Genomic characterization of mithun (Bos frontalis) populations using high density SNP array

Abstract

Mithun (Bos frontalis) is a bovine species found in the four North-Eastern Hilly States of India viz., Nagaland, Arunachal, Manipur and Mizoram. The 770k BovineHDBeadChip (Illumina, CA), which is basically a highdensity SNP array was utilized for genomic characterization of four mithun populations and to study genetic diversity present in the populations. SNP genotyping of a total 24 samples representing four mithun populations as per their geographic locations were carried out. The results indicated that the majority of polymorphic SNPs were found to be in HWE. Observed heterozygosity ranged between 0.263±0.040 (Nagaland) to 0.299±0.044 (Arunachal). Inbreeding coefficient ranged from 0.087±0.139 for Nagaland to 0.186±0.053 for Manipur mithun. The result of the Principal Component Analysis (PCA) indicated all the mithuns were distributed together in close proximity and no clear separation of the four populations was observed.The first and second principal components (PC1 and PC2) explained 9.59% and 88.0% of the total variation, respectively. The results of the STRUCTURE analysis also showed no population substructure as inferred from an increasing plot of cross validation error, similar to PCA. In our knowledge, this is the first study on genomic characterization of any Indian livestock species, through analysis of population structure and genetic diversity using high density SNP array. The baseline information generated in our study will help in developing proper strategies for implementing genomic selection and conservation of mithun.