Characterization of INDEL Polymorphisms in Selected Genes of Chickens
Author(s)
Selahaddin Kiraz , Ayfer BOZKURT KIRAZ ,
Download Full PDF Pages: 17-23 | Views: 9 | Downloads: 2 | DOI: 10.5281/zenodo.17840588
Abstract
InDel (Insertion–Deletion) polymorphisms are structural genetic variations that occur as a result of the insertion or deletion of one or more base pairs in the DNA sequence. These variations are generally observed in short sequences (1–100 bp) and may occur in the promoter, exon, intron, or UTR regions of genes. In chickens, InDel polymorphisms can affect gene transcriptional activity, mRNA stability, or protein structure, thereby influencing economically important traits such as growth, egg production, carcass characteristics, fat deposition, muscle development, and disease resistance. Analyzing gene expression in different genotypes helps determine the regulatory (modulatory) role of InDel polymorphisms. At the molecular level, InDel polymorphisms play an important role in the development of genetic improvement strategies. Therefore, InDel markers are considered powerful genetic tools that can be used in selection programs aimed at improving economic efficiency in poultry breeding.
Keywords
indel polymorphism, chickens genetics, molecular markers, chickens
References
[1] Andersson, L., & Georges, M. (2004). Domestic-animal genomics: Deciphering the genetics of complex traits. Nature Reviews Genetics, 5(3), 202–212. https://doi.org/10.1038/nrg1315
[2] Dekkers, J. C. M. (2012). Application of genomics tools to animal breeding. Current Genomics, 13(3), 207–212. https://doi.org/10.2174/138920212800543066
[3] Fu, R., Ren, T. H., Li, W. Y., Liang, J. Y., Mo, G. D., Luo, W., He, D. L., Liang, S. D., & Zhang, X. Q. (2020). A novel 65-bp indel in the GOLGB1 gene is associated with chicken growth and carcass traits. Animals, 10(3), 475. https://doi.org/10.3390/ani10030475
[4] Li, T., Chen, B., Wei, C., Hou, D., Qin, P., Jing, Z., Ma, H., Niu, X., Wang, C., Han, R., Li, H., Liu, X., Xu, H., Kang, X., & Li, Z. (2021). A 104-bp structural variation of the ADPRHL1 gene is associated with growth traits in chickens. Frontiers in Genetics, 12, 691272. https://doi.org/10.3389/fgene.2021.691272
[5] Li, T., Qin, P., Chen, B., Niu, X., Wang, Y., Niu, Y., Wei, C., Hou, D., Ma, H., Han, R., Li, H., Liu, X., Kang, X., & Li, Z. (2022). A novel 27-bp indel in the intron region of the YBX3 gene is associated with growth traits in chickens. British Poultry Science. https://doi.org/10.1080/00071668.2022.2059340
[6] Liang, K., Wang, X. N., Tian, X. X., et al. (2019). Molecular characterization and an 80-bp indel polymorphism within the prolactin receptor (PRLR) gene and its associations with chicken growth and carcass traits. 3 Biotech, 9(8), 296. https://doi.org/10.1007/s13205-019-1827-0
[7] Liu, D., Han, R., Wang, X., Li, W., Tang, S., Wang, Y., Jiang, R., Yan, F., Wang, C., & Liu, X. (2019). A novel 86-bp indel of the motilin receptor gene is significantly associated with growth and carcass traits in Gushi-Anka F-2 reciprocal cross chickens. British Poultry Science, 60(6), 649–658. https://doi.org/10.1080/00071668.2019.1655710
[8] Liu, D., Liu, X., Ma, X., Li, C., Li, J., Li, Q., Zhang, N., Cao, Y., Li, Z., Kang, X., Tian, Y., & Li, W. (2021). Two novel InDels within the promoter of SIRT1 are associated with growth traits in chickens. British Poultry Science, 63(1), 78–86. https://doi.org/10.1080/00071668.2021.2014400
