Abstract
The present study was carried out on 96 animals representing three distinct colour variants of Badri cattle to investigate the genetic diversity, population structure and substitution mutations in the genetic codons due to single nucleotide variations. The DNA samples of 96 Badri cows were genotyped using a double digestion restriction associated DNA (ddRAD) sequencing approach. A standardized bioinformatics pipeline was employed to identify single nucleotide polymorphisms (SNPs), initially detecting 7,168,552 SNPs through alignment with the Bos indicus reference genome assembly. Subsequent stringent quality filtration yielded 65,483 high-confidence SNPs for downstream analysis. Genetic diversity analysis of the Badri cattle population resulted in average values of 0.145, 0.088, and 0.091 for Shannon’s diversity Index (I), Simpson’s Diversity (h), and Simpson’s Unbiased Diversity (uh), respectively. Genetic similarities between the black and brown, black and grey, and brown and grey Badri variants were found to be 0.9972, 0.9980 and 0.9970, respectively. Tajima’s D diversity value was observed to be significant and positive for 99.29% of high-confidence SNPs (65,483). STRUCTURE analysis showed admixture among the three Badri colour variants, suggesting a lack of genetic differentiation. Annotation of high-confidence SNPs regarding genetic codon changes indicated maximum substitutions in the GGC with GGT (22 occurrences), followed by AAC to AGC (20 occurrences), GAA to TAA (19 occurrences) and CAA to CAG (19 occurrences). The study concludes there are genetic similarities among colour variants, lack of rare alleles, balancing selection, sudden population contraction and genetic codon substitutions within the Badri cattle population. Insights derived from SNP data analysis hold potential significance for conservation initiatives and breed improvement programs for indicine cattle.
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Data availability
The data sets generated and analysed during the current study are available in the European Variation Archive-EMBL- EBI repository under accession number: Project: PRJEB59419 Analyses: ERZ16007574.
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Acknowledgements
The authors are thankful to the Director of Research, Dean, College of Veterinary and Animal Sciences and Dean, PGS, G B Pant University of Agriculture and Technology and Director and Veterinary Officer Animal Breeding Farm, Champawat for providing the essential facilities for conducting this study.
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Financial support for this study was provided by the Department of Biotechnology, New Delhi, under Project No. 8002, titled North-Western Himalayan Bioinformatics Grid. The first author was the recipient of an SRF fellowship from the Indian Council of Agricultural Research-New Delhi.
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JUR, DK, SPS, BNS, AKG and AK conceived and designed the study; JUR, AP, and MKV collected blood samples; JUR conducted experiments, bioinformatic analysis and drafted manuscript’ AHD, and SFA provided critical inputs during the data analysis and manuscript preparation.
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Rahman, J.U., Kumar, D., Singh, S.P. et al. Genetic diversity, population structure analysis and codon substitutions of Indicine Badri cattle using ddRAD sequencing. 3 Biotech 14, 46 (2024). https://doi.org/10.1007/s13205-023-03894-4
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DOI: https://doi.org/10.1007/s13205-023-03894-4