SNP characterization of DSG3 gene for high-altitude adaptation in Chaugarkha goat of Kumaon Himalaya

Abstract

Livestock in high-altitude environments have developed genetic adaptations, including physiological and morphological changes, to thrive in challenging conditions. The DSG3 gene (Desmoglein 3) on chromosome 24 of goats has been identified as a key player in the adaptation of goat breeds at high altitudes. A study focused on DSG3 revealed 27 SNPs variants between lowland and highland goat breeds, with three non-synonymous SNPs (R597E, T595I, and G572S) located in exon 5. To address the gap in knowledge regarding the genetic basis of high-altitude adaptation, this study aimed to characterize non-synonymous SNPs in exon 5 in DSG3 gene by analyzing Sanger sequences from 100 Chaugarkha goats. Sanger sequencing data were analyzed to identify genetic variation and assess the functional impact of non-synonymous SNPs. DNA and amino acid sequences were aligned to the San Clemente goat reference genome (ARS 1.2 Assembly) using MEGA11 with the ClustalW algorithm, and translations were performed using ExPASy. The functional effects of amino acid substitutions were predicted using Mutation Assessor, and protein stability changes were evaluated through structural modeling with the Site-Directed Mutator (SDM) tool. Variants were screened for insertions/deletions and premature stop codons using MEGA11. The potential effects of coding variants on pre-mRNA splicing were assessed using sequence-based splice prediction approaches using Human Splicing Finder, NNSPLICE, and GeneSplicer. Haplotype relationships were inferred using a median-joining network in NETWORK v10. Additionally, 100 diploid Chaugarkha goats were genotyped for three biallelic SNPs, allele frequencies, heterozygosity, and Hardy–Weinberg equilibrium were evaluated using chi-square and exact tests. Analysis revealed two non-synonymous SNPs (G572S and T595I) and one synonymous SNP in exon 5 of Chaugarkha goats. The two SNPs (chr24:g.25794771G>A and chr24:g.25794695C>T) showed complete heterozygosity in all individuals and strong deviation from Hardy–Weinberg equilibrium, whereas a third SNP (chr24:g.25794621G>C) was rare and conformed to equilibrium. Functional prediction analyses indicated that the associated amino acid substitutions (G572S and T595I) do not affect DSG3 protein function, stability, splicing, or structure. Haplotype analysis identified three haplotypes, with one predominant and one rare haplotype defined by a private mutation. Overall, the variants exhibited distinct genetic patterns but no predicted functional impact. In conclusion, the in silico tools predicted no drastic impact, despite the occurrence of non-synonymous SNPs in the gene, as this gene plays some of the very important biological roles. The experimental assays are needed to confirm the in silico prediction.