More than 35,000 SNPs
GeneSeek ® Genomic Profiler™ indicus
The portfolio of GeneSeek Genomic Profiler (GGP) tools provide an accurate evaluation of genetic merit, genome-wide selection, GWAS studies, and excellent imputation accuracy. The GGP portfolio is utilized globally by leading researchers, beef and dairy bull studs, and breeding associations.
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genomics.neogen.com • 402-435-0665 • [email protected]
Utilize the power of the next generation of bovine genotyping technologies — The GGP indicus leverages Neogen’s leading SNP selection process to precisely choose the most informative SNPs for your genomic selection or research goals. These advantages plus a host of causative mutations, make the GGP indicus an instant leader in its class.
• The GGP indicus chip consists of 35,090 SNPs that are optimally selected using the SelectSNP software package that features MOLO optimization (Wu et al., 2016). The chip also includes Bos indicus specific SNPs for parentage testing, and causative assays for genetic diseases.
• The highly optimized 35K SNP panel features:
Average SNP spacing of 77kb across all autosomal chromosomes
19K backbone SNP targets, highly informative according to a weighted MAF
3K highly informative (breed-specific MAF > 0.40) SNPs for Brahman and Nelore, respectively
2K highly informative (breed-specific MAF > 0.40) SNPs for Guzera and Gyr, respectively
3K highly informative (breed-specific MAF > 0.40) SNPs for Droughtmaster, Santa Gertrudis and Tropical Composite, respectively
An additional set of 1000 map-optimal SNPs (weighted MAF > 0)
Imputation accuracy (to the Illumina Bovine HD) averages greater than 97% for all evaluated breeds
Comparing the breed average minor allele frequency (MAF) of the GGP indicus chip and other commonly utilized arrays
Breed GGP indicus GGP Bovine LD GGP Bovine HDi Illumina SNP50 Illumina BovineHDBrahman 0.3603 0.2637 0.3168 0.1385 0.1899
Guzera 0.3291 0.222 0.2746 0.1151 0.1566
Gyr 0.3357 0.2311 0.285 0.1117 0.1595
Nelore 0.3527 0.2401 0.2969 0.1161 0.1638
Droughtmaster 0.3687 0.3062 0.329 0.2121 0.2643
Santa Gertrudis 0.32 0.2781 0.2712 0.2143 0.2467
Tropical Composite 0.3346 0.2958 0.2865 0.2251 0.2629
Other indicus 0.3545 0.2642 0.3186 0.1509 0.2055
Mean 0.3445 0.2626 0.2973 0.1604 0.2061
Data were collected from more than 32,000 genotyped animals and applied optimally for SNP selection. The animal breeds included in this analysis were Nelore, Brahman, Gyr, Guzera, Droughtmaster, Santa Gertrudis, Tropical composite, and those of unknown indicus cross breeds.
SNP selection was based on the following breed weightings of the allele frequencies for each breed (by percentage).
SNP chips Number of common SNPsGeneSeek Genomic Profiler Bovine LD (v4) 8,680
Illumina Bovine SNP50 2,557
GeneSeek Genomic Profiler HDi 12,189
Illumina BovineHD 35,090
Breeds
Number of animals with
BovineHD genotype
Imputation Accuracy
Min Max MeanBrahman 349 96.43% 98.36% 97.43%
Nelore 6,026 98.19% 99.87% 99.08%
Droughtmaster 300 94.59% 97.28% 96.44%
Santa Gertrudis 299 96.85% 98.39% 97.77%
Tropical Composite 199 92.14% 96.53% 94.83%
Brahman
Guzera
Gyr
Nelore
Droughtmaster
Santa Gertrudis
Tropical composite
other indicus
15%
15%
15%35%
5%5%5%
5%
The number of common SNPs between the GGP indicus chip and several commonly utilized commercial SNP chips.
Imputation accuracies from GGP indicus to Bovine HD (777k)
The breed weightings of the allele frequencies for each breed
©2017 Neogen Corporation. Neogen and GeneSeek are registered trademarks and Genomic Profiler is a trademark of Neogen Corporation, Lansing, Mich. All other trademarks are property of their respective companies.
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Please contact Neogen’s GeneSeek Operations for more information
402-435-0665
