Genome-wide Association Study of Birth Weight in Bali Cattle (Bos javanicus)
Abstract
The genome-wide association study is popularly used to identify markers associated with high economic traits in cattle breeds worldwide. However, this method has never been applied to Bali cattle (Bos javanicus), which are indigenous to Indonesia. Therefore, this study aimed to determine whether the GWAS can also be employed to figure out genomic regions potentially affecting Bali cattle's birth weight trait. In this study, phenotypic and genotypic data of 48 Bali cattle were used to figure out genomic regions which are potentially affecting the birth weight trait of Bali cattle. Those samples were genotyped using an Illumina bead chip array with 53.218 single nucleotide polymorphisms (SNPs). The estimation of the variance proportion explained by each SNP was conducted by a restricted maximum likelihood (REML) approach. The result showed that the birth weight trait in Bali cattle was affected by multiple regions dispersed over the genome, especially chromosomes 20 and 21. This study demonstrated that GWAS can be used effectively and discovered two intriguing regions related to quantitative trait loci and genes, namely STXBP6 and TERT, which previously had been linked to cattle birth weight and growth. These findings are important for developing and refining genomic-based selection programs for Bali cattle in Indonesia.
References
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Buzanskas, M. E., D. A. Grossi, R. V. Ventura, F. S. Schenkel, M. Sargolzaei, S. L. C. Meirelles, F. B. Mokry, R. H. Higa, M. A. Mudadu, M. V. G. B. da Silva, S. C. M. Niciura, R. A. A. T. Júnior, M. M. Alencar, L. C. A. Regitano, & D. P. Munari. 2014. Genome-wide association for growth traits in Canchim beef cattle. PLoS ONE 9:e94802. https://doi.org/10.1371/journal.pone.0094802
Cahyadi, M., S. Sukaryo, M. I. Dhiaurridho, T. A. Bramastya, Y. Yanti, J. Riyanto, S. D. Volkandari, & P. Sudrajad. 2022. Association of pleomorphic adenoma gene 1 with body weight and measurement of Bali cattle (Bos javanicus). Vet. World 15:782–788. https://doi.org/10.14202/vetworld.2022.782-788
Casas, E. & M. Kehrli Jr. 2016. A review of selected genes with known effects on performance and health of cattle. Front. Vet. Sci. 3:113. https://doi.org/10.3389/fvets.2016.00113
Chang, C. C., C. C. Chow, L. C. A. M. Tellier, S. Vattikuti, S. M. Purcell, & J. J. Lee. 2015. Second-generation PLINK: Rising to the challenge of larger and richer datasets. GigaScience 4:1-16. https://doi.org/10.1186/s13742-015-0047-8
Crispim, A. C., M. J. Kelly, S. E. F. Guimarães, F. F. de Silva, M. R. S. Fortes, & R. R. Wenceslau. 2015. Multi-trait GWAS and new candidate genes annotation for growth curve parameters in Brahman cattle. PLoS ONE 10:e0139906. https://doi.org/10.1371/journal.pone.0139906
Durán, A. M., S. I. R. Ponce, F. J. R. López, E. G. Padilla, C. G. V. Peláez, A. Bagnato, & M. G. Strillacci. 2016. Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers. J. Anim. Breed. Genet. 134:49–59. https://doi.org/10.1111/jbg.12238
Eggen, A. 2012. The development and application of genomic selection as a new breeding paradigm. Anim. Front. 2:10–15. https://doi.org/10.2527/af.2011-0027
Elsik, C. G., D. R. Unni, C. M. Diesh, A. Tayal, M. L. Emery, H. N. Nguyen, & D. E. Hagen. 2016. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. Nucleic Acids Res. 44:D834–D839. https://doi.org/10.1093/nar/gkv1077
Flores, R., A. Plascencia, A. Barreras, J. Salinas-Chavira, N. Torrentera, & R. A. Zinn. 2022. Influence of arrival weight of Holstein steers of similar age on feedlot growth performance, dietary energetics, and carcass characteristics. J. Adv. Vet. Anim. Res. 9:59–65. https://doi.org/10.5455/javar.2022.i569
Gilchrist, G. C., P. Kurjanowicz, F. V. Mereilles, W. A. King, & J. LaMarre. 2015. Telomere length and telomerase activity in bovine pre-implantation embryos in vitro. Reprod. Domest. Anim. 50:58–67. https://doi.org/10.1111/rda.12449
