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1000 Titel
  • Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle
1000 Autor/in
  1. , Mehrnush |
  2. Ansari Mahyari, Saeid |
  3. Baes, Christine |
  4. Melzer, Nina |
  5. Schenkel, Flavio Schramm |
  6. Sargolzaei, Mehdi |
1000 Erscheinungsjahr 2018
1000 LeibnizOpen
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2018-01-27
1000 Erschienen in
1000 Quellenangabe
  • 19:98
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2018
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.1186/s12864-018-4453-z |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5787230/ |
1000 Ergänzendes Material
  • https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4453-z#Decs |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • BACKGROUND: While autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulation was performed and inbreeding estimates based on runs of homozygosity (ROH), pedigree, and the genomic relationship matrix were compared to true inbreeding. Inbreeding based on ROH was estimated using SNP1101, PLINK, and BCFtools software with different threshold parameters. The effects of different selection methods on ROH patterns were also compared. Furthermore, inbreeding coefficients were estimated in a sample of genotyped North American Holstein animals born from 1990 to 2016 using 50 k chip data and ROH patterns were assessed before and after genomic selection. RESULTS: Using ROH with a minimum window size of 20 to 50 using SNP1101 provided the closest estimates to true inbreeding in simulation study. Pedigree inbreeding tended to underestimate true inbreeding, and results for genomic inbreeding varied depending on assumptions about base allele frequencies. Using an ROH approach also made it possible to assess the effect of population structure and selection on distribution of runs of autozygosity across the genome. In the simulation, the longest individual ROH and the largest average length of ROH were observed when selection was based on best linear unbiased prediction (BLUP), whereas genomic selection showed the largest number of small ROH compared to BLUP estimated breeding values (BLUP-EBV). In North American Holsteins, the average number of ROH segments of 1 Mb or more per individual increased from 57 in 1990 to 82 in 2016. The rate of increase in the last 5 years was almost double that of previous 5 year periods. Genomic selection results in less autozygosity per generation, but more per year given the reduced generation interval. CONCLUSIONS: This study shows that existing software based on the measurement of ROH can accurately identify autozygosity across the genome, provided appropriate threshold parameters are used. Our results show how different selection strategies affect the distribution of ROH, and how the distribution of ROH has changed in the North American dairy cattle population over the last 25 years.
1000 Sacherschließung
lokal Runs of homozygosity
lokal Inbreeding
lokal Genomic selection
lokal BLUP selection
1000 Fachgruppe
  1. Biologie |
  2. Agrarwissenschaften |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. http://orcid.org/0000-0002-8145-1035|https://frl.publisso.de/adhoc/creator/QW5zYXJpIE1haHlhcmksIFNhZWlk|https://frl.publisso.de/adhoc/creator/QmFlcywgQ2hyaXN0aW5l|https://frl.publisso.de/adhoc/creator/TWVsemVyLCBOaW5h|https://frl.publisso.de/adhoc/creator/U2NoZW5rZWwsIEZsYXZpbyBTY2hyYW1t|https://frl.publisso.de/adhoc/creator/U2FyZ29semFlaSwgTWVoZGk=
1000 Label
1000 Förderer
  1. Iran’s Ministry of Science, Research and Technology
  2. Deutsche Forschungsgemeinschaft (DFG)
  3. Dairy Research Cluster Initiative
  4. Natural Sciences and Engineering Research Council of Canada
  5. DairyGen Council
  6. Semex Alliance Canada
1000 Fördernummer
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  2. -
  3. -
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1000 Förderprogramm
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  4. Collaborative Research and Development
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1000 Dateien
1000 Objektart article
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1000 @id frl:6410733.rdf
1000 Erstellt am 2018-10-23T11:37:32.022+0200
1000 Erstellt von 122
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1000 Bearbeitet von 218
1000 Zuletzt bearbeitet 2020-01-31T00:31:02.327+0100
1000 Objekt bearb. Tue Dec 18 12:43:32 CET 2018
1000 Vgl. frl:6410733
1000 Oai Id
  1. oai:frl.publisso.de:frl:6410733 |
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