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.

Fig. 1

ROH in 33 OB cattle with average sequencing depth greater than 10-fold. a Average genomic inbreeding and corresponding standard error for the 29 autosomes. b Average genomic inbreeding (F_ROH) calculated from short (50–100 kb), medium (0.1–2 Mb) and long (> 2 Mb) ROH. (c) Average number of short, medium and long ROH

Fig. 2

Cumulative genomic inbreeding (%) in animals born between 1965 and 1989 (blue lines) and 1990–2012 (red lines) from ROH sorted on length and binned in windows of 10 kb. Thin dashed lines represent individuals and thick solid lines represent the average cumulative genomic inbreeding of the two groups of animals

Fig. 3

Genome wide distribution of top 0.5% signatures of selection from CLR (a) and iHS (b) analyses and their overlap (c). Each point represents a non-overlapping window of 40 kb along the autosomes

Fig. 4

Detailed view of a top candidate selection region on chromosome 11 in OB that was detected using CLR tests (a) and iHS (b). Each point represents a non-overlapping window of 40 kb. The dotted horizontal lines indicate the cutoff values (top 0.5%) for CLR (210) and iHS (2.13) statistics. The allele frequencies of the derived (red) or alternate alleles (black) (c and d) and genes (e and f) in the peak region (67.5–68.2 Mb) of the top CLR (66–68.5 Mb) and iHS (68.4–69.2 Mb) regions. Green and black colour indicates genes on the forward and reverse strand of DNA, respectively

Fig. 5

Top CLR candidate region on chromosome 6 (a). Each point represents a non-overlapping window of 40 kb. The frequencies of the derived (red) or alternate alleles (black) (b) and genes (c) annotated between 38.5 and 39.4 Mb. Green and black colour indicates genes on the forward and reverse strand of DNA, respectively