International Journal of Agriculture Extension and Social Development

author(s)
Utsav Surati, Ravina, Dharamshaw CA, Gaurav Patel, Chandana Sree Chinnareddyvari, Pallavi Rathi, Rangasai Chandra Goli, Kiyevi G Chishi, Ayushi Singh¬ and Kanaka KK

abstract
Deleterious mutations in genomes, particularly those occurring in germ cells, can have heritable consequences. Next Generation Sequencing (NGS) technology has facilitated the discovery and prediction of novel mutations. Computational algorithms and robust bioinformatics pipelines play a crucial role in identifying genetic mutations, especially in scenarios lacking animal records and in vivo testing. In this study, genomic sequence data from twenty Sus scrofa (pig) samples obtained from the European Variation Archive repository was annotated using VEP-Ensembl. A total of 178,745 variants were processed, including 530 novel variants. Subsequently, only sex chromosomes were considered for further analysis to identify sex-linked mutations, resulting in the processing of 2300 variants, including 28 non-synonymous SNPs (nsSNPs). Using various predictive tools such as SIFT, PANTHER, Predict SNP, Polyphen-1, Polyphen-2, and SNAP, four nsSNPs were identified as deleterious, with one nsSNP found deleterious across all tools. Additionally, the I-mutant tool confirmed a decrease in protein stability for all deleterious nsSNPs. This study identified four deleterious mutations (S261F, D664N, A704, and I76N) mapped to two genes (HUWE1 and NKRF) in pigs. One mutation name D664N (HUWEI) was found to be deleterious by all tools. While most deleterious mutations in pigs have been reported in exotic breeds, limited information exists for Indian native pig breeds. The in-silico identification of deleterious SNPs in this study provides a foundation for further investigation into the biological consequences of these mutations in Indian pig breeds through in vivo studies.