Comparative Analysis of Romanian and Swiss Bovine Populations Using Whole Genome Sequencing and SNP Microarrays

Abstract

The use of SNP microarrays has gained distinguished attention in recent years and the identification of numerous SNPs has proven valuable for genetic evaluation and selection in farm animals. In the current study we compared several bovine populations from Romania and Switzerland at the level of SNPs. Romanian Brown (N=39) and Romanian Spotted (N=245) cattle were genotyped using the Axiom Bovine BovMDv3 SNP microarray. For the Swiss population, we acquired sequencing data from the NCBI SRA database for 80 individuals from three breeds: Brown Swiss (N=20), Original Braunvieh (N=20) and Simmental (N=40). Sequencing data were processed using the Bcbio-nextgen data analysis pipeline and variants were called based on the UMD3.1 reference genome. Common SNPs found from both microarray and sequencing data were retained and genotypes from all the Romanian and Swiss animals were pooled together, resulting in a combined dataset of 48,291 SNPs for 364 individuals. Pairwise comparisons were assessed on the five subpopulations according to Weir and Cockerham’s FST index. Small genetic differences (FST < 0.05) were found between the Romanian Brown and Swiss Brown Swiss subpopulations and between Romanian Spotted and Swiss Simmental subpopulations. For all the other pairwise comparisons, FST values were between 0.05 and 0.1, indicating a moderate level of genetic difference among the corresponding subpopulations. The results of fastSTRUCTURE indicated that the most likely number (K) of subpopulations from the pooled dataset was between 8 and 12. Bar plots for K = 5, 8 and 12 confirmed that Romanian Brown and Swiss Brown Swiss subpopulations were genetically similar. However, they also revealed a surprisingly high level of heterogeneity among the Romanian Spotted individuals. As such, future research is required to zoom in on the genetic make-up and explain the most likely sources of heterogeneity for the Romanian Spotted breed. Current results will facilitate a better understanding of genomic selection and its application for improved breeding programs in Romanian cattle breeds.

Keywords

• whole genome sequencing
• variant calling
• snp microarray
• population structure