Knowledge on runs of homozygosity (ROH) and linkage disequilibrium (LD) has contributed to the application of studies with genomic information and to understand population structure, which improve the animal breeding practices. However, due to historical and structural differences between populations, studies have reported that even in short distances, Bos taurus indicus showed lower LD compared to Bos taurus taurus and crossbreds. These findings suggest the use of higher density SNP panels improves the performance of genomic approaches for this subspecies. Studies of imputation are used to fill in the gaps left by unknown markers to reduce costs in genomic selection and they are applied to obtain genotypes for ungenotyped animals. Imputation is also an important tool to combine data from different SNP panels which allows to increase the density of SNPs with high LD for Bos taurus indicus. The combination of different high density arrays may improve the genome coverage when compared to the use of each array independently. Therefore, the present study aims to identify runs of homozygosity (ROH), evaluate imputation using high density arrays (Illumina and Affymetrix) and customized array in Nelore beef cattle; estimate linkage disequilibrium (LD) and haplotype blocks conformation of high density arrays both individuality and after imputation.
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