Sequence characterization, structural analysis, SNP detection and expression profiling of SLC11A1 gene in Indian goats

Abstract

The Solute Carrier Family 11 Member A1 (SLC11A1) is a candidate gene, encodes a divalent cation transporter, SLC11A1 protein, localizes in the phagolysosome membrane in macrophages, essential for immunity and resistance to intracellular pathogens. The indigenous goats of Kerala are known for disease resistance and adaptability, but the underlying genetic causes are to be unraveled. This study comprised of characterization of the caprine SLC11A1 gene, to detect SNPs and compare the relative abundance of SLC11A1 mRNA by quantitative-PCR in native goats (Attappady Black and Malabari) and crossbreds. The 1702 bp cDNA of SLC11A1 comprised of 15 exons, an ORF of 1647 bp, encoding a protein of 548 amino acids. SLC11A1 amino acid sequence was 83–99% identical to that of other species. SLC11A1 peptide contains 10 serine and 2 threonine phosphorylation loci and 12 transmembrane domains. The study indicated the presence of four synonymous and three non-synonymous mutations (p.Ile132Thr; p.Phe294Leu; p.Gln541His). The amino acid substitution p.Ile132Thr was deleterious and p.Phe294Leu and p.Gln541His were neutral. p.Phe294Leu was located in the 7th transmembrane helix. The relative abundance of the SLC11A1 mRNA in leukocytes in Malabari and Attappady Black were significantly higher than crossbreds (P < 0.01). The significantly higher SLC11A1 expression in native goats indicates higher disease resistance than crossbreds, gives an insight into the necessity of conservation of native breeds, important role of SLC11A1 in disease resistance. The detected SNPs would benefit the use of this gene as a candidate gene for disease resistance in goat breeding programs.