Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle

Abstract

Background Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods. ResultsWhen using 600 K single nucleotide polymorphisms (SNPs), the inbreeding coefficient (probability of sampling an HBD locus in an individual) was on average 0.303 (ranging from 0.258 to 0.375). HBD-classes associated to historical ancestors (with small segments ≤ 200 kb) accounted for 21.6% of the genome length (71.4% of the total length of the genome in HBD segments), whereas classes associated to more recent ancestors accounted for only 22.6% of the total length of the genome in HBD segments. However, these recent classes presented more individual variation than more ancient classes. Although inbreeding coefficients obtained with low SNP densities (7 and 32 K) were much lower (0.060 and 0.093), they were highly correlated with those obtained at higher density (r = 0.934 and 0.975, respectively), indicating that they captured most of the individual variation. At higher SNP density, smaller HBD segments are identified and, thus, more past generations can be explored. We observed very high correlations between our estimates and those based on homozygosity (r = 0.95) or on runs-of-homozygosity (r = 0.95). As expected, pedigree-based estimates were mainly correlated with recent HBD-classes (r = 0.56).ConclusionsAlthough we observed high levels of autozygosity associated with small HBD segments in BBB cattle, recent inbreeding accounted for most of the individual variation. Recent autozygosity can be captured efficiently with low-density SNP arrays and relatively simple models (e.g., two HBD classes). The HMM framework provides local HBD probabilities that are still useful at lower SNP densities.Electronic supplementary materialThe online version of this article (10.1186/s12711-017-0370-x) contains supplementary material, which is available to authorized users.

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

“…The average F ROH estimated from WGS data was 0.14 in OB. This is lower than WGS-based F ROH in Holstein (0.18), Jersey (0.24), Old Danish Red (0.23) and Belgian Blue (0.3) cattle [47,48]. However, the genomic inbreeding is slightly higher in OB than New Red Danish cattle (0.11), an admixed breed that contains genes from old Danish and other red breeds [47].…”

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

“…Original Braunvieh is a local cattle breed with approximately 10,000 cows registered in the breeding population and 4,500 calves entering the herd book every year (Additional file 1). In spite of the small population size, the nucleotide diversity (π = 1.6 × 10 -3 ) is higher in OB than many European taurine cattle breeds with considerably more breeding animals [84,85]. However, genomic inbreeding is slightly higher in OB than New Red Danish cattle (0.11), an admixed breed that contains genes from old Danish and other red breeds [84].…”

RZooRoH: An R package to characterize individual genomic autozygosity and identify homozygous‐by‐descent segments

“…More precisely, single HBD class models may underestimate the autozygosity when multiple generations contribute to it . We also illustrated with cattle data that the use of single HBD class models results in lower estimates of autozygosity and that the distribution of identified HBD segments is more concentrated at intermediary sizes (Solé et al, 2017)…”

“…Our multiple HBD classes model allows to fit more realistic situations where ancestors contributing to autozygosity trace back to different generations in the past (e.g. Solé et al, 2017). The HBD classes are indeed related to the age of common ancestors contributing to them : classes with longer (shorter) segments, i.e.…”