Genetic diversity in kappa casein gene and its impact on milk composition and quantity in the Achai cattle ( <i>Bos indicus</i> )

Background The kappa casein ( κ‐CN ) gene exhibits notable structural variations compared with other caseins and plays a vital role in both the quality and quantity of milk. Aim(s) This study was conducted to investigate the different genotypes of κ‐CN and their association with milk composition, quality and protein structural stability in the Achai cow. Methods To investigate the different genotypes of the κ‐CN gene, PCR‐RFLP and Sanger sequencing were used. The protein structural stability of mutant and wild‐type proteins was explored using online bioinformatics tools and molecular dynamics simulations. Major Findings Three genotypes (AA, CC and AC) were investigated in the Achai cow. The genotypic frequencies of κ‐CN were AC&gt;AA&gt;CC (60%, 27% and 13%), while the allelic frequencies were 0.57 for A and 0.43 for C. It was indicated that χ 2 &gt; P (5.81 &gt; 3.841); therefore, there was no Hardy–Weinberg equilibrium among the genotypes. The association of genotypes with milk performance revealed that the levels of total SNF, lactose, protein, density and yield were highest in the CC genotype. Furthermore, a D169A mutation has been identified in the protein of the CC genotype. The mutation has been validated as a stable substitution through Ramachandran plot analysis (65.2% of residues were in the favoured region), Z ‐score (−8.63) and RMSD (2.062 Å). It is concluded that the significant molecular marker (CC genotype) can be used to improve milk quality and quantity. Scientific and Industrial Implications Different genotypes can influence milk performance in cattle; therefore, a marker‐assisted selection method has been used to select the best trait. The results of this study indicate that the genotype CC and the D169A mutant have good milk performance and can be used as markers for marker‐assisted selection in the Achai cow.