Identification of FREM2 SNPs in Bali cattle for improving meat quality
Article Sidebar
Abstract Views: 312
File Views: 184
Main Article Content
Abstract
Abstract. Pertiwi EA, Maskur, Rozi T, Muhsinin M, Ulum MF, Muharram F, Jakaria. 2026. Identification of FREM2 SNPs in Bali cattle for improving meat quality. Biodiversitas 27 (1): d270127. https://doi.org/10.13057/biodiv/d270127. Bali cattle (Bos javanicus) are indigenous to Indonesia and valued for beef quality traits influenced by genetic variation. The FREM2 gene is recognized as one of the genetic factors that regulate marbling scores in beef cattle. This gene has been extensively studied in various livestock breeds, but has rarely been explored in local livestock breeds in Indonesia. This study aims to identify SNPs in Bali cattle as a first step in determining genetic markers to help improve meat quality, especially in Bali cattle. Blood samples were collected from 20 unrelated Bali cattle. Genomic DNA was extracted via the phenol-chloroform method. A 662 bp fragment encompassing exon 6 and intron 7 of the FREM2 gene was amplified by Polymerase Chain Reaction (PCR) and sequenced bidirectionally using Sanger technology. Sequence alignment and SNP detection were performed in MEGA X, with chromatogram inspection in FinchTV to confirm base calls. Population genetic parameters, including allele frequencies, observed and expected heterozygosity, and Polymorphic Information Content (PIC), were calculated using PopGen 3.2. Two novel SNPs were identified: g.89573C>T in exon 6, resulting in a non-synonymous Pro→Leu substitution, and g.89633G>A in intron 7. The g.89573C>T SNP deviated significantly from Hardy-Weinberg equilibrium (χ² = 4.62, p = 0.032), with observed heterozygosity (Ho = 0.50) exceeding expected heterozygosity (He = 0.455) and a PIC of 0.343. The intronic g.89633G>A variant conformed to equilibrium (p = 0.345) with a PIC of 0.269. These FREM2 markers enable marker-assisted selection to improve meat quality in Bali cattle while supporting breed conservation through genomic selection.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Agung PP, Anwar S, Putra WPB, Said S. 2017. Keragaman gen Growth Hormone (GH) pada beberapa rumpun sapi lokal Indonesia. Pros Sem Nas Masy Biodiv Indon 3 (3): 304-308. https://doi.org/10.13057/psnmbi/m030304. [Indonesian]
Agustina KK, Cahya IMRD, Widyantara GM, Swacita IBN, Dharmayudha AAGO, Rudyanto MD. 2021. Nilai gizi dan kualitas fisik daging Sapi Bali berdasarkan jenis kelamin dan umur. Buletin Veteriner Udayana 9 (2): 156-163. https://doi.org/ 10.21531/bulvet.2017.9.2.156. [Indonesian]
Aritonang SB, Yuniati R, Abinawanto, Imron M, Bowolaksono A. 2017. Studies of adaptive traits of Bali cattle in Buleleng district, Bali and Barru district, South Sulawesi. AIP Conf Proc 1844: 060003. https://doi.org/10.1063/1.4983443.
Bedhane M, van der Werf J, Gondro C, Duijvesteijn N, Lim D, Park B, Park MN, Hee RS, Clark S. 2019. Genome-wide association study of meat quality traits in Hanwoo beef cattle using imputed whole-genome sequence data. Front Genet 10: 1235. https://doi.org/10.3389/fgene.2019.01235.
Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32 (3): 314-331.
Coddington M. 2020. Missense, Nonsense and Frameshift Mutations: A Genetic Guide. Technology Networks.
Dairoh, Ulum MF, Jakaria, Sumantri C. 2024. Calpain 1 gene expression in liver tissue and the association of novel calpain 1 Single-Nucleotide Polymorphisms (SNPs) with meat quality in Bali cattle. Arch Anim Breed 67 (3): 311-321. https://doi.org/10.5194/aab-67-311-2024.
Dalimunthe SR, Siregar LAM, Putri LAP, Chairunnisa T, Hairmansis A. 2020. Polymorphism levels of some SSR markers (Simple Sequence Repeat) for parental line identification on low temperature tolerance. IOP Conf Ser: Earth Environ Sci 454: 012165. https://doi.org/10.1088/1755-1315/454/1/012165.
Delpero M, Arends D, Freiberg A, Brockmann GA, Hesse D. 2022. OPEN QTL-mapping in the obese Berlin fat mouse identifies additional candidate genes for obesity and fatty liver disease. Sci Rep 12: 10471. https://doi.org/10.1038/s41598-022-14316-5.
