Novel variations in 5′ flanking region of the α-Lactalbumin gene in exotic and indigenous cattle

α-Lactalbumin (α-La) gene is involved in milk production traits in dairy animals. The variability in milk production potentials of different animals have been attributed to the polymorphism existing within this gene. The study was carried out to detect polymorphism in PCR amplified DNA fragments encompassing to − 363 to + 80 of the α-La gene in 50 Holstein Friesians (HF), 63 Jersey and 49 endogenous Kashmiri cattle. The polymorphism was detected by sequence analysis of amplified products. Three genotypes designated as AA, AB, BB were observed during the course of the study. The two alleles were differentiated on the basis of three single nucleotide polymorphism (SNP) each at position − 250, − 89, and − 46 of the promoter region of the α-La gene. All the three nucleotide variations involved base transition viz., A to G, T to C and A to G, respectively. The haplotype with nucleotide A, T and A at positions − 250, − 89 and − 46 was designated as A whereas the haplotype with nucleotide G, C and G at positions − 250, − 89 and − 46 was designated as allele B. The genotypic frequencies were observed to be 90.50% (n = 57) for AA allele and 9.50% (n = 06) for AB allele in Jersey, however no animal with genotype of BB allele was observed. The genotypic frequencies of homozygous A, homozygous B and heterozygous AB were 30% (n = 15), 22% (n = 11) and 47% (n = 23), respectively in Kashmiri cattle. Like in Jersey breed of cattle, no homozygous animal was observed to harbor BB genotype in HF cattle and the frequencies of AA and AB genotypes were 70% (n = 35) and 30% (n = 15), respectively. The allele frequencies for A and B allele were 95.25% and 4.75% in Jersey, 85% and 15% in HF and 54% and 46% in Kashmiri cattle, respectively. In view of the breed averages and preponderance of A allele in Bos taurus, it can be largely inferred that the polymorphism in 5′ flanking region of the α-La gene could be a potential molecular marker for production traits in dairy cattle. However, to authenticate it further evaluation through association studies are warranted.