Single-step prediction of genomic breeding value in a small dairy cattle population with strong import of foreign genes

Abstract

The main goal of the inclusion of molecular genetic information (MG) in the evaluation of breeding animals is to evaluate young animals without performance records.The inclusion of MG was first carried out based on the relationship between several genetic markers with QTLs (Přibyl, 1995). This information was combined with the polygenic breeding value (EBV) determined by a BLUP Animal Model. A large number of genetic markers can be determined due to the development of laboratory techniques that influence the methods of EBV prediction. A large number of partial regressions are estimated for a given trait based on many SNP genetic markers. These partial regressions are summed into one total criterion used for the animal's selection for breeding. This criterion predicts the direct genetic value (DGV) and in combination with the Single-step prediction of genomic breeding value in a small dairy cattle population with strong import of foreign genes The older data set included 526 genotyped bulls, in which the daughters' milk performance was known for 210 individuals. All of the genotyped animals were included in the newer data set. Of the young genotyped bulls from the older set, 279 had more than 50 daughters with performance records in the newer set. Genomic relationship matrices (G) were constructed from the allele frequencies of the current genotyped population or by assuming a constant value of 0.5 for all loci. Using current allele frequencies, the correlation of G with the pedigree relationship (A) was 0.74, while it was 0.77 when the constant value was used. G was blended with A with weights of 80 or 99%. The average EBV of the genotyped bulls exceeded the mean EBV of the entire population by 3 SD. Although the number of reference bulls was small, genotyping resulted in an increase of approximately 0.05 in the correlation of the GEBV of young bulls with their results after progeny testing. Only small differences in correlations were found in dependency on the methods used for the determination of G and in dependency on the weight used in blending G with A. Both EBV and GEBV in the older set showed higher correlations with the GEBV of the newer set than the EBV of the newer set.

Domestic estimated breeding values and genomic enhanced breeding values of bulls in comparison with their foreign genomic enhanced breeding values

“…Manifestation of greater differences among methods would be expected as first lactation records of daughters became available. On the other hand, we are using more proven genotyped sires in reference population than in previous studies (Přibyl et al, 2012(Přibyl et al, , 2013a. If the number of proven genotyped sires increased in the reference population, results improved as well.…”

“…In addition, domestic GEBVs, which reflect domestic production conditions, are calculated for imported young genotyped bulls. Přibyl et al (2012Přibyl et al ( , 2013aPřibyl et al ( and 2014 verified genomic predictions for milk production in the Czech Holstein population using a cut-off study based on comparing results of young sires from an earlier span of years to those from a later span when their progeny results are known. With the passage of time, the number of genotyped animals increases, leading to increased reliability of results.…”

“…where Y is the vector of first lactation milk yield of cow, or DRP of milk production of bull; X, Z the design matrices for fixed and random effects, respectively (Přibyl et al, 2012 and2013a); β the vector of fixed effects covering contemporary groups within a herd in a 3-month calving period (HYS), linear and quadratic regression for calving age and linear and quadratic regression for days open; an the EBV of animal, random effect with assumption of covariance structure an~N(0, Aσ 3. RRBLUP -prediction on the basis of regression coefficients of all single nucleotide polymorphism (SNP) loci exploiting of pseudo-phenotype data DRPs of proven genotyped bulls only.…”

“…Blending ssGBLUP -calculation of GEBV, utilizing DRP of all 112 880 genotyped and un-genotyped bulls from Interbull (analysis 5i). Evaluation is according to analysis 1i (approach 1), but with relationship matrix H substituted for matrix A, where H is the pedigree additive relationship matrix A augmented by genomic relationship matrix G. Weights of 80% G and 20% additive pedigree relationship matrix, only for genotyped animals A 22 was used for incorporation into H (Misztal et al, 2009;Christensen and Lund, 2010;Přibyl et al, 2012); 6. ssGBLUP with combined data -calculation of GEBV, joint evaluation in one step of the entire domestic population and entire Interbull file (analysis 6di). To avoid double counting in these combined analyses, Interbull DRPs were used only when sires did not have daughters in the domestic population.…”

“…This method effectively combines nation-wide production records and pedigree databases with genomic information to directly predict GEBV. Přibyl et al (2012) used this methodology for the genetic evaluation of the relatively small Czech Holstein population. Gao et al (2012) and used DRP of sires instead of phenotypic production records as input data in ssGBLUP, naming the procedure the one-step blending approach.…”