Runs of homozygosity and analysis of inbreeding depression
| Autor: | Samuel E. Aggrey, Andrew J. Roberts, El Hamidi Hay, Romdhane Rekaya, Sajjad Toghiani, Pattarapol Sumreddee |
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| Rok vydání: | 2020 |
| Předmět: |
Genotype
Population Pedigree chart Single-nucleotide polymorphism Runs of Homozygosity Biology Polymorphism Single Nucleotide 03 medical and health sciences Statistics Genetics Inbreeding depression Animals Inbreeding education 030304 developmental biology 0303 health sciences education.field_of_study Inbreeding Depression Homozygote Animal Genetics and Genomics 0402 animal and dairy science 04 agricultural and veterinary sciences General Medicine 040201 dairy & animal science Pedigree Mutation (genetic algorithm) Trait Cattle Animal Science and Zoology Food Science |
| Zdroj: | J Anim Sci |
| ISSN: | 1525-3163 0021-8812 |
| DOI: | 10.1093/jas/skaa361 |
| Popis: | Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments ( |
| Databáze: | OpenAIRE |
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