Inbreeding depression across the genome of Dutch Holstein Friesian dairy cattle
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RESEARCH ARTICLE
Ge n e t i c s Se l e c t i o n Ev o l u t i o n
Open Access
Inbreeding depression across the genome of Dutch Holstein Friesian dairy cattle Harmen P. Doekes1,2* , Piter Bijma1, Roel F. Veerkamp1, Gerben de Jong3, Yvonne C. J. Wientjes1 and Jack J. Windig1,2
Abstract Background: Inbreeding depression refers to the decrease in mean performance due to inbreeding. Inbreeding depression is caused by an increase in homozygosity and reduced expression of (on average) favourable dominance effects. Dominance effects and allele frequencies differ across loci, and consequently inbreeding depression is expected to differ along the genome. In this study, we investigated differences in inbreeding depression across the genome of Dutch Holstein Friesian cattle, by estimating dominance effects and effects of regions of homozygosity (ROH). Methods: Genotype (75 k) and phenotype data of 38,792 cows were used. For nine yield, fertility and udder health traits, GREML models were run to estimate genome-wide inbreeding depression and estimate additive, dominance and ROH variance components. For this purpose, we introduced a ROH-based relationship matrix. Additive, dominance and ROH effects per SNP were obtained through back-solving. In addition, a single SNP GWAS was performed to identify significant additive, dominance or ROH associations. Results: Genome-wide inbreeding depression was observed for all yield, fertility and udder health traits. For example, a 1% increase in genome-wide homozygosity was associated with a decrease in 305-d milk yield of approximately 99 kg. For yield traits only, including dominance and ROH effects in the GREML model resulted in a better fit (P 87.5%, either red or black), which calved in the period 2012–2016 in 233 herds, were included. The same dataset was used as in Doekes et al. [8]. Genotype and phenotype data were provided by the Dutch-Flemish cattle improvement co-operative (CRV; Arnhem, the Netherlands). Cows were genotyped with the Illumina BovineSNP50 BeadChip (v1 and v2) or CRV custommade 60 k Illumina panel (v1 and v2). Genotypes were
Doekes et al. Genet Sel Evol
(2020) 52:64
imputed to approximately 76 k, following Druet et al. [18]. The 75,538 SNPs used by Doekes et al. [8] were remapped to the ARS-UCD1.2 assembly, using the NAGRP Data Repository [19] and the NCBI Genome Remapping Service [20]. The final dataset comprised 75,377 successfully remapped SNPs. The distribution of the allelic frequencies of these SNPs was approximately uniform [see Additional file 1: Figure S1]. Phenotypic data included yield, fertility and udder health traits. For yield, the 305-day milk yield (MY; in kg), 305-day fat yield (FY; in kg) and 305-day protein yield (PY; in kg) were included. For fertility, the calving interval (CI; in days), interval calving to first insemination (ICF; in days), interval first to last insemination (IFL; in days) and conception rate (CR; in %) were included. For udder health, the mean somatic cell scores for day 5 through to 150 (SCS150; in units) and
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