Mutation Analysis and Restriction Site Mapping of GDF9 in Indonesian Bligon Goat
Abstract
Bligon goat is one of the crossbred goats raised in Indonesia, which has a prolific nature, potentially increasing the economic benefits. The gene that particularly influences prolific traits is Growth Differentiation Factor 9 (GDF9). This study aims to identify the mutation analysis (SNPs and amino acid changes) and restriction enzymes map in the GDF9 of Bligon goats. Six pairs of primers were used to amplify target sequences of GDF9 by polymerase chain reaction method and continued by sequencing. The sequence products were analyzed to get information on the SNPs and restriction enzyme (RE) around the SNPs for genotyping by PCR-RFLP method. A total of 15 SNPs were found in position g.1956A>C, g.2248G>T, g.2470A>T, g.2172DelA (shift T, Heterozygote), g.2807C>T, g.2919C>T, g.2996C>T, g.3615T>C, g.3855A>C, g.3879A>G, g.3924A>G, g.3943G>T, g.3969G>A, g.3981G>A, and g.4314C>T. Eight out of fifteen SNPs are located at the exon. Thus, the amino acid shows one synonymous at Exon 1 (Leucine to Leucine) and seven non synonymous at exon 2 with varied amino acid alteration (Valine to Alanine, Glutamine to Proline, Lysine to Arginine, Lysine to Arginine, Glutamine to Histidine, Arginine to Lysine, and Serine to Asparagine, respectively). Two SNPs at position g.1956A>C in Exon 1 and g.3855A>C in exon 2 show the homozygote CC and heterozygote AC. The most sample at those two position 67% and 83% homozygote type, respectively. Recognitions of site restriction enzymes BsaI and BsmAI were found at g.1956A>C or g.667C>M (Exon I). SNP g.3855A>C or g.2566C>M was recognized by three restriction enzymes (MspI, HapII, and HpaII). Two SNPs were not recognized by the restriction enzyme, and two other SNPs have more than 12 fragmented sequences, and as a consequence, it is very difficult to analyze the genotype. In conclusion, fifteen site mutations were identified; however, only two potential genetic markers with transversion mutations in Exon 1 and Exon 2 were recognized by restriction enzymes (BsaI, HapII, and MspI). These enzymes were recommended as candidate markers for further genotype identification using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.
References
Bi, Y., X. Wang, L. He, K. Lan, L. Qu, X. Lan, X. Song, & C. Pan. 2020. Two novel rare strongly linked missense SNPs (P27R and A85G) within the GDF9 gene were significantly associated with litter size in Shaanbei White Cashmere (SBWC) goats. Front. Vet. Sci. 7:406. https://doi.org/10.3389/fvets.2020.00406
Chu, M. X., Z. H. Wu, T. Feng, G. L. Cao, L. Fang, R. Di, D. W. Huang, X. W. Li, & N. Li. 2011. Polymorphism of GDF9 gene and its association with litter size in goats. Vet. Res. Commun. 35:329–336. https://doi.org/10.1007/s11259-011-9476-8
Das, A., M. Shaha, M. D. Gupta, A. Dutta, & O. M. Miazi. 2021. Polymorphism of fecundity genes (BMP15 and GDF9) and their association with their litter size in Bangladesh prolific Balck Bengal goat. Trop. Anim. Health Prod. 53:230-238. https://doi.org/10.1007/s11250-021-02679-2
Du, Z. Y., J. B. Lin, C. Tan, J. F. Wang, & X. Q. Ran. 2008. Study on the polymorphisms of Exon 2 of GDF9 gene in Guizhou white goat. Anim. Husb. Vet. Med. 40:46–48.
El-Maaty, A. M. A., A. A. Mohamed, & F. M. Karima. 2022. Effect of diet restriction and polymorphism of bone morphogenetic protein-15 and growth differentiation factor-9 (GDF9) on reproductive performance of three Egyptian fat tail sheep breeds. J. Adv. Vet. Res. 12:18-24.
