Molecular genetics and bioinformatics analysis of EDG1 and AKIRIN2 genes in Iranian fat-tailed and nonfat-tailed sheep breeds

Abstract

This study was conducted to detect different allelic forms and its association with fat-tail traits, and also investigation of domains variants in 5/- and 3/-UTR regions of EDG1 and AKIRIN2 genes in Iranian fat-tailed (Lori-Bakhtiari) and nonfat-tailed (Zel) sheep breeds. Blood samples were randomly collected from 300 sheep (150 samples per each breed) and genomic DNA was extracted by modified salting out method. Two primer pairs were designed by oligo7 software for amplification of fragments with the length of 516 and 454bp from EDG1 and AKIRIN2 genes, respectively. The results of genotyping by SSCP assay and silver nitrate staining showed that, in both breeds, there was no incidence of mutation in AKIRIN2 gene. But, the EDG1 was highly polymorph in studied sheep breeds, so that, six banding patterns with different frequencies of A (36.73 and 31.19%), B (8.84 and 21.6%), C (7.48 and 41.12%), D (29.93 and 34.50%), E (13.61 and 34.10%) and F (3.40 and 38.1%) were observed for Zel and Lori-Bakhtiari breeds, respectively. Comparison of banding pattern frequencies by Chi-square test showed significant difference between two breeds (P<0.01). One sample from each banding patterns were sequenced. The alignment and motif analysis of sequences by BioEdit and DNASIS MAX software showed incidence of 11 single nucleotide polymorphism (SNP) and 18 DNA motifs in EDG1 marker site. According to different SNPs, the paternal and maternal haplotypes were determined by phase software. The association study showed significant association between EDG1 gene haplotypes and banding patterns with fat-tail traits in Lori-Bakhtiari sheep except for height of fat-tail. This study was the first effort for evaluate of these genes in sheep. Therefore, more studies on other breeds of sheep and on coding sequence of these genes are recommended.