Gondro, C., S. H. Lee, H. K. Lee, & L. R. Porto-Neto. 2013. Quality Control for Genome-Wide Association Studies. In: Gondro et al. (ed.). Genome-Wide Association Studies and Genomic Prediction. Springer Science+Business Media, London. pp.129–147. https://doi.org/10.1007/978-1-62703-447-0_5
Gunawan, A. & Jakaria. 2011. Genetic and non-genetics effect on birth, weaning, and yearling weight of Bali cattle. Med. Pet. 34:93–98. https://doi.org/10.5398/medpet.2011.34.2.93
Hartwig, F. P., F. Nedel, T. V. Collares, S. B. C. Tarquinio, J. E. Nör, & F. F. Demarco. 2012. Telomeres and tissue engineering: the potential roles of TERT in VEGF-mediated angiogenesis. Stem Cell Rev. Rep. 8:1275–1281. https://doi.org/10.1007/s12015-012-9414-3
Iqbal, K., W. A. Kues, U. Baulain, W. Garrels, D. Herrmann, & H. Niemann. 2011. Species-specific telomere length differences between blastocyst cell compartments and ectopic telomere extension in early bovine embryos by human telomerase reverse transcriptase. Biol. Reprod. 84:723–733. https://doi.org/10.1095/biolreprod.110.087205
Kaswati, Sumadi, & N. Ngadiyono. 2013. Estimasi nilai heritabilitas berat lahir, sapih, dan umur satu tahun pada sapi Bali di Balai Pembibitan Ternak Unggul Sapi Bali. Buletin Peternakan 37:74–78. https://doi.org/10.21059/buletinpeternak.v37i2.2424
Kumar, S. K., M. W. Feldman, D. H. Rehkopf, & S. Tuljapurkar. 2015. Limitations of GCTA as a solution to the missing heritability problem. Proc. Natl. Acad. Sci. USA 113:E61-E70. https://doi.org/10.1073/pnas.1520109113
Lai, E., A. L. Danner, T. R. Famula, & A. M. Oberbauer. 2020. Genome-wide association studies reveal susceptibility loci for digital dermatitis in Holstein cattle. Animals 10:2009. https://doi.org/10.3390/ani10112009
Lopez, B. I., K. G. Santiago, K. Seo, T. Jeong, J. E. Park, H. H. Cai, W. Park, & D. Lim. 2020. Genetic parameter of birth weight and weaning weight and their relationship with gestation length and age at first calving in Hanwoo (Bos taurus coreanae). Animals 10:1083. https://doi.org/10.3390/ani10061083
Lyu, S., P. Yang, Y. Liu, T. Song, Z. Zhang, Q. Shi, F. Chen, X. Liu, Z. Li, B. Ru, C. Cai, J. Xie, C. Lei, H. Chen, Z. Xu, E. Wang, & Y. Huang. 2021. Genetic effects of MOGAT1 gene SNP in growth traits of Chinese cattle. Gene 769:145201. https://doi.org/10.1016/j.gene.2020.145201
Martínez, R., D. Bejarano, Y. Gómez, R. Dasoneville, A. Jiménez, G. Even, J. Sölkner, & G. Mészáros. 2017. Genome-wide association study for birth, weaning and yearling weight in Colombian Brahman cattle. Genet. Mol. Biol. 40:453–459. https://doi.org/10.1590/1678-4685-gmb-2016-0017
Martojo, H. 2012. Indigenous Bali cattle is most suitable for sustainable small farming in Indonesia. Reprod. Domest. Anim. 47:10–14. https://doi.org/10.1111/j.1439-0531.2011.01958.x
McDaneld, T. G., L. A. Kuehn, M. G. Thomas, W. M. Snelling, T. P. L. Smith, E. J. Pollak, J. B. Cole, & J. W. Keele. 2014. Genomewide association study of reproductive efficiency in female cattle. J. Anim. Sci. 92:1945–1957. https://doi.org/10.2527/jas.2012-6807
Mohamad, K., M. Olsson, G. Andersson, B. Purwantara, H. T. A. van Tol, H. Rodriguez-Martinez, B. Colenbrander, & J. A. Lenstra. 2019. The origin of Indonesia cattle and conservation genetics of the Bali cattle. Reprod. Domest. Anim. 47:1-4. https://doi.org/10.1111/j.1439-0531.2011.01960.x
Nazar, M., X. Lu, I. M. Abdalla, N. Ullah, Y. Fan, Z. Chen, A. A. I. Arbab, Y. Mao, & Z. Yang. 2021. Genome-wide association study candidate genes on mammary system-related teat-shape conformation traits in Chinese Holstein cattle. Genes 12:1–15. https://doi.org/10.3390/genes12122020
Ren, S., X. Yang, T. Peng, X. Qiu, X. Wang, X. Yin, X. Wan, Y. Sun, & H. Chen. 2022. Establishment of a fetal cow (Bos Borus) skin fibroblasts cell line with immortalized characterization through human telomerase reverse transcriptase (hTERT) ectopic expression. J. Virol. Methods 309:114605. https://doi.org/10.1016/j.jviromet.2022.114605
Riwu, A. R. & J. N. Kihe. 2015. Heritabilitas bobot lahir sapi Bali dan persilangannya yang dipelihara secara semi-intensif di Kabupaten Kupang. Jurnal Nukleus Peternakan 2:15–22.
