Weighting genomic and genealogical information for genetic parameter estimation and breeding value prediction in tropical beef cattle

A combined matrix that exploits genealogy together with marker-based information could improve the selection of elite individuals in breeding programs. We present genetic parameters for adaptive and growth traits in beef cattle by exploring linear combinations of pedigree-based (A) and marker-based (G) relationship matrices. We use a data set with 2,111 Brahman (BB) and 2,550 Tropical Composite (TC) cattle with genotypes for 729,068 SNP, and phenotypes for five traits. A weighted relationship matrix (WRM) combining G and A was constructed as WRM = λG + (1 - λ)A. The weight (λ) was explored at values from 0.0 to 1.0, at 0.1 intervals. Additionally, four alternative G matrices, in the WRM, were evaluated according to the selection of SNP used to generate them: 1) Gw: all autosomal SNP with minor allele frequency (MAF) > 1%; 2) Gg: autosomal SNP with MAF > 1% and mapped inside to gene coding regions; 3) Gp: autosomal SNP with MAF > 1% and previously reported to have significant pleiotropic effect in these two populations; and 4) Gc: autosomal SNP with MAF > 1% and with significant correlated effects previously reported in both BB and TC populations. In addition, two A matrices were evaluated: 1) A: all relationships between animals were considered after tracing back known ancestors; and 2) Ad: a distorted A matrix where a random 1% of the off-diagonal nonzero values were set to zero to simulate relationship errors. Five independent Ad matrices were explored each with a different random 1% of relationships masked. Criteria for comparing the resulting WRM included estimates of heritability (h2) and cross-validation accuracy (ACC) of genomic estimated breeding values. The choice of WRM had a greater impact on h2 than on ACC estimates. The 1% errors introduced in pedigree relationships generated large distortion in genetic parameters and ACC estimates. However, employing a λ > 0.7 was an efficient mechanism to compensate for the errors in A. Additionally, although significant (P-value < 0.0001), we found no consistent relationship between the type of SNP used to compute G and h2 or ACC estimates. We devised the optimal value of λ for maximum h2 and ACC at λ = 0.7 suggesting a 70% and 30% weighting to genomic and genealogical information, respectively, as an optimal strategy to compensate for pedigree errors, to improve genetic parameters estimates and lead to more accurate selection decisions.