Design Markers | Process BeadChip | Analyze Data

BovineSNP50 v3 BeadChip
Featuring 53,218 evenly spaced and strategically placed SNPs across the bovine genome.
Highlights• Excellent call rates and accuracy> 99% average call rates and 99.9% reproducibility• Comprehensive and uniform coverage
Evenly distributed polymorphic SNPs with a median spacingof 37.4 kb• Simple workflow
PCR- and ligation-free protocol• High-throughput format
Up to 24 samples can be interrogated in parallel

Introduction
In collaboration with the United States Department of Agriculture(USDA) Agricultural Research Service (ARS), the University ofMissouri, and the University of Alberta, Illumina has developed thethird generation of the BovineSNP50 v3 BeadChip (Figure 1). This
high-density, genome-wide genotyping array (Table 1) features
53,218 informative single nucleotide polymorphism (SNP) probes thatuniformly span the entire bovine genome to enable interrogation ofgenetic variation in cattle. The BeadChip empowers applications suchas genome-wide–enabled selection, identification of quantitative trait
loci, evaluation of genetic merit of individuals, and comparative genetic
studies with imputation power in beef and dairy cattle.
Using the iScan System, integrated analysis software, and theInfinium high-throughput screening (HTS) assay, this 24-sample
BeadChip provides exceptionally high call rates, allows for flexible
content deployment, and enables the detection and measurementof copy number variation. In addition, PCR-free, single-tube sample
preparation3,4 significantly reduces labor and potential samplehandling errors.
™

BovineSNP50 v3 BeadChip content
High-value content was derived from publicly available sources
such as the Bos taurus (bovine) reference genome,1 and the Bovine
Genome Consortia.2 Illumina scientists and collaborators developed
an informative and high-density SNP genotyping microarray that could
be used to investigate genetic variation in any cattle breed. More than
12,000 probes were designed to target validated common SNPs (MAF≥ 0.05) described by the Bovine HapMap Consortium. BeadChip
developers also mined publicly available resources for commonSNPs including Btau and whole-genome shotgun reads assembledby researchers at the Baylor College of Medicine5. Additional content
sources include parentage markers identified by researchers fromthe US Meat Animal Research Center and Clay Center.6 Content also
includes SNPs identified by researchers at the USDA ARS throughthe comparison of Holstein bacterial artificial chromosome (BAC)
sequence data7 to the bovine genome assembly (Table 2).

For Research Use Only. Not for use in diagnostic procedures.

Figure 1: BovineSNP50 v3 BeadChip—The BovineSNP50 v3 BeadChip
features 53,218 evenly spaced SNPs across the entire bovine genome.

Table 1: Product informationa
FeatureDescriptionSpecies

Bos taurus (bovine)

Total number of markers

53,218Capacity for custom bead types

600,000

Number of samples per BeadChip

24DNA input requirement

200 ng genomic DNA

Assay chemistry

Infinium HTS

Instrument supportiScan System

Maximum iScan System sample
throughputa~5760 samples/week

Scan time per sample

30 minutes

a. Approximate values, scan times, and maximum throughput may vary depending onlaboratory and system configurations.

More than 24,000 SNP probes featured on the BovineSNP50
BeadChip target novel SNP loci discovered by sequencing threepooled populations of economically important beef and dairy cattle.
Illumina scientists and collaborators discovered more than 62,000
putative SNPs by deeply sequencing approximately 2% of the Bos
taurus taurus genome8. More than 23,800 SNPs derived from thisnovel data source were chosen based on their spacing, expectedminor allele frequency (MAF, and Infinium HTS Assay performance.
In addition, BeadChip developers selected loci that target the largest
unmapped contigs to ensure comprehensive coverage. All 53,218
SNP probes on the BovineSNP50 v3 BeadChip have been validated in
19 common beef and dairy breeds (Table 3).
The BeadChip targets evenly distributed SNPs that are polymorphic
across the breeds tested, provides an average probe spacing of 50.6kb and a median spacing of 37.4 kb, and presents an average MAF of
0.25 across all loci. Current research on linkage disequilibrium (LD) in

