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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MDPI AG
2021-10-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/11/11/3105 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T04:36:11Z |
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| id | doaj.art-bfadfe598aa349bda2c7c08a08fe9039 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-09T04:36:11Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
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| series | Animals |
| spelling | doaj.art-bfadfe598aa349bda2c7c08a08fe90392023-12-03T13:27:37ZengMDPI AGAnimals2076-26152021-10-011111310510.3390/ani11113105Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 HerefordBethany Pilon0Kelly Hinterneder1El Hamidi A. Hay2Breno Fragomeni3Department of Animal Science, University of Connecticut, Storrs, CT 06269, USADepartment of Animal Science, University of Connecticut, Storrs, CT 06269, USAFort Keogh Livestock and Range Research Laboratory, ARS, USDA, Miles City, MT 59301, USADepartment of Animal Science, University of Connecticut, Storrs, CT 06269, USAThe 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.https://www.mdpi.com/2076-2615/11/11/3105inbreedingruns of homozygosityHereford cattle |
| spellingShingle | 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 Animals inbreeding runs of homozygosity Hereford cattle |
| title | 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_short | 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 |
| topic | inbreeding runs of homozygosity Hereford cattle |
| url | https://www.mdpi.com/2076-2615/11/11/3105 |
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