Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians

K.J.E. van Hulzen, G.C.B. Schopen, J.A.M. van Arendonk, M. Nielen, A.P. Koets, C. Schrooten, H.C.M. Heuven

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22 Citations (Scopus)

Abstract

Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.
LanguageEnglish
Pages2740-2748
JournalJournal of Dairy Science
Volume95
Issue number5
DOIs
Publication statusPublished - 2012

Fingerprint

Mycobacterium avium subsp. paratuberculosis
Paratuberculosis
Mycobacterium avium
Genome-Wide Association Study
paratuberculosis
Antibody Formation
Single Nucleotide Polymorphism
Milk
Holstein
milk
antibodies
single nucleotide polymorphism
Breeding
Chromosomes, Human, Pair 4
sires
Mothers
Chromosomes, Human, Pair 15
Chromosomes, Human, Pair 14
breeding value
chromosomes

Keywords

  • single nucleotide polymorphisms
  • estimated breeding values
  • quantitative trait loci
  • genetic-variation
  • johnes-disease
  • linkage disequilibrium
  • short-communication
  • us holsteins
  • infection
  • cattle

Cite this

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title = "Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians",
abstract = "Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70{\%}, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.",
keywords = "single nucleotide polymorphisms, estimated breeding values, quantitative trait loci, genetic-variation, johnes-disease, linkage disequilibrium, short-communication, us holsteins, infection, cattle",
author = "{van Hulzen}, K.J.E. and G.C.B. Schopen and {van Arendonk}, J.A.M. and M. Nielen and A.P. Koets and C. Schrooten and H.C.M. Heuven",
year = "2012",
doi = "10.3168/jds.2011-5005",
language = "English",
volume = "95",
pages = "2740--2748",
journal = "Journal of Dairy Science",
issn = "0022-0302",
publisher = "American Dairy Science Association",
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}

Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians. / van Hulzen, K.J.E.; Schopen, G.C.B.; van Arendonk, J.A.M.; Nielen, M.; Koets, A.P.; Schrooten, C.; Heuven, H.C.M.

In: Journal of Dairy Science, Vol. 95, No. 5, 2012, p. 2740-2748.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians

AU - van Hulzen, K.J.E.

AU - Schopen, G.C.B.

AU - van Arendonk, J.A.M.

AU - Nielen, M.

AU - Koets, A.P.

AU - Schrooten, C.

AU - Heuven, H.C.M.

PY - 2012

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N2 - Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.

AB - Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.

KW - single nucleotide polymorphisms

KW - estimated breeding values

KW - quantitative trait loci

KW - genetic-variation

KW - johnes-disease

KW - linkage disequilibrium

KW - short-communication

KW - us holsteins

KW - infection

KW - cattle

U2 - 10.3168/jds.2011-5005

DO - 10.3168/jds.2011-5005

M3 - Article

VL - 95

SP - 2740

EP - 2748

JO - Journal of Dairy Science

T2 - Journal of Dairy Science

JF - Journal of Dairy Science

SN - 0022-0302

IS - 5

ER -