Technical note: Impact of pedigree depth on convergence of single-step genomic BLUP in a purebred swine population

Ivan Pocrnic, D. A. L. Lourenco, H. L. Bradford, C. Y. Chen, I. Misztal

Research output: Contribution to journalArticlepeer-review

Abstract

ABSTRACT: In genomic evaluations, it is desirable
to have low computing cost while retaining high
accuracy of evaluation for young animals. When the
population is large but only few animals have phenotypes,
especially for low heritability traits, the
convergence rate of BLUP or single-step genomic
BLUP (ssGBLUP) can be very slow. This study
investigates the effect of pedigree truncation on convergence
rate and solutions of ssGBLUP for data
exhibiting slow convergence. The data consisted of
216,000, 221,000, 732,000, and 579,000 phenotypes
on 4 traits. Heritabilities were less than 0.1 for 2 traits
and greater than 0.2 for the other 2 traits. The full
pedigree consisted of 2.4 million animals. Genotypes
were available for 33,000 animals and consisted of
60,000 SNP. Two bivariate animal models were fit
using pedigree-based BLUP or ssGBLUP. Either a
regular or the algorithm for proven and young (APY)
inverse was used for the genomic relationship matrix.
Different pedigree depths were analyzed including full
pedigree and 1 to 5 ancestral generations. Pedigree
depths were defined as n ancestral generations for animals
with phenotypes. The number of animals in the
reduced pedigrees varied from 226,000 and 760,000
for 1 generation to 228,000 and 767,000 for 5 generations.
Genomic EBV (GEBV) for genotyped animals
had correlations greater than 0.99 between runs with
the full and reduced pedigrees with 2 to 5 generations.
A single generation of pedigree was not sufficient to
obtain the same GEBV as full pedigree. The convergence
rate was the worst with the full pedigree and
generally improved with reduced pedigrees. Using
ssGBLUP with the APY inverse improved convergence
without affecting accuracy. Reducing pedigrees
and the APY are important tools to reduce the computational
cost in the implementation of ssGBLUP.
Original languageEnglish
JournalJournal of Animal Science
DOIs
Publication statusPublished - 1 Aug 2017

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