Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle
Abstract Background Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), a...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | deu |
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BMC
2024-01-01
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| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-024-00878-7 |
| _version_ | 1797276232554905600 |
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| author | Maulana Mughitz Naji José Luis Gualdrón Duarte Natalia Soledad Forneris Tom Druet |
| author_facet | Maulana Mughitz Naji José Luis Gualdrón Duarte Natalia Soledad Forneris Tom Druet |
| author_sort | Maulana Mughitz Naji |
| collection | DOAJ |
| description | Abstract Background Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding. Methods We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (F PED), on the correlation between uniting gametes (F UNI), on the genomic relationship matrix (F GRM), on excess homozygosity (F HET), or on homozygous-by-descent (HBD) segments (F HBD). Results F UNI and F GRM were sensitive to used allele frequencies, whereas F HET and F HBD were more robust. We detected significant ID for four traits related to height and length; F HBD and F UNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments. Conclusions Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding. |
| first_indexed | 2024-03-07T15:24:25Z |
| format | Article |
| id | doaj.art-fc284748c89d42608fff622ea865801a |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-03-07T15:24:25Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-fc284748c89d42608fff622ea865801a2024-03-05T17:25:02ZdeuBMCGenetics Selection Evolution1297-96862024-01-0156111010.1186/s12711-024-00878-7Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattleMaulana Mughitz Naji0José Luis Gualdrón Duarte1Natalia Soledad Forneris2Tom Druet3Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of LiègeUnit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of LiègeUnit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of LiègeUnit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of LiègeAbstract Background Cattle populations harbor generally high inbreeding levels that can lead to inbreeding depression (ID). Here, we study ID with different estimators of the inbreeding coefficient F, evaluate their sensitivity to used allele frequencies (founder versus sample allele frequencies), and compare effects from recent and ancient inbreeding. Methods We used data from 14,205 Belgian Blue beef cattle genotyped cows that were phenotyped for 11 linear classification traits. We computed estimators of F based on the pedigree information (F PED), on the correlation between uniting gametes (F UNI), on the genomic relationship matrix (F GRM), on excess homozygosity (F HET), or on homozygous-by-descent (HBD) segments (F HBD). Results F UNI and F GRM were sensitive to used allele frequencies, whereas F HET and F HBD were more robust. We detected significant ID for four traits related to height and length; F HBD and F UNI presenting the strongest associations. Then, we took advantage of the classification of HBD segments in different age-related classes (the length of an HBD segment being inversely related to the number of generations to the common ancestors) to determine that recent HBD classes (common ancestors present approximately up to 15 generations in the past) presented stronger ID than more ancient HBD classes. We performed additional analyses to check whether these observations could result from a lower level of variation in ancient HBD classes, or from a reduced precision to identify these shorter segments. Conclusions Overall, our results suggest that mutational load decreases with haplotype age, and that mating plans should consider mainly the levels of recent inbreeding.https://doi.org/10.1186/s12711-024-00878-7 |
| spellingShingle | Maulana Mughitz Naji José Luis Gualdrón Duarte Natalia Soledad Forneris Tom Druet Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle Genetics Selection Evolution |
| title | Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle |
| title_full | Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle |
| title_fullStr | Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle |
| title_full_unstemmed | Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle |
| title_short | Inbreeding depression is associated with recent homozygous-by-descent segments in Belgian Blue beef cattle |
| title_sort | inbreeding depression is associated with recent homozygous by descent segments in belgian blue beef cattle |
| url | https://doi.org/10.1186/s12711-024-00878-7 |
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