Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data

Background: Local cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to harsh environments and scarce food conditions. One such local Swiss cattle breed is Original Braunvieh (OB) which is used for beef and milk production in alpine areas. Using whole-genome sequencing data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results: We annotated 15.7 million SNPs and 1.5 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding (FROH=0.14) was relatively low in OB cattle. However, genomic inbreeding increased in recent years due to a higher number of long (> 1 Mb) runs of homozygosity in cattle born in more recent generations. Using two complementary approaches, i.e., composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (p