Association analysis for young stock survival index with imputed whole-genome sequence variants in Nordic Holstein cattle

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Association analysis for young stock survival index with imputed whole-genome sequence variants in Nordic Holstein cattle. / Wu, Xiaoping; Guldbrandtsen, Bernt; Nielsen, Ulrik Sander; Lund, Mogens Sandø; Sahana, Goutam.

In: Journal of Dairy Science, Vol. 100, No. 8, 2017, p. 6356-6370.

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Wu, Xiaoping ; Guldbrandtsen, Bernt ; Nielsen, Ulrik Sander ; Lund, Mogens Sandø ; Sahana, Goutam. / Association analysis for young stock survival index with imputed whole-genome sequence variants in Nordic Holstein cattle. In: Journal of Dairy Science. 2017 ; Vol. 100, No. 8. pp. 6356-6370.

Bibtex

@article{b6d66fbf79264e1f9536e8cd1ea9712f,
title = "Association analysis for young stock survival index with imputed whole-genome sequence variants in Nordic Holstein cattle",
abstract = "Identification of the genetic variants associated with calf survival in dairy cattle will aid in the elimination of harmful mutations from the cattle population and the reduction of calf and young stock mortality rates. We used de-regressed estimated breeding values for the young stock survival (YSS) index as response variables in a genome-wide association study with imputed whole-genome sequence variants. A total of 4,610 bulls with estimated breeding values were genotyped with the Illumina BovineSNP50 (Illumina, San Diego, CA) single nucleotide polymorphism (SNP) genotyping array. Genotypes were imputed to whole-genome sequence variants. After quality control, 15,419,550 SNP on 29 Bos taurus autosomes (BTA) were used for association analysis. A modified mixed-model association analysis was used for a genome scan, followed by a linear mixed-model analysis for selected genetic variants. We identified 498 SNP on BTA5 and BTA18 that were associated with the YSS index in Nordic Holstein. The SNP rs440345507 (Chr5:94721790) on BTA5 was the putative causal mutation affecting YSS. Two haplotype-based models were used to identify haplotypes with the largest detrimental effects on YSS index. For each association signal, 1 haplotype region with harmful effects and the lead associated SNP were identified. Detected haplotypes on BTA5 and BTA18 explained 1.16 and 1.20%, respectively, of genetic variance for the YSS index. We examined whether YSS quantitative trait loci (QTL) on BTA5 and BTA18 were associated with stillbirth. YSS QTL on BTA18 overlapped a QTL region for stillbirth, but most likely 2 different causal variants were responsible for these 2 QTL. Four component traits of the YSS index, defined by sex and age, were analyzed separately by the modified mixed-model approach. The same genomic regions were associated with both bull and heifer calf mortality. Several genes (EPS8, LOC100138951, and KLK family genes) contained a lead associated SNP or were included in haplotypes with large detrimental effects on YSS in Nordic Holstein cattle.",
keywords = "Journal Article, M{\ae}lkeafgiftsfonden, GUDP",
author = "Xiaoping Wu and Bernt Guldbrandtsen and Nielsen, {Ulrik Sander} and Lund, {Mogens Sand{\o}} and Goutam Sahana",
note = "Copyright {\textcopyright} 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.",
year = "2017",
doi = "10.3168/jds.2017-12688",
language = "English",
volume = "100",
pages = "6356--6370",
journal = "Journal of Dairy Science",
issn = "0022-0302",
publisher = "Elsevier Inc.",
number = "8",

}

RIS

TY - JOUR

T1 - Association analysis for young stock survival index with imputed whole-genome sequence variants in Nordic Holstein cattle

