Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins

Abstract Background Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, but rather could be distinctly associated with more recent or more anci...

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Main Authors: Bayode O. Makanjuola, Christian Maltecca, Filippo Miglior, Flavio S. Schenkel, Christine F. Baes
Format: Article
Language:English
Published: BMC 2020-09-01
Series:BMC Genomics
Subjects:
Online Access:http://link.springer.com/article/10.1186/s12864-020-07031-w
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spelling doaj-61ef943c4f8149c3b62787d4279529522020-11-25T02:43:12ZengBMCBMC Genomics1471-21642020-09-0121111510.1186/s12864-020-07031-wEffect of recent and ancient inbreeding on production and fertility traits in Canadian HolsteinsBayode O. Makanjuola0Christian Maltecca1Filippo Miglior2Flavio S. Schenkel3Christine F. Baes4Centre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of GuelphCentre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of GuelphCentre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of GuelphCentre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of GuelphCentre for Genomic Improvement of Livestock, Department of Animal Biosciences, University of GuelphAbstract Background Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, but rather could be distinctly associated with more recent or more ancient inbreeding. Therefore, splitting inbreeding into different age classes could help in assessing detrimental effects of different ages of inbreeding. Hence, this study sought to investigate the effect of recent and ancient inbreeding on production and fertility traits in Canadian Holstein cattle with both pedigree and genomic records. Furthermore, inbreeding coefficients were estimated using traditional pedigree measure (F PED ) and genomic measures using segment based (F ROH ) and marker-by-marker (F GRM ) based approaches. Results Inbreeding depression was found for all production and most fertility traits, for example, every 1% increase in F PED , F ROH and F GRM was observed to cause a − 44.71, − 40.48 and − 48.72 kg reduction in 305-day milk yield (MY), respectively. Similarly, an extension in first service to conception (FSTC) of 0.29, 0.24 and 0.31 day in heifers was found for every 1% increase in F PED , F ROH and F GRM , respectively. Fertility traits that did not show significant depression were observed to move in an unfavorable direction over time. Splitting both pedigree and genomic inbreeding into age classes resulted in recent age classes showing more detrimental inbreeding effects, while more distant age classes caused more favorable effects. For example, a − 1.56 kg loss in 305-day protein yield (PY) was observed for every 1% increase in the most recent pedigree age class, whereas a 1.33 kg gain was found per 1% increase in the most distant pedigree age class. Conclusions Inbreeding depression was observed for production and fertility traits. In general, recent inbreeding had unfavorable effects, while ancestral inbreeding had favorable effects. Given that more negative effects were estimated from recent inbreeding when compared to ancient inbreeding suggests that recent inbreeding should be the primary focus of selection programs. Also, further work to identify specific recent homozygous regions negatively associated with phenotypic traits could be investigated.http://link.springer.com/article/10.1186/s12864-020-07031-wInbreeding depressionRecent and ancient inbreedingPedigree and genomic inbreeding
collection DOAJ
language English
format Article
sources DOAJ
author Bayode O. Makanjuola
Christian Maltecca
Filippo Miglior
Flavio S. Schenkel
Christine F. Baes
spellingShingle Bayode O. Makanjuola
Christian Maltecca
Filippo Miglior
Flavio S. Schenkel
Christine F. Baes
Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins
BMC Genomics
Inbreeding depression
Recent and ancient inbreeding
Pedigree and genomic inbreeding
author_facet Bayode O. Makanjuola
Christian Maltecca
Filippo Miglior
Flavio S. Schenkel
Christine F. Baes
author_sort Bayode O. Makanjuola
title Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins
title_short Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins
title_full Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins
title_fullStr Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins
title_full_unstemmed Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins
title_sort effect of recent and ancient inbreeding on production and fertility traits in canadian holsteins
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2020-09-01
description Abstract Background Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, but rather could be distinctly associated with more recent or more ancient inbreeding. Therefore, splitting inbreeding into different age classes could help in assessing detrimental effects of different ages of inbreeding. Hence, this study sought to investigate the effect of recent and ancient inbreeding on production and fertility traits in Canadian Holstein cattle with both pedigree and genomic records. Furthermore, inbreeding coefficients were estimated using traditional pedigree measure (F PED ) and genomic measures using segment based (F ROH ) and marker-by-marker (F GRM ) based approaches. Results Inbreeding depression was found for all production and most fertility traits, for example, every 1% increase in F PED , F ROH and F GRM was observed to cause a − 44.71, − 40.48 and − 48.72 kg reduction in 305-day milk yield (MY), respectively. Similarly, an extension in first service to conception (FSTC) of 0.29, 0.24 and 0.31 day in heifers was found for every 1% increase in F PED , F ROH and F GRM , respectively. Fertility traits that did not show significant depression were observed to move in an unfavorable direction over time. Splitting both pedigree and genomic inbreeding into age classes resulted in recent age classes showing more detrimental inbreeding effects, while more distant age classes caused more favorable effects. For example, a − 1.56 kg loss in 305-day protein yield (PY) was observed for every 1% increase in the most recent pedigree age class, whereas a 1.33 kg gain was found per 1% increase in the most distant pedigree age class. Conclusions Inbreeding depression was observed for production and fertility traits. In general, recent inbreeding had unfavorable effects, while ancestral inbreeding had favorable effects. Given that more negative effects were estimated from recent inbreeding when compared to ancient inbreeding suggests that recent inbreeding should be the primary focus of selection programs. Also, further work to identify specific recent homozygous regions negatively associated with phenotypic traits could be investigated.
topic Inbreeding depression
Recent and ancient inbreeding
Pedigree and genomic inbreeding
url http://link.springer.com/article/10.1186/s12864-020-07031-w
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