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

Christian Maltecca,Filippo Miglior,Flavio S. Schenkel,Christine F. Baes,Bayode O. Makanjuola

doi:10.1186/s12864-020-07031-w

Christian Maltecca, Filippo Miglior + Show 3 more

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https://doi.org/10.1186/s12864-020-07031-w

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Abstract

BackgroundPhenotypic 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 (FPED) and genomic measures using segment based (FROH) and marker-by-marker (FGRM) based approaches.ResultsInbreeding depression was found for all production and most fertility traits, for example, every 1% increase in FPED, FROH and FGRM 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 FPED, FROH and FGRM, 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.ConclusionsInbreeding 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.

Highlights

Phenotypic performances of livestock animals decline with increasing levels of inbreeding, 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
For every 1% increase in inbreeding coefficients based on FPED, FROH and FGRM, a corresponding reduction of 44.71, 40.48 and 48.72 kg was estimated, respectively, representing 0.49, 0.45 and 0.54% of the phenotypic means for the traits
The effect of inbreeding was noticeable for fertility traits with heifers having a statistically significant (P < 0.05) increase of 0.29, 0.24 and 0.31 days in first service to conception (FSTC) for every 1% increase in inbreeding coefficients based on FPED, FROH and FGRM, respectively, which represents 1.50, 1.24 and variances

Summary

Introduction

Phenotypic performances of livestock animals decline with increasing levels of inbreeding, 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. Inbreeding depression is the noticeable decline in the phenotypic mean of economically important traits within a given population [3]. This decline is often attributable to decreasing heterozygosity and increasing recessive homozygosity resulting from inbreeding and random genetic drift. Depression could result when inbreeding reduces the combination of favorable heterozygous genotypes across multiple loci [6]. From these hypotheses, partial dominance has been widely reported to account for most of the observed inbreeding depression [4, 7, 8]

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