Design of a Bovine Low-Density SNP Array Optimized for Imputation

被引：144

作者：

Boichard, Didier ^{[1
]}

Chung, Hoyoung ^{[2
,3
]}

Dassonneville, Romain ^{[1
,4
]}

David, Xavier ^{[5
]}

Eggen, Andre ^{[6
]}

Fritz, Sebastien ^{[5
]}

Gietzen, Kimberly J. ^{[6
]}

Hayes, Ben J. ^{[7
,8
,9
]}

Lawley, Cynthia T. ^{[6
]}

Sonstegard, Tad S. ^{[3
]}

Van Tassell, Curtis P. ^{[3
]}

VanRaden, Paul M. ^{[10
]}

Viaud-Martinez, Karine A. ^{[6
]}

Wiggans, George R. ^{[10
]}

机构：

[1] Natl Inst Agr Res INRA, Anim Genet & Integrat Biol UMR1313, Jouy En Josas, France

[2] Natl Inst Anim Sci, Anim Genet Improvement Div, Seonghwan, Cheonan, South Korea

[3] ARS, Bovine Funct Genom Lab, USDA, Beltsville, MD USA

[4] Inst Elevage, Paris, France

[5] Natl Assoc Livestock & Artificial Inseminat Coope, Paris, France

[6] Illumina, San Diego, CA USA

[7] Dept Primary Ind Victoria, Biosci Res Div, Melbourne, Vic, Australia

[8] Dairy Futures Cooperat Res Ctr, Bundoora, Vic, Australia

[9] La Trobe Univ, Bundoora, Vic, Australia

[10] ARS, Anim Improvement Programs Lab, USDA, Beltsville, MD USA

来源：

PLOS ONE | 2012年 / 7卷 / 03期

基金：

美国食品与农业研究所;

关键词：

MISSING GENOTYPES; PREDICTION; SELECTION; MARKERS; PANELS; MODEL;

D O I：

10.1371/journal.pone.0034130

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The Illumina BovineLD BeadChip was designed to support imputation to higher density genotypes in dairy and beef breeds by including single-nucleotide polymorphisms (SNPs) that had a high minor allele frequency as well as uniform spacing across the genome except at the ends of the chromosome where densities were increased. The chip also includes SNPs on the Y chromosome and mitochondrial DNA loci that are useful for determining subspecies classification and certain paternal and maternal breed lineages. The total number of SNPs was 6,909. Accuracy of imputation to Illumina BovineSNP50 genotypes using the BovineLD chip was over 97% for most dairy and beef populations. The BovineLD imputations were about 3 percentage points more accurate than those from the Illumina GoldenGate Bovine3K BeadChip across multiple populations. The improvement was greatest when neither parent was genotyped. The minor allele frequencies were similar across taurine beef and dairy breeds as was the proportion of SNPs that were polymorphic. The new BovineLD chip should facilitate low-cost genomic selection in taurine beef and dairy cattle.

引用

页数：10

共 22 条

[1] Haplotype phasing: existing methods and new developments [J].

Browning, Sharon R. ;

Browning, Brian L. .

NATURE REVIEWS GENETICS, 2011, 12 (10) :703-714

[2] Imputation of Missing Genotypes From Sparse to High Density Using Long-Range Phasing [J].

Daetwyler, Hans D. ;

Wiggans, George R. ;

Hayes, Ben J. ;

Woolliams, John A. ;

Goddard, Mike E. .

GENETICS, 2011, 189 (01) :317-U1028

[3] Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations [J].

Dassonneville, R. ;

Brondum, R. F. ;

Druet, T. ;

Fritz, S. ;

Guillaume, F. ;

Guldbrandtsen, B. ;

Lund, M. S. ;

Ducrocq, V. ;

Su, G. .

JOURNAL OF DAIRY SCIENCE, 2011, 94 (07) :3679-3686

[4]

Dassonneville R, 2012, J DAIRY SCI IN PRESS

[5] Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle [J].

Druet, T. ;

Schrooten, C. ;

de Roos, A. P. W. .

JOURNAL OF DAIRY SCIENCE, 2010, 93 (11) :5443-5454

[6] A Hidden Markov Model Combining Linkage and Linkage Disequilibrium Information for Haplotype Reconstruction and Quantitative Trait Locus Fine Mapping [J].

Druet, Tom ;

Georges, Michel .

GENETICS, 2010, 184 (03) :789-U237

[7] Dual Origins of Dairy Cattle Farming - Evidence from a Comprehensive Survey of European Y-Chromosomal Variation [J].

Edwards, Ceiridwen J. ;

Ginja, Catarina ;

Kantanen, Juha ;

Perez-Pardal, Lucia ;

Tresset, Anne ;

Stock, Frauke ;

Gama, Luis T. ;

Penedo, M. Cecilia T. ;

Bradley, Daniel G. ;

Lenstra, Johannes A. ;

Nijman, Isaac J. .

PLOS ONE, 2011, 6 (01)

[8] Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds [J].

Gibbs, Richard A. ;

Taylor, Jeremy F. ;

Van Tassell, Curtis P. ;

Barendse, William ;

Eversoie, Kallye A. ;

Gill, Clare A. ;

Green, Ronnie D. ;

Hamernik, Debora L. ;

Kappes, Steven M. ;

Lien, Sigbjorn ;

Matukumalli, Lakshmi K. ;

McEwan, John C. ;

Nazareth, Lynne V. ;

Schnabel, Robert D. ;

Taylor, Jeremy F. ;

Weinstock, George M. ;

Wheeler, David A. ;

Ajmone-Marsan, Paolo ;

Barendse, William ;

Boettcher, Paul J. ;

Caetano, Alexandre R. ;

Garcia, Jose Fernando ;

Hanotte, Olivier ;

Mariani, Paola ;

Skow, Loren C. ;

Williams, John L. ;

Caetano, Alexandre R. ;

Diallo, Boubacar ;

Green, Ronnie D. ;

Hailemariam, Lemecha ;

Hanotte, Olivier ;

Martinez, Mario L. ;

Morris, Chris A. ;

Silva, Luiz O. C. ;

Spelman, Richard J. ;

Taylor, Jeremy F. ;

Mulatu, Woudyalew ;

Zhao, Keyan ;

Abbey, Colette A. ;

Agaba, Morris ;

Araujo, Flabio R. ;

Bunch, Rowan J. ;

Burton, James ;

Gill, Clare A. ;

Gorni, Chiara ;

Olivier, Hanotte ;

Harrison, Blair E. ;

Luff, Bill ;

Machado, Marco A. ;

Mariani, Paola .

SCIENCE, 2009, 324 (5926) :528-532

[9]

Heffner EL, 2011, PLANT GENOME-US, V4, P65, DOI [10.3835/plantgenome2010.12.0029, 10.3835/plantgenome.2010.12.0029]

[10] A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes [J].

Hickey, John M. ;

Kinghorn, Brian P. ;

Tier, Bruce ;

Wilson, James F. ;

Dunstan, Neil ;

van der Werf, Julius H. J. .

GENETICS SELECTION EVOLUTION, 2011, 43

← 1 2 3 →