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Design Markers | Process BeadChip | Analyze Data

multiple breeds of cattle suggests haplotype blocks of approximately
70 kb on average.9 This indicates that the resolution offered by theBovineSNP50 v3 BeadChip is well within that of LD in cattle. Morethan 53,000 SNP probes on the BovineSNP50 v3 BeadChip map to
UMD 3.0, the most current bovine reference genome assembly.
Table 2: BovineSNP50 BeadChip content sources
BovineSNP50
v1 Probes

BovineSNP50
v2 Probes

BovineSNP50
v3 Probes

Novel SNPs derived
from sequencing
common cattle breeds
using the Illumina
GenomeAnalyzer

23,84024,181

22,299Bovine HapMap Data
Set

12,29812,342

11,607

Btau Assembly SNPs

9361

9404

9086

Whole-Genome Shotgun
Readsa

5808

6038

5485

Holstein BAC Sequence
Data

1409

Source1411

1238

Parentageb116

120200

Otherc

1169

1113

3384

Total

54,001

54,60953,218a. Reads derived from 6 cows/breeds (Norwegian Red, Holstein, Brahman, Angus, Jersey,and Limousin) compared against Btau2.0.
b. Highly curated parentage markers that include 30 duplicates.
c. Includes common SNPs validated by the Institute for Food and Agricultural Sciences
Alberta and INRA and the French International Institute of Agriculture.

High-quality data
The 53,218 SNP probes on the BovineSNP50 v3 BeadChip weresubjected to rigorous functional testing to ensure strong performanceusing the Infinium HTS assay. Whole-genome association studies
are successful, in part, due to high call rates and accurately called
genotypes. Because complex traits often have relatively small geneeffects, potential associations may be missed if the assayed SNP inlinkage disequilibrium (LD) with the SNP of interest has a low call rate
or incorrect genotype call. Illumina ensures that every BovineSNP50 v3
BeadChip offers > 99% call rate (Table 3).
Internal validation of content on the BovineSNP50 v3 BeadChip
using samples provided by the Bovine HapMap Consortium showed
outstanding results (Table 4). Product developers identified andretained 4290 loci that appear to have an adjacent or underlying
deletion among the breeds sampled. These loci yield lower call rates
when compared to the other loci on the panel. However, they wereretained because they may provide biologically relevant information for
traits of interest and for future improvements in the genome build.
The performance and content validation results clearly show thereliability and outstanding data quality the BovineSNP50 v3 BeadChip
delivers. With this BeadChip, researchers can predict the genetic
merit for phenotypes of interest and investigate the genetic basis ofvariation among a multitude of cattle breed types. The BovineSNP50
v3 BeadChip demonstrates the commitment by Illumina to provide
innovative tools for research and production needs to support thelivestock industry.

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Table 3: BovineSNP50 v3 BeadChip performance
Productspecification

Parameter

Results

Average Call Ratea

99.7%

> 99%

Reproducibilityb

100%> 99.9%Mendelian inconsistencies

0.06%< 0.1%

a. Based on 274 individuals from 17 major cattle breeds, 31 trios, and 1 replicate.
b. Based on 4 Holstein trios.

