Dataset Information

Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle.

ABSTRACT:

Background

Parasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance.

Results and conclusion

To quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the approximately 10% most and least infected daughters within each family (selective genotyping). Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position.

SUBMITTER: Coppieters W

PROVIDER: S-EPMC2657155 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

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Publications

Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle.

Coppieters Wouter W Mes Ted H M TH Druet Tom T Farnir Frédéric F Tamma Nico N Schrooten Chris C Cornelissen Albert W C A AW Georges Michel M Ploeger Harm W HW

BMC genomics 20090302

<h4>Background</h4>Parasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance.<h4>Results and conclusion</h4>To quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch ...[more]

PMID: 19254385

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Project description:BackgroundInbreeding 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).MethodsGenotype (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.ResultsGenome-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 < 0.05) than a model with only additive effects. After correcting for the effect of genome-wide homozygosity, dominance and ROH variance explained less than 1% of the phenotypic variance for all traits. Furthermore, dominance and ROH effects were distributed evenly along the genome. The most notable region with a favourable dominance effect for yield traits was on chromosome 5, but overall few regions with large favourable dominance effects and significant dominance associations were detected. No significant ROH-associations were found.ConclusionsInbreeding depression was distributed quite equally along the genome and was well captured by genome-wide homozygosity. These findings suggest that, based on 75 k SNP data, there is little benefit of accounting for region-specific inbreeding depression in selection schemes.

Project description:BACKGROUND:Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Recent inbreeding is expected to be more harmful than ancient inbreeding, because selection decreases the frequency of deleterious alleles over time. Selection efficiency is increased by inbreeding, a process called purging. Our objective was to investigate effects of recent and ancient inbreeding on yield, fertility and udder health traits in Dutch Holstein-Friesian cows. METHODS:In total, 38,792 first-parity cows were included. Pedigree inbreeding ([Formula: see text]) was computed and 75 k genotype data were used to compute genomic inbreeding, among others based on regions of homozygosity (ROH) in the genome ([Formula: see text]). RESULTS:Inbreeding depression was observed, e.g. a 1% increase in [Formula: see text] was associated with a 36.3 kg (SE?=?2.4) decrease in 305-day milk yield, a 0.48 day (SE?=?0.15) increase in calving interval and a 0.86 unit (SE?=?0.28) increase in somatic cell score for day 150 through to 400. These effects equalled -?0.45, 0.12 and 0.05% of the trait means, respectively. When [Formula: see text] was split into generation-based components, inbreeding on recent generations was more harmful than inbreeding on more distant generations for yield traits. When [Formula: see text] was split into new and ancestral components, based on whether alleles were identical-by-descent for the first time or not, new inbreeding was more harmful than ancestral inbreeding, especially for yield traits. For example, a 1% increase in new inbreeding was associated with a 2.42 kg (SE?=?0.41) decrease in 305-day fat yield, compared to a 0.03 kg (SE?=?0.71) increase for ancestral inbreeding. There were no clear differences between effects of long ROH (recent inbreeding) and short ROH (ancient inbreeding). CONCLUSIONS:Inbreeding depression was observed for yield, fertility and udder health traits. For yield traits and based on pedigree, inbreeding on recent generations was more harmful than inbreeding on distant generations and there was evidence of purging. Across all traits, long and short ROH contributed to inbreeding depression. In future work, inbreeding depression and purging should be assessed in more detail at the genomic level, using higher density information and genomic time series.

Dataset Information

Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle.

Background

Results and conclusion

Publications

Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle.

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