Data Sheet: Agrigenomics illumina • Comprehensive and Uniform Coverage Evenly distributed polymorphic SNPs with a median < 3 kb gap spacing • Unrivaled Call Rates and Accuracy > 99% average call rates and > 99.9% reproducibility • Simple Workflow • High-Throughput Format Up to 8 samples can be interrogated in parallel The BovineHD BeadChip (Figure 1) is the most comprehensive genome-wide genotyping array, providing superior power to interrogate genetic variation across any breed of beef and dairy cattle. Illumina has developed this product in collaboration with major bovine agricultural thought leaders, including USDA-ARS, UNCEIA-INRA, Pfizer Animal Genetics, and the University of Missouri. Featuring more than 777,000 SNPs that uniformly span the entire bovine genome, the BovineHD BeadChip enables a broad range of applications such as genome-wide selection, identification of quantitative trait loci, evaluation of genetic merit, cross-breed mapping, linkage disequilibrium studies, comparative genetic studies, and breed characterization for evaluating biodiversity. This multi-sample genotyping panel is powered by the Infinium® HD Assay, delivering the industry's highest call rates and reproducibility, along with precise detection and measurement of copy number variation (CNV) (Table 1). The assay's PCR-free single-tube sample preparation significantly reduces labor and potential sample handling errors.1'2 A multi-sample format further reduces experimental variability and overall project cost by allowing researchers to interrogate up to 8 samples in parallel. The combination of proprietary Illumina assay technology, unconstrained locus selection, and high-throughput format presents the most comprehensive solution for whole-genome studies in beef and dairy cattle. Illumina scientists and collaborators strategically selected informative markers across the bovine genome. The BovineHD BeadChip covers SNPs validated in economically important beef and dairy cattle, encompassing temperate and tropically adapted species Bos taurus taurus (Btt), Bos taurus indicus (Bti), and several Bti x Btt breeds. The average minor allele frequency (MAF) across all loci is 0.25 for Btt and 0.17 for Bti. More than 749,000 SNPs were validated across all breeds with a MAF > 0.05 (Table 2, “polymorphic loci”). Over 99% of the markers are mapped to the UMD3 bovine genome assembly,3 which include coverage of autosomal, mitochondrial, and sex-linked (X/Y) SNPs. Uniform genomic coverage, with an average gap size of 3.43 kb and a median gap size of 2.68 kb, provides excellent SNP density to power robust genome-association studies and CNV detection in cattle (Figure 2).4 The BovineHD BeadChip is the most comprehensive tool in the Illumina portfolio of bovine products. More than 93% of SNPs featured on the BovineHD BeadChip target novel SNP loci that were discovered by sequencing > 20 individual breeds of economically important beef and dairy cattle (Table 3). Using Illumina next-generation paired-end sequencing technology, > 90% of the included SNPs were identified from over 180x coverage of the mappable Btt genome. Prioritization for SNP selection included the following parameters: 1) breed-specific expected MAF, 2) Infinium HD design score, 3) unmapped contig coverage, 4) breed weighting, 5) breed-specific spacing, and 6) and position based on region of genome (ie, exon, repetitive, segmental duplication/CNV). The 777,962 SNPs on the BovineHD BeadChip were subjected to rigorous functional testing on multiple breeds to ensure strong performance using the Infinium HD Assay. High call rates and accurate genotype calls are important for successful whole-genome association studies. Because complex traits often have relatively small gene effects, potential associations can be missed if the assayed SNP in linkage disequilibrium with the SNP of interest has a low call rate or incorrect genotype call. Illumina ensures that every BovineHD BeadChip offers > 99% average call rate across common beef and dairy cattle breeds. Figure 1: BovineHD BeadChip—The BovineHD BeadChip features more than 777,000 evenly spaced SNPs across the entire bovine genome.

Data Sheet: Agrigenomics BovineHD BeadChip Probe Spacing (Chromosome 1-29, X) Figure 2: BovineHD BeadChip Probe Spacing—The BovineHD BeadChip provides uniform coverage across the entire UMD3 genome. Table 1 shows the results from internal validation testing of the BovineHD BeadChip content using samples provided by collaborators and the Bovine HapMap Consortium.5 Illumina scientists and collaborators identified and retained 29,968 loci that appear to have an adjacent polymorphism or deletion among the breeds sampled. Although these loci yielded lower call rates when compared to most loci on the...

Data Sheet: Agrigenomics Table 2: BeadChip Content Validation Species Breed Bos taurus taurus Angus Bos taurus taurus Blonde d’Aquitaine Bos taurus taurus Brown Swiss Bos taurus taurus Charolais Bos taurus taurus Guernsey Bos taurus taurus Hereford Bos taurus taurus Holstein Bos taurus taurus Jersey Bos taurus taurus Lagunaire Bos taurus taurus Limousin Bos taurus taurus Montbeliard Bos taurus taurus N’Dama Bos taurus taurus Normande Bos taurus taurus Norwegian Red Bos taurus taurus Piedmontese Bos taurus taurus Red Angus Bos taurus taurus Romagnola Bos taurus taurus Senepol Bos taurus taurus...

Data Sheet: Agrigenomics Novel content derived > 180x coverage of > 20 y 9 Holstein BAC sequence data 1,229 Whole-genome shotgun readsb 5,435 SNPs from Baylor genome build Btau2.0 8,703 Bovine Hapmap data setc 11,723 a. Highly curated parentage markers that include 30 duplicates. b. Reads derived from 6 cows/breeds (Norwegian Red, Holstein, Brahman, Angus, Jersey, and Limousin) compared against Btau2.0. c. Includes common SNPs validated by the Institute for Food and Agricultural Sciences Alberta and INRA, the French International Institute of Agriculture. 1. Gunderson KL, Steemers FJ, Lee G,...