Identifcation and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr.

Abstract

Whole genome sequencing of bovine breeds has allowed identifcation of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identifed genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted efects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii)

protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcrip- tion factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identifed in the caseins (CSN1S1,

CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identifed. LALBA Ile60Val was predicted to afect protein stability and fexibility, by reducing the number the disulfde bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly afect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn afect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of afecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identifcation of potentially functional variants for milk protein genes.