50,000 SNPs

GeneSeek ® Genomic Profiler™ Bovine 50K

GGPBovine 50K

• Evenly spaced and highly polymorphic SNPs with a mean gap of 59 kb

• Strategic, higher density marker placement on the chromosome that increases imputation accuracy

• Imputation accuracy greater than 99% in most well-characterized breeds

• Call rate success averages above 99%

• Includes a large percentage of SNP overlap with other commercially available arrays including the original Illumina Bovine SNP50k

Powered by Illumina

One Sample, One Simple Comprehensive Solution

www.neogen.com • 402-435-0665 • geneseekinfo@neogen.com

Utilize the power of the next generation of bovine genotyping technologies—The NEW GeneSeek Genomic Profiler (GGP) Bovine 50K lassos the knowledge of industry leading scientists who have designed and processed more animal genotyping arrays than any other organization. The new generation GGP Bovine 50K leverages Neogen GeneSeek’s leading SNP selection processes to precisely choose the best 50,000 SNPs. This delivers more accurate evaluation of genetic merit, genome wide selection, comparative genetic studies, and higher density imputation.

These advantages, plus a host of causative mutations, make the GGP Bovine 50K, an instant leader in its class.

The GGP Bovine 50K contains all the content from popular lower density commercial arrays. Additionally, it has validated and retained the most informative SNPs from the original Illumina Bovine SNP50 and Illumina Bovine HD Bead Chips.

Utilize the best content from the most commonly used commercial genotyping arrays, and for a low affordable price, PLUS comprehensive parentage, disease and trait relevant SNPs.

After 10 years and millions of animals genotyped, the world is ready for the ultimate in 50K SNP genotyping product. Tap in to the power of GeneSeek for the new generation in commercial bovine SNP genotyping products.

• Includes approximately 16,000 of the most informative SNPs from the original Illumina Bovine SNP50k

• 39,000 SNP overlap with the GGP Bovine 150K and greater than 12,000 SNPs from the previous version of the GGP-LD array are included

• More than 44,000 SNPs overlap with the Illumina Bovine HD array

SNPs were selected for maximum informativeness in the following cattle breeds:

Angus, Red Angus, Beefmaster, Brangus, Charolais, Gelbvieh, Hereford, Limousin, Simmental, Holstein, Jersey, and Brown Swiss.

Illumina BovineLD SNP Spacing and Chromosome Coverage GGP Bovine 50K SNP Spacing and Chromosome Coverage

The average SNP spacing on the GGP Bovine 50K is approximately 59 kb (the Illumina 7K chip has average spacing at 383 kb for comparison), with a higher concentration on the telomeric regions of the chromosome

The following table details the SNP overlap among several heavily utilized bovine genotyping arrays:

Illumina LD GGP Bovine LD v4 Illumina 50K GGP Bovine 50K GGP Bovine150K Illumina HD

Illumina LD 7,931 7,917 6,900 7,783 7,392 7,757

GGP Bovine LD v4 7,917 30,125 10,256 12,900 28,670 28,909

Illumina 50K 6,900 10,290 54,069 15,779 41,857 49,345

GGP Bovine 50K 7,783 12,900 15,779 48,268 38,665 44,733

GGP Bovine150K 7,392 28,670 41,857 38,665 140,668 134,686

Illumina HD 7,757 28,909 49,435 44,733 134,686 777,962

www.neogen.com • 402-435-0665 • geneseekinfo@neogen.com

GeneSeek Genomic Profiler (GGP) Bovine 50K Minor Allele Frequency (MAF) Summary

Breed AVG MAF

Percentage of SNPs

0<=MAF<0.2 0.2<=MAF<0.4 0.4<=MAF<0.5 MAF=0.5

Angus 0.3399 16.32% 42.25% 41.41% 0.03%

Gelbvieh 0.3598 9.58% 46.27% 44.02% 0.12%

Holstein 0.3308 18.88% 41.44% 39.58% 0.10%

Jersey 0.2826 30.95% 40.28% 27.87% 0.89%

Limousin 0.3472 13.02% 45.30% 38.01% 3.67%

RedAngus 0.3373 16.04% 44.15% 39.81% 0.00%

Simmental 0.3539 11.52% 45.37% 43.09% 0.03%

0.26 0.26 0.260.28

0.26 0.26

0.22

0.270.26

0.270.26

0.340.33 0.33

0.36

0.30

0.33

0.29

0.350.34

0.360.33

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0.45

0.50

Angus BeefMaster Brangus Gelbvieh Hereford Holstein Jersey Limousin RedAngus Simmental Weighted AVG