Du L, Duan X, An B, Chang T, Liang M, Xu L, Zhang L, Li J, Guangxin E, Gao H. 2021. Genome-wide association study based on random regression model reveals candidate genes associated with longitudinal data in Chinese simmental beef cattle. Animals 11 (9): 2524. https://doi.org/10.3390/ani11092524.
FAO [Food and Agriculture Organization]. 2020. Status and trends of animal genetic resources: 2020. Food and Agriculture Organization of the United Nations.
Gariri PN, Sutopo S, Setiaji A, Mustofa F, Haris FZ, Da’i MAM, Prahara PG, Kamila FT, Philco SV, Tamanningrum TD, Suratman S. 2025. Enhancing production efficiency: The role of inflection points in non-linear growth of Bali cattle. IOP Conf Ser: Earth Environ Sci 1460: 012001. https://doi.org/10.1088/1755-1315/1460/1/012001.
Gerard D. 2022. Comment on three papers about Hardy-Weinberg equilibrium tests in autopolyploids. Front Genet 13: 1027209. https://doi.org/10.3389/fgene.2022.1027209.
Greguła-Kania M, Gruszecki TM, Junkuszew A, Juszczuk-Kubiak E, Florek M. 2019. Association of CAST gene polymorphism with carcass value and meat quality in two synthetic lines of sheep. Meat Sci 154: 69-74. https://doi.org/10.1016/j.meatsci.2019.04.007.
Grigoletto L, Ferraz JBS, Oliveira HR, Eler JP, Bussiman FO, Silva BCA, Baldi F, Brito LF. 2020. Genetic architecture of Carcass and meat quality traits in Montana Tropical® composite beef cattle. Front Genet 11: 123. https://doi.org/10.3389/fgene.2020.00123.
Hapsari RD, Nugroho T, Pambuko G, Pradista LA, Riyanto J, Widyas N, Prastowo S. 2025. Genetic variation in the bovine heat shock protein gene in Indonesian Bali cattle (Bos javanicus): A marker candidate for heat stress tolerance trait. Open Vet J 15 (6): 2861-2874. https://doi.org/10.5455/ovj.2025.v15.i6.55.
Hunde D, Tadesse Y, Tadesse M, Abegaz S, Getachew T. 2024. Community-based breeding programs can realize sustainable genetic gain and economic benefits in tropical dairy cattle systems. Front Genet 15: 1106709. https://doi.org/10.3389/fgene.2024.1106709.
Indra W. 2021. Detection of Gen C / EBPα Encodes the Meat Quality. Akademik Jurnal Mahasiswa Sain dan Teknologi 1 (1): 24-32.
Jordan VK, Beck TF, Hernandez-Garcia A et al. 2018. The role of FREM2 and FRAS1 in the development of congenital diaphragmatic hernia. Hum Mol Genet 27 (12): 2064-2075. https://doi.org/10.1093/hmg/ddy110.
Kwong AM, Blackwell TW, Lefaive J et al. 2021. Robust, flexible, and scalable tests for Hardy-Weinberg equilibrium across diverse ancestries. Genetics 218 (1): iyab044. https://doi.org/10.1093/genetics/iyab044.
Lee HJ, Jin S, Kim H-J, Bhuiyan MSA, Lee DH, Lee SH, Jang SB, Han MH, Lee SH. 2019. Validation study of SNPs in CAPN1-CAST genes on the tenderness of muscles (Longissimus thoracis and Semimembranosus) in Hanwoo (Korean cattle). Animals 9 (9): 691. https://doi.org/10.3390/ani9090691.
Margawati ET, Volkandari SD, Indriawati I, Ridwan M. 2019. Genetic diversity and relationship among Bali cattle from Several locations in Indonesia based on ETH10 microsatellite marker. Jurnal Ilmu Ternak Veteriner 23 (4): 168-173. https://doi.org/10.14334/jitv.v23i4.1915.
Maruki T, Lynch M. 2015. Genotype-frequency estimation from high-throughput sequencing data. Genetics 201 (2): 473-486. https://doi.org/10.1534/genetics.115.179077.
Maskur MM, Depamede SN. 2023. Identification of fecXG and fecB mutations and its association with litter size in Kacang and Boerka goat. Adv Anim Vet Sci 11 (1): 124-131.
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, Oxford.
Oakley CG, Winn AA. 2012. Effects of population size and isolation on heterosis, mean fitness, and inbreeding depression in a perennial plant. New Phytol 196 (1): 261-270. https://doi.org/10.1111/j.1469-8137.2012.04240.x.
