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 br... Mehr ...
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Dokumenttyp: | Datenquelle |
Erscheinungsdatum: | 2017 |
Verlag/Hrsg.: |
Figshare
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Schlagwörter: | Medicine / Genetics / FOS: Biological sciences / Evolutionary Biology / 59999 Environmental Sciences not elsewhere classified / FOS: Earth and related environmental sciences / Ecology / 69999 Biological Sciences not elsewhere classified / 19999 Mathematical Sciences not elsewhere classified / FOS: Mathematics / Cancer / Plant Biology |
Sprache: | unknown |
Permalink: | https://search.fid-benelux.de/Record/base-28885324 |
Datenquelle: | BASE; Originalkatalog |
Powered By: | BASE |
Link(s) : | https://dx.doi.org/10.6084/m9.figshare.c.3961515 |
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. Results When 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 ...