[9] Maw, A. A., Shimogiri, T., Riztyan, K., Kawabe, K., Kawamoto, Y., & Okamoto, S. (2012). Genetic diversity of Myanmar and Indonesia native chickens together with two jungle fowl species by using 102 indels polymorphisms. Asian-Australasian Journal of Animal Sciences, 25(7), 927–934. https://doi.org/10.5713/ajas.2011.11511
[10] Mills, R. E., et al. (2006). An initial map of insertion and deletion (InDel) variation in the human genome. Genome Research, 16(9), 1182–1190. https://doi.org/10.1101/gr.4565806
[11] Qin, P., Liu, Y., Niu, X., Liu, Y., Zhang, Y., Niu, Y., Wang, Y., Chen, B., Han, R., Tian, Y., Liu, X., Kang, X., Jiang, R., & Li, Z. (2023). Molecular characterization, expression profile, and a 21-bp indel within the ASB9 gene and its associations with chicken production traits. Genes, 14(2), 339. https://doi.org/10.3390/genes14020339
[12] Ren, T., Li, W., Liu, D., et al. (2019). Two insertion/deletion variants in the promoter region of the QPCTL gene are significantly associated with body weight and carcass traits in chickens. Animal Genetics, 50(3), 279–282. https://doi.org/10.1111/age.12741
[13] Ren, T., Zhang, Z., Fu, R., Yang, Y., Li, W., Liang, J., Mo, G., Luo, W., & Zhang, X. (2020). A 51-bp indel polymorphism within the PTH1R gene is significantly associated with chicken growth and carcass traits. Animal Genetics, 51(4), 568–578. https://doi.org/10.1111/age.12942
[14] Ren, T. H., Yang, Y., Lin, W. J., Li, W. Y., Xian, M. J., Fu, R., Zhang, Z. H., Mo, G. D., Luo, W., & Zhang, X. Q. (2020). A 31-bp indel in the 5′ UTR region of GNB1L is significantly associated with chicken body weight and carcass traits. BMC Genetics, 21(1), 91. https://doi.org/10.1186/s12863-020-00900-z
[15] Wang, R., Wang, T., Lu, W., et al. (2015). Three indel variants in chicken LPIN1 exon 6/flanking region are associated with performance and carcass traits. British Poultry Science, 56(6), 621–630. https://doi.org/10.1080/00071668.2015.1113502
[16] Wang, X. N., Li, Z. J., Guo, Y. P., et al. (2019). Identification of a novel 43-bp insertion in the heparan sulfate 6-O-sulfotransferase 3 (HS6ST3) gene and its associations with growth and carcass traits in chickens. Animal Biotechnology, 30(3), 252–259. https://doi.org/10.1080/10495398.2018.1479712
[17] Wang, X. N., Wang, X. L., Chen, B. J., Guo, Y. P., Tang, H. H., Li, D. H., Liu, D. L., Wang, Y. B., Li, G. X., & Kang, X. T. (2020). Association of a new 99-bp indel of the CEL gene promoter region with phenotypic traits in chickens. Scientific Reports, 10(1), 3215. https://doi.org/10.1038/s41598-020-60168-2
[18] Väli, Ü., Einarsson, A., Waits, L., & Ellegren, H. (2008). Insertion–deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genetics, 9(1), 8. https://doi.org/10.1186/1471-2156-9-8
[19] Wei, C., Hou, D., Feng, Y., Li, T., Jing, Z. Z., Li, W. Y., Han, R. L., Li, G. X., Sun, G. R., & Tian, Y. D. (2020). Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens. Gene, 761, 145046. https://doi.org/10.1016/j.gene.2020.145046
[20] Wei, C., Niu, Y., Chen, B., Qin, P., Wang, Y., Hou, D., Li, T., Li, R., Wang, C., Yin, H., Han, R., Xu, H., Tian, Y., Liu, X., Kang, X., & Li, Z. (2022). Genetic effect of an InDel in the promoter region of the NUDT15 and its effect on myoblast proliferation in chickens. BMC Genomics, 23(1), 144. https://doi.org/10.1186/s12864-022-08362-6
[21] Zhang, S., Han, R. L., Gao, Z. Y., Zhu, S. K., Tian, Y. D., Sun, G. R., & Kang, X. T. (2014). A novel 31-bp indel in the paired box 7 (PAX7) gene is associated with chicken performance traits. British Poultry Science, 55(1), 31–36. https://doi.org/10.1080/00071668.2013.860215
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