Genetic diversity among three camel populations reared in Egypt using mitochondrial COX-3 gene

Abstract

Abstract Maintaining genetic diversity among native Egyptian breeds is important towards genetic resource conservation. Examining the mitochondrial genome in different or within breeds can be helpful in determining the genetic variety of populations. This study examined the mitochondrial COX-3 gene of Egyptian Camelus dromedaries using bioinformatics and phylogenetic analysis, revealing two distinct haplotypes based on single nucleotide polymorphisms at positions 280 and 325. These two haplotypes' amplified PCR products were uploaded to GenBank/NCBI with accession numbers OP994029 and OP994030 with protein id = WHO17331.1" and WHO17330.1, respectively. Comparison of nucleotide and amino acid sequences of the Egyptian camel populations' three-dimensional COX-3 structure showed how closely related these two haplotypes are genetically. Haplotype 1 was more predominant and found in Baldi and Sudani populations whereas haplotype 2 was more abundant in Maghrebi population. The two polymorphic sites have diversity and theta (per site): Theta (W: 0.00208); high variety of haplotypes (Hd: 0.667). These two haplotypes are the most genetically distant from camels in the Camelidae family, according to phylogenetic study. Based on the nucleotide sequences A + T and C + G have frequencies between 51.15% and 48.85%, respectively. The two non-synonymous SNPs caused the P94S amino acid substitution in the coiled region while I109V substitution located in the strand, which was neutral. Analysis of amino acid substitutions via protein prediction showed that the two amino acids were semi-conserved in which the resultant amino acid has different properties from the original amino acid and can affect the protein structure. The protein stability diminished according to the I-Mutant and MUpro tools. I109V nSNP and increased for P94S nSNP. This finding suggested that COX-3 gene variability in camels is important to preserve this genetic resource and creating future breeding programmes, conservation strategies that will increase camel production.