Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were us...

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Autores principales:	Bethany Pilon, Kelly Hinterneder, El Hamidi A. Hay, Breno Fragomeni
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	inbreeding runs of homozygosity Hereford cattle Veterinary medicine SF600-1100 Zoology QL1-991
Acceso en línea:	https://doaj.org/article/bfadfe598aa349bda2c7c08a08fe9039
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spelling	oai:doaj.org-article:bfadfe598aa349bda2c7c08a08fe90392021-11-25T16:15:32ZInbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford10.3390/ani111131052076-2615https://doaj.org/article/bfadfe598aa349bda2c7c08a08fe90392021-10-01T00:00:00Zhttps://www.mdpi.com/2076-2615/11/11/3105https://doaj.org/toc/2076-2615The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes’ ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.Bethany PilonKelly HinternederEl Hamidi A. HayBreno FragomeniMDPI AGarticleinbreedingruns of homozygosityHereford cattleVeterinary medicineSF600-1100ZoologyQL1-991ENAnimals, Vol 11, Iss 3105, p 3105 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	inbreeding runs of homozygosity Hereford cattle Veterinary medicine SF600-1100 Zoology QL1-991
spellingShingle	inbreeding runs of homozygosity Hereford cattle Veterinary medicine SF600-1100 Zoology QL1-991 Bethany Pilon Kelly Hinterneder El Hamidi A. Hay Breno Fragomeni Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford
description	The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes’ ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.
format	article
author	Bethany Pilon Kelly Hinterneder El Hamidi A. Hay Breno Fragomeni
author_facet	Bethany Pilon Kelly Hinterneder El Hamidi A. Hay Breno Fragomeni
author_sort	Bethany Pilon
title	Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford
title_short	Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford
title_full	Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford
title_fullStr	Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford
title_full_unstemmed	Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford
title_sort	inbreeding calculated with runs of homozygosity suggests chromosome-specific inbreeding depression regions in line 1 hereford
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/bfadfe598aa349bda2c7c08a08fe9039
work_keys_str_mv	AT bethanypilon inbreedingcalculatedwithrunsofhomozygositysuggestschromosomespecificinbreedingdepressionregionsinline1hereford AT kellyhinterneder inbreedingcalculatedwithrunsofhomozygositysuggestschromosomespecificinbreedingdepressionregionsinline1hereford AT elhamidiahay inbreedingcalculatedwithrunsofhomozygositysuggestschromosomespecificinbreedingdepressionregionsinline1hereford AT brenofragomeni inbreedingcalculatedwithrunsofhomozygositysuggestschromosomespecificinbreedingdepressionregionsinline1hereford
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Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

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