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

Abstract

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 (F ROH =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 < 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 genomic variation segregating in Swiss OB cattle. Using whole-genome sequencing 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 harsh environments. Considering the low population size and increasing rates of genomic inbreeding in the past generations, the implementation and adoption of genomic mating programs 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 ± 5 K) 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 [ 26 ]. 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 breeds considered [ 27 ].…”

Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

“…Previous studies have elucidated that using genomic data to evaluate the extent of inbreeding was more accurate than using pedigree data ( Purfield et al, 2012 ; Zanella et al, 2016 ) because the pedigree data were always incomplete and failed to capture the influence of relatedness among individuals in the population. The level of ROH reflects the ancient and recent inbreeding history of a population, which has been widely applied to explore the extent of inbreeding in the population of any species ( Deniskova et al, 2019 ; Xu et al, 2019 ; Bhati et al, 2020 ). As shown in previous report, the average ROH levels varied considerably among Chinese pigs, ranging from the lowest value of 20.6 Mb in wild boars to the largest value of 168 Mb in DSE pigs ( Wang et al, 2018 ).…”

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 high-productive, 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.…”