Header: Proceedings of the World Congress on Genecs Applied to Livestock Producon Insert your paper number here: Design of a low-density SNP chip for Bos indicus: GGP indicus technical characterization and imputation accuracy to higher density SNP genotypes J.B.S. Ferraz 1 , X. Wu 2,3 , H. Li 2,3 , J. Xu 2,4 , R. Ferretti 2 , B. Simpson 2 , J. Walker 2 , L.R. Silva 2 , J.F. Garcia 5 ,R.G. Tait Jr. 2 , S. Bauck 2 1 Dept of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Rua Duque de Caxias Norte, 225, 13635-970, Pirassununga, SP, Brazil jbferraz@usp.br (corresponding author) 2 Biostatistics and bioinformatics, Neogen GeneSeek, Lincoln, NE 68504,USA 3 Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA 4 Department of Statistics, University of Nebraska, Lincoln, NE 68583, USA 5 Dept. of Animal Production and Health, College of Veterinary Medicine, UNESP, 16050-680, Araçatuba, SP, Brazil Summary The majority of commercial bovine SNP chips were developed based on information from Bos taurus animals, which results in a considerable percentage of the SNP being monomorphic in Bos indicus populations. Although costs of genotyping are decreasing over time, low-cost SNP chips need to be developed for broader use in Bos indicus, a species or subspecies which account for a large proportion of beef production in tropical and subtropical regions, and beef trade around the world. A new low-density (LD) GeneSeek Genomic Profiler SNP chip was developed specifically for Bos indicus (GGP indicus), which consists of 34,000 SNPs optimally selected by a multiple-objective, local-optimization (MOLO) algorithm, plus 1,000 SNPs reserved for those on Y chromosome, “causative” mutations for a variety of economically relevant traits, genetic health conditions, and international society for animal genetics (ISAG) globally recognized parentage markers for those breeds of cattle. SNPs on this new LD Bos indicus SNP chip were selected from a pool of 788,879 SNPs genotyped on 40,092 Zebu cattle (and crossbreds) of more than seven breeds, which included Australian Brahman, Droughtmaster, Guzerath, Gyr, Nellore (including polled Nellore), Santa Gertrudis, and Tropical Composite. Of them, a majority (69.32%) of the reference animals were from the Nellore breed, the most important breed in the Brazilian beef industry. The results showed that the new LD SNP chip was highly informative and the selected SNPs were well positioned on each chromosome. Relative to Illumina BovineHD SNP Chip, weighted minor allele frequency (WMAF) increased from 0.1829 to 0.4293 for the selected 35K SNPs and average locus-wise Shannon Entropy, which measured the average locus-wise information of SNPs, increased from 0.6019 to 0.9674. Average maximum gap by chromosome on the new 35K SNP chip was 89.44% as much as the gap on the existing GeneSeek GGP high-density Bos indicus (HDi) SNP