A model‐based approach to characterize individual inbreeding at both global and local genomic scales

• DOI: 10.1111/mec.14324
• Publication Date: 2017-08-17T07:21:48Z
• Authors: T. Druet; M. Gautier
• Keywords: Identity by descent

Abstract Inbreeding results from the mating of related individuals and may be associated with reduced fitness because it brings together deleterious variants in one individual. In general, inbreeding is estimated respect to an arbitrary base population consisting ancestors that are assumed unrelated. We herein propose a model‐based approach estimate characterize individual at both global local genomic scales by assuming genome mosaic homozygous‐by‐descent (HBD) non‐HBD segments. The HBD segments originate tracing back different periods past defining distinct age‐related classes. lengths exponentially distributed class‐specific parameters reflecting older origin generates on average shorter stretches observed homozygous markers. model implemented hidden Markov framework uses marker allele frequencies, genetic distances, genotyping error rates sequences genotypes. Note errors, low‐fold sequencing or genotype‐by‐sequencing data easily accommodated under this framework. Based simulations inference model, we show genomewide coefficients accurately estimated. addition, when several classes simulated, captures them if their ages sufficiently different. Complementary analyses, either sets simulated more realistic models human, dog sheep real data, illustrate range applications how can reveal recent demographic histories among populations (e.g., very bottlenecks founder effects). method also allows clearly identify resulting extreme consanguineous matings.