Genetic polymorphisms of the 5' untranslated regions of the gene in Indonesian cattle populations.

BACKGROUND AND AIM

Heat shock proteins (HSPs) are a group of proteins that play a significant role in protecting cells against cellular stress. is a conserved, sensitive, and abundant gene associated with heat stress's physiological adaptability. The objective of this study was to reveal the polymorphisms of the partial sequences of the gene (5' untranslated region [UTR]) in seven cattle populations in Indonesia.

MATERIALS AND METHODS

Polymerase chain reaction products (551 bp) of the gene amplified from 102 animals representing seven cattle populations (Bali, Belgian Blue x Peranakan Ongole [PO] cross, Galekan, Jabres, Madura, PO, and Rambon) were sequenced by DNA sequencing method.

RESULTS

Fourteen single-nucleotide polymorphisms (SNPs), generally found at a low frequency, were detected. Among these SNPs, only 1117G>A, 1125A>C, and 1204T>C were polymorphic in all the analyzed breeds. A Chi-square test showed that the majority of the loci were in Hardy-Weinberg equilibrium (p0.05). Varying levels of observed (0.050-0.571) and expected heterozygosity (0.049-0.500) were noted. The polymorphism information content values (0.048-0.375) indicated that the SNPs in the gene showed low-to-moderate polymorphism in the studied populations. Thirty-six haplotypes were defined according to the identified SNPs, of which haplotype Hap5 (CGACGAGAGTGTCC) and Hap4 (CGACGAGAGTGCCC) were generally dominant in the studied samples. The phylogenetic tree showed a close relationship between Bali and Rambon cattle and between Galekan and Jabres cattle, while the Belgian Blue x PO crossbred cattle were farther apart.

CONCLUSION

The polymorphisms in the 5' UTR of the geneidentified in this study should be further investigated in a larger population to unravel the association between the SNPs and thermotolerance in Indonesian local cattle populations.