Óvilo C, Trakooljul N, Núñez Y, Hadlich F, Murani E, Ayuso M, García-Contreras C, Vázquez-Gómez M, Rey AI, Garcia F, García-Casco JM, López-Bote C, Isabel B, González-Bulnes A, Wimmers K, Muñoz M. 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.
Pertiwi EA, Ulum MF, Jakaria J. 2024. SNP detection in FREM2 gene and its association with Carcass quality in Bali beef. Trop Anim Sci J 47 (2): 149-154. https://doi.org/10.5398/tasj.2024.47.2.149.
Pratiwi N, Maskur M, Priyanto R, Jakaria J. 2016. Novel SNP of Calpain-1 (CAPN1) gene and its association with Carcass and meat characteristics traits in Bali cattle. J Indones Trop Anim Agric 41 (3): 109-116. https://doi.org/10.14710/jitaa.41.3.109-116.
Romero JV, Olleta JL, Resconi VC, Santolaria P, Campo MdelM. 2024. Genetic markers associated with beef quality: A review. Livest Sci 289: 105583. https://doi.org/10.1016/j.livsci.2024.105583.
Sandhu KS, Merrick LF, Sankaran S, Zhang Z, Carter AH. 2022. Prospectus of genomic selection and phenomics in cereal, legume and oilseed breeding programs. Front Genet 12: 829131. https://doi.org/10.3389/fgene.2021.829131.
Schiavo G, Bovo S, Tinarelli S, Bertolini F, Dall’Olio S, Gallo M, Fontanesi L. 2019. Genome-wide association analyses for several exterior traits in the autochthonous Casertana pig breed. Livest Sci 230: 103842. https://doi.org/10.1016/j.livsci.2019.103842.
Shi M, Huang L, Meng S, Wang H, Zhang J, Miao Z, Li Z. 2024. Identification of several lncRNA-mRNA pairs associated with marbling trait between Nanyang and Angus cattle. BMC Genomics 25: 696. https://doi.org/10.1186/s12864-024-10590-x.
Shiddieqy MI, Pratiwi N, Soewandi BDP. 2019. Utilization of molecular marker to improve Cattle Carcass quality in Indonesia. Indones Bull Anim Vet Sci 29 (4): 193. https://doi.org/10.14334/wartazoa.v29i4.2009.
Su T-Y, Xia Y. 2025. A quantitative comparison of the deleteriousness of missense and nonsense mutations using the structurally resolved human protein interactome. Protein Sci 34 (6): e70155. https://doi.org/10.1002/pro.70155.
Sun X, Wu X, Fan Y, Mao Y, Ji D, Huang B, Yang Z. 2018. Effects of polymorphisms in CAPN1 and CAST genes on meat tenderness of Chinese Simmental cattle. Arch Anim Breed 61 (4): 433-439. https://doi.org/10.5194/aab-61-433-2018.
Tahuk PK, Budhi SPS, Panjono P, Baliarti E. 2018. Carcass and meat characteristics of male Bali cattle in Indonesian smallholder farms fed ration with different protein levels. Trop Anim Sci J 41 (3): 215-223. https://doi.org/10.5398/tasj.2018.41.3.215.
Tian R, Mahmoodi M, Tian J, Koshkoiyeh SE, Zhao M, Saminzadeh M, Li H, Wang X, Li Y, Esmailizadeh A. 2024. Leveraging functional genomics for understanding beef quality complexities and breeding beef cattle for improved meat quality. Genes 15 (8): 1104. https://doi.org/10.3390/genes15081104.
Timmer JR, Mak TW, Manova K, Anderson KV, Niswander L. 2005. Tissue morphogenesis and vascular stability require the FREM2 protein, product of the mouse myelencephalic blebs gene. Proc Natl Acad Sci USA 102 (33): 11746-11750. https://doi.org/10.1073/pnas.0505404102.
Ur Rehman S, Ali R, Zhang H, Zafar MH, Wang M. 2023. Research progress in the role and mechanism of Leucine in regulating animal growth and development. Front Physiol 14: 1252089. https://doi.org/10.3389/fphys.2023.1252089.
Zhao Y, Pu Y, Liang B, Bai T, Liu Y, Jiang L, Ma Y. 2022. A study using single-locus and multi-locus genome-wide association study to identify genes associated with teat number in Hu sheep. Anim Genet 53 (2): 203-211. https://doi.org/10.1111/age.13169.