Elvin, J. A., A. T. Clark, P. Wang, N. M. Wolfman, & M. M. Matsuk. 1999. Paracrine action of growth differentiation factor 9 in mammalian ovary. Mol. Endocrinol. 13:1035-1048. https://doi.org/10.1210/mend.13.6.0310
Feng, T., C. X. Geng , X. Z. Lang, M. X. Chu, G. L. Cao, R. Di, L. Fang, H. Q. Chen, X. L. Liu, & N. Li. 2011. Polymorphisms of caprine GDF9 gene and their association with litter size in Jining Grey goats. Mol. Biol. Rep. 38:5189–5197. https://doi.org/10.1007/s11033-010-0669-y
Garibyan, L. & N. Avashia. 2013. Research techniques made simple: Polymerase Chain Reaction (PCR). J. Invest. Dermatol. 133:1-8. https://doi.org/10.1038/jid.2013.1
Ghoreishi, H., S. Fathi-Yosefabad, J. Shayegh, & A. Barzegari. 2019. Identification of mutations in BMP15 and GDF9 genes associated with prolificacy of Markhoz goats. Arch. Anim. Breed. 62:565–570. https://doi.org/10.5194/aab-62-565-2019
Hanrahan, J. P., S. M. Gregan, P. Mulsant, M. Mullen, G. H. Davis, R. Powell, & S. M. Galloway. 2004. Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both increased ovulation rate and sterility in cambridge and belclare sheep (Ovis aries). Biol. Reprod. 70:900–909. https://doi.org/10.1095/biolreprod.103.023093
Hossain, F., A. S. Sharmin, & S. A. B. Mohammad. 2020. Association of GDF9 gene polymorphisms with litter size in indigenous sheep of Bangladesh. Research Agriculture Livestock Fisheries 7:283-292. https://doi.org/10.3329/ralf.v7i2.48871
Pingoud, A. & A. Jeltsch. 2001. Survey and summary: Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29:3705–3727. https://doi.org/10.1093/nar/29.18.3705
Perdana, Y. C. & T. Hartatik. 2022. Restriction mapping of MC4R gene on Bali Cattle (Bos sondaicus) as genetic marker for breeding program in compared to Bos taurus and Bos indicus. J. Trop. Biodivers. Biotechnol. 7:1-8. https://doi.org/10.22146/jtbb.67636
Polley, S., S. De, S. Batabyal, R. Kausik, P. Yadav, J. S. Arora, S. Chattopadhyay, S. Pan, B. Brahma, T. K. Datta, & S. L. Goswami. 2009. Polymorphism of fecundity genes (BMPR1B, BMP15, and GDF9) in the Indian prolific Black Bengal goat. Small Rumin. Res. 85:122−129. https://doi.org/10.1016/j.smallrumres.2009.08.004
Silva, J. R. V., R. V. D. Hurk, V. Tol, B. A. J. Roelen, & J. R. Figuiredo. 2004. Expression of growth differentiation factor 9 (GDF9), Bone morphogenetic protein 15 (BMP15), and BMP receptors in the ovaries of goats. Mol. Reprod. Dev. 70:11-19. https://doi.org/10.1002/mrd.20127
Wang, X., Y. Qing, Z. Sihuan, Z. Xiaoyo, P. Chuanying, C. Hong, Z. Haijing, & L. Xianyong. 2019. Genetic effects of single nucleotide polymorphisms in the goat GDF9 gene on prolificacy: True or false positive? Animals 9:1-20. https://doi.org/10.3390/ani9110886
Wang, F., M. Chu, L. Pan, X. Wang, X. He, R. Zhang, L. Tao, Y. La, L. Ma, & R. Di. 2021. Polymorphism detection of GDF9 gene and its association with litter size in Luzhong mutton sheep (Ovis aries). Animals 11:571. https://doi.org/10.3390/ani11020571
Wouobeng, P., J. S. Kouam, F. Meutchieye, M. Yacouba, G. Achieng, J. Tutah, C. Mutai, & M. Agaba. 2020. Polymorphism of prolificacy genes (BMP15, BMPR 1B, and GDF9) in the native goat (Capra hircus) of Cameroon. Genetics & Biodiversity Journal 4:28-43. https://doi.org/10.46325/gabj.v4i1.69
Yuliana, R., Sumadi, & T. Hartatik. 2019. Identification of single nucleotide polymorphisms in GDF9 gene associated with litter size in Garut sheep. Indones. J. Biotechnol. 24:51-56. https://doi.org/10.22146/ijbiotech.42095
Zhang, Y., W. Cui, H. Yang, M. Wang, H. Yan, H. Zhu, J. Liu, L. Qu, X. Lan, & C. Pan. 2019. A novel missense mutation (L280V) within POU1F1 gene strongly affects litter size and growth traits in goat. Theriogenology 135:198-203. https://doi.org/10.1016/j.theriogenology.2019.06.021
Authors
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Authors submitting manuscripts should understand and agree that copyright of manuscripts of the article shall be assigned/transferred to Tropical Animal Science Journal. The statement to release the copyright to Tropical Animal Science Journal is stated in Form A. This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA) where Authors and Readers can copy and redistribute the material in any medium or format, as well as remix, transform, and build upon the material for any purpose, but they must give appropriate credit (cite to the article or content), provide a link to the license, and indicate if changes were made. If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.
Article Details
