Stepwise Detection of Copy Number Variations in Whole Genome Sequence of Buffalo

Authors

  • Aishwarya Dash Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal -132001, Haryana, India.
  • Jayakumar Sivalingam ICAR-Directorate of Poultry Research, Hyderabad, Telangana, India.
  • Kangabam Bidyalaxmi Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal -132001, Haryana, India.
  • Kousalya Devi M Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal -132001, Haryana, India.
  • Nidhi Sukhija Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal -132001, Haryana, India.
  • Ravi Kumar D Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal -132001, Haryana, India.
  • Saket Kumar Niranjan ICAR-National Bureau of Animal Genetics and Breeding, Karnal-132001, Haryana, India
  • Madhu Sudan Tantia ICAR-National Bureau of Animal Genetics and Breeding, Karnal-132001, Haryana, India
  • Ishwar Dayal Gupta Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal -132001, Haryana, India.

DOI:

https://doi.org/10.48165/ijvsbt.19.3.07

Keywords:

Buffalo, Copy number variations (CNVs), Read Depth, Whole genome sequencing (WGS)

Abstract

Genetic variants cause changes in genetic composition and are accountable for uniqueness of genomes of individuals. Copy number variations (CNVs) cause genetic variations due to loss or gain of DNA segments varying from 50 bp to several mega base pairs (Mb) compared with a reference genome. These unbalanced structural variants are heritable and have potentially greater effect than SNPs. The present study was conducted on whole genome resequencing (WGS) data of swamp buffalo for identification of CNVs. Sample of swamp buffalo was collected from Manipur and karyotyped and confirmed to be of swamp type. After quality and quantity checking it was sent for sequencing with Illumina Hiseq 2000 platform. Paired end reads of WGS data were analysed using Read depth (RD) based approach aligning to the reference Mediterranean riverine buffalo assembly. CNVs were identified using CNVnator with standardized parameters and total 587 CNVs were found in swamp buffalo. Among CNV events, 405 deletions and 182 duplications were identified. These variations comprised of 5.82% of reference genome. This was the first Genome-wide CNV study in indigenous swamp buffalo with reference to buffalo genome using Read Depth based approach.

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References

Abyzov, A., Urban, A.E., Snyder, M., & Gerstein, M. (2011). CNVnator: An approach to discover, genotype and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research, 21(6), 974-984.

Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data.

Bickhart, D.M., Hou, Y., Schroeder, S.G., Alkan, C., Cardone, M.F., Matukumalli, L.K., et al. (2012). Copy number variation of individual cattle genomes using next-generation sequencing. Genome Research, 22(4), 778-790.

Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.

Coghlan, A. (2013). Avrilomics: Using CNVnator to find copy number variation. Avrilomics.

Fernandes, A.C., da Silva, V.H., Goes, C.P., Moreira, G.C.M., Godoy, T.F., Ibelli, A.M.G., et al. (2021). Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics, 22(1), 1-18.

Gao, Y., Jiang, J., Yang, S., Hou, Y., Liu, G.E., Zhang, S., et al. (2017). CNV discovery for milk composition traits in dairy cattle using whole genome resequencing. BMC Genomics, 18, 1-12.

Ghosh, S., Qu, Z., Das, P.J., Fang, E., Juras, R., Cothran, E.G. et al. (2014). Copy number variation in the horse genome. PLoS Genetics, 10(10), e1004712.

Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14): 1754–1760.

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079.

Li, W., Bickhart, D.M., Ramunno, L., Iamartino, D., Williams, J.L., & Liu, G.E. (2019). Comparative sequence alignment reveals river buffalo genomic structural differences compared with cattle. Genomics, 111(3), 418-425.

Liu, S., Kang, X., Catacchio, C.R., Liu, M., Fang, L., Schroeder, S.G., et al. (2019). Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo (Bubalus bubalis). Functional and Integrative Genomics, 19(3), 409-419.

Mills, R.E., Walter, K., Stewart, C., Handsaker, R.E., Chen, K., Alkan, C., et al. (2011). Mapping copy number variation by population-scale genome sequencing. Nature, 470(7332), 59-65.

Nandolo, W., Mészáros, G., Wurzinger, M., Banda, L.J., Gondwe, T.N., Mulindwa, H.A., et al. (2021). Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics, 22(1), 1-15.

Pinto, D., Darvishi, K., Shi, X., Rajan, D., Rigler, D., Fitzgerald, T., et al. (2011). Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nature Biotechnology, 29(6), 512-520.

Pirooznia, M., Goes, F.S., & Zandi, P.P. (2015). Whole-genome CNV analysis: Advances in computational approaches. Frontiers in Genetics, 6, 138.

Qiu, Y., Ding, R., Zhuang, Z., Wu, J., Yang, M., Zhou, S., et al. (2021). Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs. BMC Genomics, 22(1), 1-16.

Salehian-Dehkordi, H., Xu, Y.X., Xu, S.S., Li, X., Luo, L.Y., Liu, Y.J., et al. (2021). Genome-wide detection of copy number variations and their association with distinct phenotypes in the world’s sheep. Frontiers in Genetics, 12, 670582.

Strillacci, M.G., Moradi-Shahrbabak, H., Davoudi, P., Ghoreishifar, S.M., Mokhber, M., Masroure, A.J., et al. (2021). A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes. BMC Genomics, 22(1), 1-14.

Sudmant, P.H., Rausch, T., Gardner, E.J., Handsaker, R.E., Abyzov, A., Huddleston, J., et al. (2015). An integrated map of structural variation in 2,504 human genomes. Nature, 526(7571), 75-81.

Zhang, L., Jia, S., Yang, M., Xu, Y., Li, C., Sun, J., et al. (2014). Detection of copy number variations and their effects in Chinese bulls. BMC Genomics, 15, 1-9.

Zhou, J., Liu, L., Reynolds, E., Huang, X., Garrick, D., & Shi, Y. (2022). Discovering copy number variation in dual-purpose Xin Jiang Brown cattle. Frontiers in Genetics, 12, 747431.

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Published

2023-05-09

Issue

Vol. 19 No. 3 (2023): The Indian Journal of Veterinary Sciences and Biotechnology (IJVSBT) (May- Jun) 2023

Section

Articles

License

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

How to Cite

Dash, A., Sivalingam, J., Bidyalaxmi, K., M, K.D., Sukhija, N., D, R.K., … Gupta, I.D. (2023). Stepwise Detection of Copy Number Variations in Whole Genome Sequence of Buffalo. Indian Journal of Veterinary Sciences and Biotechnology, 19(3), 30–33. https://doi.org/10.48165/ijvsbt.19.3.07
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