AU - Wu, Xiaoping

AU - Guldbrandtsen, Bernt

AU - Nielsen, Ulrik Sander

AU - Lund, Mogens Sandø

AU - Sahana, Goutam

N1 - Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

PY - 2017

Y1 - 2017

N2 - Identification of the genetic variants associated with calf survival in dairy cattle will aid in the elimination of harmful mutations from the cattle population and the reduction of calf and young stock mortality rates. We used de-regressed estimated breeding values for the young stock survival (YSS) index as response variables in a genome-wide association study with imputed whole-genome sequence variants. A total of 4,610 bulls with estimated breeding values were genotyped with the Illumina BovineSNP50 (Illumina, San Diego, CA) single nucleotide polymorphism (SNP) genotyping array. Genotypes were imputed to whole-genome sequence variants. After quality control, 15,419,550 SNP on 29 Bos taurus autosomes (BTA) were used for association analysis. A modified mixed-model association analysis was used for a genome scan, followed by a linear mixed-model analysis for selected genetic variants. We identified 498 SNP on BTA5 and BTA18 that were associated with the YSS index in Nordic Holstein. The SNP rs440345507 (Chr5:94721790) on BTA5 was the putative causal mutation affecting YSS. Two haplotype-based models were used to identify haplotypes with the largest detrimental effects on YSS index. For each association signal, 1 haplotype region with harmful effects and the lead associated SNP were identified. Detected haplotypes on BTA5 and BTA18 explained 1.16 and 1.20%, respectively, of genetic variance for the YSS index. We examined whether YSS quantitative trait loci (QTL) on BTA5 and BTA18 were associated with stillbirth. YSS QTL on BTA18 overlapped a QTL region for stillbirth, but most likely 2 different causal variants were responsible for these 2 QTL. Four component traits of the YSS index, defined by sex and age, were analyzed separately by the modified mixed-model approach. The same genomic regions were associated with both bull and heifer calf mortality. Several genes (EPS8, LOC100138951, and KLK family genes) contained a lead associated SNP or were included in haplotypes with large detrimental effects on YSS in Nordic Holstein cattle.

AB - Identification of the genetic variants associated with calf survival in dairy cattle will aid in the elimination of harmful mutations from the cattle population and the reduction of calf and young stock mortality rates. We used de-regressed estimated breeding values for the young stock survival (YSS) index as response variables in a genome-wide association study with imputed whole-genome sequence variants. A total of 4,610 bulls with estimated breeding values were genotyped with the Illumina BovineSNP50 (Illumina, San Diego, CA) single nucleotide polymorphism (SNP) genotyping array. Genotypes were imputed to whole-genome sequence variants. After quality control, 15,419,550 SNP on 29 Bos taurus autosomes (BTA) were used for association analysis. A modified mixed-model association analysis was used for a genome scan, followed by a linear mixed-model analysis for selected genetic variants. We identified 498 SNP on BTA5 and BTA18 that were associated with the YSS index in Nordic Holstein. The SNP rs440345507 (Chr5:94721790) on BTA5 was the putative causal mutation affecting YSS. Two haplotype-based models were used to identify haplotypes with the largest detrimental effects on YSS index. For each association signal, 1 haplotype region with harmful effects and the lead associated SNP were identified. Detected haplotypes on BTA5 and BTA18 explained 1.16 and 1.20%, respectively, of genetic variance for the YSS index. We examined whether YSS quantitative trait loci (QTL) on BTA5 and BTA18 were associated with stillbirth. YSS QTL on BTA18 overlapped a QTL region for stillbirth, but most likely 2 different causal variants were responsible for these 2 QTL. Four component traits of the YSS index, defined by sex and age, were analyzed separately by the modified mixed-model approach. The same genomic regions were associated with both bull and heifer calf mortality. Several genes (EPS8, LOC100138951, and KLK family genes) contained a lead associated SNP or were included in haplotypes with large detrimental effects on YSS in Nordic Holstein cattle.

KW - Journal Article

KW - Mælkeafgiftsfonden

KW - GUDP

U2 - 10.3168/jds.2017-12688

DO - 10.3168/jds.2017-12688

M3 - Journal article

C2 - 28551195

VL - 100

SP - 6356

EP - 6370

JO - Journal of Dairy Science

JF - Journal of Dairy Science

SN - 0022-0302

IS - 8

ER -