.bgm.2014.03.001
Tahuk, P. K., S. P. S. Budhi, P. Panjono, & E. Baliarti. 2018. Carcass and meat characteristics of male bali cattle in indonesian smallholder farms fed ration with different protein levels. Trop. Anim. Sci. J. 41:215–223. https://doi.org/10.5398/tasj.2018.41.3.215
Tsukahara, T. 2018. Genotyping of single nucleotide polymorphisms using the SNP-RFLP method. Biosci. Trends 12:240-246. https://doi.org/10.5582/bst.2018.01102
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Authors
PertiwiE. A., Ulum M. F., & JakariaJ. (2024). SNP Detection in FREM2 Gene and Its Association with Carcass Quality in Bali Beef. Tropical Animal Science Journal, 47(2), 149-154. https://doi.org/10.5398/tasj.2024.47.2.149
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