Estimation of Breeding Values Using Different Densities of Snp to Inform Kinship in Broiler Chickens

Abstract Background: Traditionally, breeding values are estimated based on phenotypic and pedigree information using the numerator relationship (A) matrix. With the availability of genomic information, genome-wide markers can be included in the estimation of breeding values through genomic kinship. However, the density of genomic information used can impact the cost of implementation. The aim of this study was to compare the rank, accuracy, and bias of estimated breeding values (EBV) for organs [heart (HRT), liver (LIV), gizzard (GIZ), lungs (LUN)] and carcass [breast (BRST), drumstick (DRM) and thigh (THG)] weight traits in a broiler population using pedigree-based BLUP (PBLUP) and single-step genomic BLUP (ssGBLUP) methods using various densities of SNP and variants imputed from whole-genome sequence (WGS). Results: For both PBLUP and ssGBLUP, heritability estimates varied from low (LUN) to high (HRT, LIV, GIZ, BRST, DRM and THG). Regression coefficients values of EBV on genomic estimated breeding values (GEBV) were similar for both the high density (HD) and WGS sets of SNPs, ranging from 0.87 to 0.99 across scenarios. Conclusion: Results show no benefit of using WGS data compared to HD array data using an unweighted ssGBLUP. Our results suggest that 10% of the content of the HD array can yield unbiased and accurate EBV.