Table 4: BovineSNP50 v3 BeadChip content validation
BreedSamples

Polymorphic
locia

Mean
MAF

Median
MAFbAngus

22

41,2090.22

0.23

Beefmaster

24

43,741

0.23

0.23

Bos indicus Gir

17

25,3200.11

0.03

Bos indicus Nelore

522,4220.1

0Brahman

20

33,0380.13

0.08

Charolais

14

42,6850.23

0.21

Guernsey21

37,3130.2

0.19

Hereford

20

43,9020.23

0.23

Holstein

22

41,9130.23

0.23

Jersey936,683

0.18

0.17

Limousin

1042,732

0.21

0.2

N’Dama629,0320.140.08

Piedmontese

21

42,652

0.23

0.24

Red Angus

10

43,0280.22

0.2

Romagnola

638,5210.2

0.17

Santa Gertrudis

742,675

0.21

0.21

Sheko

936,582

0.17

0.17

Overall274

47,9190.26

0.26

a. Minor allele frequency (MAF) > 0.05
b. Across all 53,218 lociSolutions for genotyping
An optional Laboratory Information Management System (LIMS) androbotic automation are available to track samples accurately andefficiently throughout the workflow. Researchers can genotype theirown samples using the Illumina GenomeStudio DNA analysis software
or FastTrack Genotyping Service.

Summary
Developed in collaboration with leading bovine researchers, theBovineSNP50 v3 BeadChip features more than 53,000 evenly spaced
SNP probes that span the bovine genome. This 24-sample BeadChip
presents a high-throughput, cost-effective solution for whole-genome
studies in beef and dairy cattle.

For Research Use Only. Not for use in diagnostic procedures.

Design Markers | Process BeadChip | Analyze Data

Ordering information
BovineSNP50-24 v3 BeadChip Kita

Description

Catalog no.

48 samples

Each package contains 2 BeadChips, along with reagents for amplifying, fragmenting,hybridizing, labeling, and detecting 48 DNA samples

20000766

288 samples

Each package contains 12 BeadChips, along with reagents for amplifying, fragmenting,hybridizing, labeling, and detecting 288 DNA samples

20000767

1152 samples

Each package contains 48 BeadChips, along with reagents for amplifying, fragmenting,hybridizing, labeling, and detecting 1152 DNA samples

20000768

Description

Catalog no.

BovineSNP50-24+ v3 BeadChip Kitb48 samples

Each package contains 2 BeadChips, and allows researchers to include up to 600,000
additional custom probes per sample for targeted studies

20000769

288 samples

Each package contains 12 BeadChips, and allows researchers to include up to 600,000
additional custom probes per sample for targeted studies

20000830

1152 samples

Each package contains 48 BeadChips, and allows researchers to include up to 600,000
additional custom probes per sample for targeted studies

20000831

a. Each BeadChip can process 24 samples and analyze ~53,000 loci.
b. Enabled for custom content.

Learn more
Learn more about the BovineSNP50-24 v3.0 BeadChip at www.
illumina.com/products/by-type/microarray-kits/bovine-snp50.html

References
1.
2.
3.

4.

5.
6.

7.
8.

9.

Ensembl Genome Browser. uswest.ensembl.org/Bos_taurus/Info/Index.
Accessed June 2, 2020.
The Bovine Genome Consortia. bovinegenome.elsiklab.missouri.edu/
bovine_genome_consortium. Accessed June 2, 2020.
Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS (2005)
A genome-wide scalable SNP genotyping assay using microarray
technology. Genet 37(5): 549–554.
Steemers FJ, Weihua Chang W, Lee G, Barker DL,Shen R, et al. (2006)
Whole-genome genotyping with the single-base extension assay.
Nat Methods 3(1): 31–33.
ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/snp/Btau20070913/READMEHeaton MP, Keen JE, Clawson ML, Harhay GP, Bauer N, et al. (2005)
Use of bovine single nucleotide polymorphism markers to verify sample
tracking in beef processing. J Am Vet Med Assoc 226(8): 1311–1314.
Matukumalli LK ,Taylor JF, and Van Tassell CP. Personal communication.
Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel, RD,et al. (2008) Simultaneous SNP discovery and allele frequency estimation by
high-throughput sequencing of reduced representation libraries.
Nat Meth (accepted).
Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JAL, et al. (2007)
A Primary Assembly of a Bovine Haplotype Block Map Basedon a 15,036-Single-Nucleotide Polymorphism Panel Genotyped in
Holstein–Friesian Cattle. Genetics 176(2): 763–772.

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