More than 50,000 SNPs

GeneSeek ® Genomic Profiler Porcine

• Includes approximately 51,000 SNPs with a mean gap of 62 kb

• Higher density marker placement at the telomeric region of the chromosome for increased imputation accuracy

• 33k SNP overlap with PorcineSNP60k

• Imputation accuracy greater than 99%

• Includes disease and performance trait markers

The Next Generation of Porcine Genotyping

Developed in collaboration with corporate and academic scientists, the second generation GeneSeek Genomic Profiler (GGP) for Porcine is built on the foundation of the most globally utilized porcine arrays ever developed. The GGP Porcine array features more than 51,000 SNPs specifically chosen for optimal chromosomal spacing and high minor allele frequency values for use in most commercial breeding lines.

The GGP Porcine array also includes several genetic markers that may directly impact disease and performance traits:

• Porcine Stress Syndrome (HAL)

• Rendement napole (RN)

• Resistance marker to E. coli (F4 ab/ac)

• PRRS tolerance marker (WUR100000125)

• SNPs that have been demonstrated to have an impact on:

Feed Intake

Conversion/Weight Gain

Lean Growth/Fat Content

Meat Quality

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The following table details the SNP overlap among the most heavily utilized porcine genotyping arrays

Chip GGP Porcine v2 ILMN PorcineSNP60 GGP Porcine HD v1

GGP Porcine v2 51,558 33,359 50,626

ILMN PorcineSNP60 33,359 63,480 42,372

GGP Porcine HD v1 50,626 42,372 70,231

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The average SNP spacing within the genome is approximately 62 kb with a higher concentration on the telomeric regions of the chromosome.

Chromosome Locus Count Length (bp)

Spacing (bp)

Mean Distance Max Disance

1 5112 315000000 61637 3731902 3389 163000000 47957 3732443 2995 144000000 48179 4431754 3200 143000000 44833 3110655 2401 112000000 46440 2801936 3544 158000000 44507 2688317 3010 135000000 44772 2612988 3007 148000000 49378 3630099 3245 154000000 47352 28418210 1668 78915339 47311 26512211 1892 87670445 46337 27824612 1343 63582536 47344 28432413 3771 219000000 57972 34947714 3430 154000000 44842 26697515 2986 158000000 52797 44298616 1930 86879315 45015 29985117 1490 69302804 46512 27646118 1342 61201108 45604 25447519 2537 144000000 56861 606416

The GGP Porcine array provides a very robust solution for imputation to higher density arrays such as the GGP Porcine HD (80k) array. The average imputation accuracy is 99.4% across all chromosomes.

The GGP Porcine array has been validated in many economically important pig breeds. In addition to spacing, SNPs were selected for high MAF values.

Chromo %

1 99.9

2 99.92

3 99.97

4 99.96

5 99.95

6 99.97

7 99.92

8 99.88

9 99.88

10 99.97

Chromo %

11 99.95

12 99.97

13 99.92

14 99.92

15 99.98

16 99.9

17 99.97

18 99.94

X 100

AVG 99.935

Breed # Polymorphic SNPs Het rate - Average

Berkshire 46470 0.2854

Chester White 47135 0.3371

Duroc 43195 0.2863

Fengjing 29754 0.191

Guam Feral 33579 0.2409

Guinea Hog 28458 0.2719

Hampshire 43719 0.2747

Hawaiian Feral 47015 0.2857

Hereford 42487 0.291

Landrace 47674 0.3641

Large Black 26929 0.2503

Mangalitsa 23189 0.2259

Meishan 28434 0.1718

Minzhu 46204 0.314

Ossabaw Island 29204 0.2526

Spotted 43565 0.3176

Tamworth 42697 0.3282

Yorkshire 47791 0.3356

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

Please contact Neogen’s GeneSeek laboratory for more information

geneseekinfo@neogen.com

402-435-0665