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.

本研究对代表 Badri 牛三种不同颜色变体的 96 只动物进行，以研究由于单核苷酸变异引起的遗传多样性、种群结构和遗传密码子的替代突变。使用双重消化限制性相关 DNA （ddRAD） 测序方法对 96 头 Badri 奶牛的 DNA 样品进行基因分型。采用标准化的生物信息学管道来识别单核苷酸多态性 （SNP），通过与 Bos indicus 参考基因组组装的比对初步检测 7,168,552 个 SNP。随后的严格质量过滤产生了 65,483 个高可信度 SNP，用于下游分析。对 Badri 牛种群的遗传多样性分析得出，香农多样性指数 （I）、辛普森多样性 （h） 和辛普森无偏多样性 （uh） 的平均值分别为 0.145、0.088 和 0.091。发现黑色和棕色、黑色和灰色以及棕色和灰色 Badri 变体之间的遗传相似性分别为 0.9972、0.9980 和 0.9970。观察到 Tajima 的 D 多样性值对 99.29% 的高置信度 SNP （65,483） 是显著的和阳性的。STRUCTURE 分析显示三种 Badri 颜色变体之间的混合，表明缺乏遗传分化。关于遗传密码子变化的高置信度 SNP 注释表明 GGC 中 GGT 的最大替换（22 次出现），其次是 AAC 到 AGC（20 次出现）、GAA 到 TAA（19 次出现）和 CAA 到 CAG（19 次出现）。该研究得出的结论是，巴德里牛种群中的颜色变异之间存在遗传相似性、缺乏稀有等位基因、平衡选择、种群突然收缩和遗传密码子替换。 从 SNP 数据分析得出的见解对印度牛的保护计划和品种改良计划具有潜在意义。