Identification of Species-Specific Indels in Bubalus bubalis, Bos taurus, Capra hircus, and Ovis aries

InDels are the second most common type of variation across eukaryote genomes. Several studies have shown that InDels are the major cause of evolutionary changes, contributing significantly to intra-interspecific divergence. The aim of this study was to identify specie-specific short-InDels for Bubalus bubalis, Bos taurus, Capra hircus, and Ovis aries. For this purpose, genomic sequences of all Artiodactyla and Perissodactyla species available in GeneBank were aligned for candidate genes associated with milk and meat qualitative and quantitative traits. The in silico investigation has evidenced that Ovis aries and Bubalus bubalis are characterized by a 14 bp deletion at the 5′UTR of the αs2-casein encoding gene (CSN1S2, KT283354.1:g.643-644delAGAAATCAAATCTT) and by a deletion of an heptamer at exon 10 (3′UTR) of the PRLR gene encoding for the Prolactin Receptor (MF461277.1:g.12162-12163delCACTACC), respectively. Likewise, the 5′UTR of the αs1-casein encoding gene (CSN1S1) of Capra hircus is characterized by a 28 bp sequence (KC951931.1:g.1989-2016insTGTACAATGCCATTAATATATTGTACAA). In particular, the first 20 nucleotides are absent in Bubalus bubalis and Bos taurus sequences, while the last 7 bp are constitutively deleted in Ovis aries. Finally, it was evidenced that Bos taurus is characterized by the deletion of 16 bp (AB076403.1:g.1207-1208delGAGTAGGTTATGGCTT) at intron 1 of the myostatin gene (MSTN). To verify the specificity of these genetic markers, four allele-specific PCR protocols were developed. The genotyping of a preliminary panel of 400 samples (100 each species, belonging to different breeds) seems to confirm the in silico analyses. These markers may become a new tool to carry out phylogenetic studies or to set up PCR methods to verify the animal origin of the components of a product.