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Area of Science:

  • Animal Breeding and Genetics
  • Quantitative Genetics
  • Genomic Selection

Background:

  • The algorithm for proven and young animals (APY) offers a computationally efficient method for approximating the inverse of the genomic relationship matrix.
  • Single-step genomic Best Linear Unbiased Prediction (ssGBLUP) is a powerful tool for genetic evaluations but can be computationally intensive with large genotyped populations.
  • Previous applications of APY have focused on single-breed or line datasets.

Purpose of the Study:

  • To evaluate the accuracy of genomic estimated breeding values (GEBV) derived from the APY (GEBVAPY) compared to those from a directly inverted genomic relationship matrix (GEBVDIRECT).
  • To assess the performance of APY in crossbreeding schemes, including F1 and F2 crosses, relevant to species like pigs and chickens.
  • To investigate the impact of core group size and composition on the accuracy of GEBVAPY in multivariate ssGBLUP.

Main Methods:

  • Simulations of a 3-way crossbreeding program were conducted to compare different approximated inverses of the genomic relationship matrix.
  • The size and breed composition of the core animal group within the APY were systematically varied.
  • Multivariate ssGBLUP was employed to evaluate GEBV accuracy in scenarios involving multiple breeds and their crosses.

Main Results:

  • GEBVAPY demonstrated accurate approximation of GEBVDIRECT in multivariate ssGBLUP analyses involving different breeds and their crosses.
  • Optimal accuracy, comparable to GEBVDIRECT, was achieved when core groups comprised diverse breeds.
  • The ideal core group size for accurate GEBVAPY was found to be between the numbers of eigenvalues explaining 98% and 99% of the genomic relationship matrix variation.

Conclusions:

  • The APY is a reliable method for approximating genomic breeding values in complex crossbreeding scenarios.
  • Careful selection of core group size and breed composition is crucial for maximizing the accuracy of GEBVAPY.
  • APY provides a computationally feasible and accurate alternative for genomic evaluation in multi-breed populations.