Sharma, A., J. S. Lee, C. G. Dang, P. Sudrajad, H. C. Kim, S. H. Yeon, H. S. Kang, & S. H. Lee. 2015. Stories and challenges of genome wide association studies in livestock — A review. Asian-Australas. J. Anim. Sci. 28:1371–1379. https://doi.org/10.5713/ajas.14.0715
Smith, J. L., M. L. Wilson, S. M. Nilson, T. N. Rowan, D. L. Oldeschulte, R. D. Schnabel, J. E. Decker, & C. M. Seabury. 2019. Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle. BMC Genom. Data 20:926. https://doi.org/10.1186/s12864-019-6231-y
Sudrajad, P., R. Y. Kusminanto, S. D. Volkandari, & M. Cahyadi. 2022. Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data. Vet. World 15:449-454. https://doi.org/10.14202/vetworld.2022.449-454
Sudrajad, P., S. Subiharta, Y. Adinata, A. Lathifah, J. H. Lee, J. A. Lenstra, & S. H. Lee. 2020. An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis. PLoS ONE 15:e0241038. https://doi.org/10.1371/journal.pone.0241038
Supriyantono, A., L. Hakim, S. Suyadi, & I. Ismudiono. 2011. Breeding programme development of Bali cattle at Bali Breeding Centre. Anim. Prod. 13:45–51.
Suwiti, N. K., I. N. K. Besung, & G. N. Mahardika. 2017. Factors influencing growth hormone levels of Bali cattle in Bali, Nusa Penida, and Sumbawa Islands, Indonesia. Vet. World 10:1250–1254. https://doi.org/10.14202/vetworld.2017.1250-1254
Uffelmann, E., Q. Q. Huang., N. S. Munung, J. de Vries., Y. Okada, A. R. Martin, H. C. Martin, T. Lappalainen, & D. Posthuma. 2021. Genome-wide association studies. Nat. Rev. Methods Primers 1:59. https://doi.org/10.1038/s43586-021-00056-9
Utsunomiya, Y. T., A. S. Do Carmo, R. Carvalheiro, H. H. Neves, M. C. Matos, L. B. Zavarez, A. M. Pérez O’Brien, J. Sölkner, J. C. McEwan, J. B. Cole, & C. P. van Tassell. 2013. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genet. 14:1–12. https://doi.org/10.1186/1471-2156-14-52
Volkandari, S. D., P. Sudrajad, D. Prasetyo, Subiharta, A. Prasetyo, J. Pujianto, & M. Cahyadi. 2020. Dampak sistem pemeliharaan intensif dan semi intensif terhadap ukuran tubuh sapi bali jantan di Balai Perbibitan Ternak Unggul (BPTU) Sapi Bali. Proceeding. Kesiapan Sumber Daya Pertanian dan Inovasi Spesifik Lokasi Memasuki Era Industri 4.0. Balai Besar Pengkajian dan Pengembangan Teknologi Pertanian, Bogor. pp. 547–551.
Weng, Z., H. Su, J. Lee, & D. Garrick. 2015. Genome-wide association study of birth and weaning weights in Brangus beef cattle. Iowa State University Animal Industry Report 12.https://doi.org/10.31274/ans_air-180814-1277
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Authors
SudrajadP., SuhadaH., PrasetyoD., GaririP. N., EddiantoE., AbiyogaA. F., KusminantoR. Y., SukaryoS., BramastyaT. A., VolkandariS. D., & CahyadiM. (2023). Genome-wide Association Study of Birth Weight in Bali Cattle (Bos javanicus). Tropical Animal Science Journal, 46(2), 151-156. https://doi.org/10.5398/tasj.2023.46.2.151
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