ILMN SNP50 GGP Bovine 50K

Comparing Minor Allele Frequencies (MAFs) between GGP Bovine 50K and Illumina Bovine SNP50

95.00%

96.00%

97.00%

98.00%

99.00%

100.00%

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

Accu

racy

Chromosome

GGP-Bovine 50K average imputation accuracy

Additional Key Features of the GGP-LD BeadChip:A majority of the SNPs were specifically chosen for high minor allele frequency values and uniform genome coverage for a majority of the Bos taurus and several of the Bos indicus breeds.

All commonly utilized USDA and ISAG parentage SNPs.

Hundreds of SNPs to enable conversion of ISAG microsatellite parentage data.

Breed identification (Holstein, Jersey, Brown Swiss)

This chip, similar to the previous GGP versions, also includes several additional SNPs that have been shown to have an impact on disease susceptibility and performance (Please note that some of the content is protected by intellectual property rights, these and many other assays may have some additional cost for data delivery due to data interpretation and translation):

©2016 Neogen Corporation. Neogen and GeneSeek are registered trademarks and Genomic Profiler is a trademark of Neogen Corporation, Lansing, Mich. AG311-0117

Neogen GeneSeek Operations • 4131 N. 48th Street, Lincoln, NE 68504877-443-6489 • www.neogen.com/genomics • genomics.neogen.com

Assay Name Assay Name

Albinism Glycogen storage disease V

Alpha Casein High Altitude (EPAS1-1816)

Angus Dwarfism Holstein bull-dog dwarfism

Ayrshire fertiltiy Haplotype 1 Holstein fertiltiy markers

Beta casein (A/B, A2, A3, C, E, F, H, I, K, L ) Horn Poll (Celtic mutation and Frisian Haplotypes)

Beta lactoglobulin Hypotrichosis (KRT71, PMEL)

Beta Mannosidosis Ichthyosis Fetalis

Black Red Coat Color Idiopathic epilepsy

Bovine Arachnomelia Syndrome Japanese black fertility SNP

Bovine Brachyspina Syndrome (BY) Jersey fertility haplotype 1 (SNP)

Bovine Citrullinemia Kappa casein (319, 355)

Bovine Leukocyte Adhesion Deficiency (BLAD) Kappa Casein C (KCN 12951)

Bovine Spinal Dysmyelination (SDM) Left Displaced Abomasum (90, 189)

Bovine Spinal Muscular Atrophy (SMA) Leptin

Brahman Dwarfism Mannosidosis (alpha & beta)

Brown Swiss Fertility Haplotype (SNP) 2 Montbeliarde Haplotype 1, 2

Calpain_316 Maple Syrup Urine Disease

Calpain_4751 Mitofusin2 (MFN2) defect

Calpain_530 Mulefoot (2719, 3595, 241, Angus)

Chediak Higashi Syndrome Myostatin (E226X,E291X,Q204X,S105,C313Y,D182N, F94L, nt419, nt821)

Cholesterol Deficiency Neuropathic Hydrocephalus

Chondrodysplastic Dwarfism (BD2, EVC2) Osteopetrosis

Complex Vertebral Malformation (CVM) PLAG1

Congenital Muscular Dystonia 1 Pompes E13, E18, E7

Congenital Muscular Dystonia 2 Protoporphyria

Congenital myasthenic syndrome Psudomyotonia (PMT)

Crooked tail syndrome Pulmonary Hypoplasia with Anasacra DEX

Developmental Duplication Pulmonary Hypoplasia with Anasacra SH

Dexter Dun Red Angus 346 coat color

DGAT Red Charlie

Dilated-Cardiomyopathy Renal Tubular Dysplesia (CL16)

Dominant Red Color Silver Dilutor

Deficiency of Uridine Monophosphate Synthase (DUMPS) Slick Coat

Epidermolysis bullosa (EB) Stearoyl-CoA desauratse

Erythrocyte Membrane Protein Band III Deficiency Thrombopathia

Factor 11 (Wagyu and Holstein) Tibial Hemimelia

Factor 13 deficiency Tibial Hemimelia - Outcast

Fish-odor Syndrome or Trimethylamlnurla Waygu IARS

Friesian Haplotype 2, 4 Weaver Haplotype

GH1-Exon5-172 Yellow Fat

Includes variants known to have an impact on the following genes or traits