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

Abstract

Background: Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) 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 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 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 derived from runs of homozygosity (ROH) was relatively low (F ROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (F ROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, 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 < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions: We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

“…We observed the highest error rate for reads aligned to the OBV-specific augmented reference graph. In 500 randomly sampled subsets of 35 sequenced cattle per breed, we discovered more sequence variants on chromosome 25 in OBV (N=305 ± 5K) than either FV (N=291 ± 3K), BSW (N=276 ± 6K) or HOL (N=259 ± 2K), reflecting that nucleotide diversity is higher in OBV than the other three breeds, which agrees with a recent study [25]. Across all alternate allele frequency thresholds considered, read mapping was more accurate for HOL than FV and OBV cattle, possibly because both genetic diversity and effective population size is less in HOL than the other three breeds considered [26].…”

Activation of cryptic splicing in bovineWDR19is associated with reduced semen quality and male fertility

“…Considering only variants that are private to BSW animals would have excluded many of the 824 variants as potential candidate causal variants. Nevertheless, such a variant filtration approach does not take into account that trait-associated recessive alleles with detrimental consequences may segregate across populations [63][64][65][66]. It is not known if the QTL detected in our study also segregates in breeds other then BSW.…”

“…The removal of variants that segregate in breeds other than BSW would have excluded many of the 824 variants as potential candidate causal variants for the impaired fertility associated with homozygosity for the BTA6 QTL. Nevertheless, such a variant filtration approach does not take into account that deleterious recessive alleles may segregate across populations [63][64][65][66].…”

Grazing Allometry: Anatomy, Movement, and Foraging Behavior of Three Cattle Breeds of Different Productivity

“…Cattle of medium productivity were represented by Original Braunvieh (OB), a dual-purpose breed traditionally kept in the Swiss Alps, with body weight, and growth rate considerably higher than that of Highland cattle (6). The Original Braunvieh is not to be confused with Brown Swiss, a highproductive, but genetically less diverse dairy breed selected from the same original population (19). The most productive breed in our experiment was Angus × Holstein crossbreed (AH), which combines the strongly muscled, heavy body of Angus beef cattle with the large-framed body and elevated milk production of Holstein dairy cows.…”