The effect of using approximate gametic variance covariance matrices on marker assisted selection by BLUP
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Date
2004-01-15
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Under additive inheritance, the Henderson mixed model equations (HMME) provide
an efficient approach to obtaining genetic evaluations by marker assisted best linear unbiased
prediction (MABLUP) given pedigree relationships, trait and marker data. For large
pedigrees with many missing markers, however, it is not feasible to calculate the exact gametic
variance covariance matrix required to construct HMME. The objective of this study was to
investigate the consequences of using approximate gametic variance covariance matrices on response
to selection by MABLUP. Two methods were used to generate approximate variance
covariance matrices. The first method (Method A) completely discards the marker information
for individuals with an unknown linkage phase between two flanking markers. The second
method (Method B) makes use of the marker information at only the most polymorphic marker
locus for individuals with an unknown linkage phase. Data sets were simulated with and without
missing marker data for flanking markers with 2, 4, 6, 8 or 12 alleles. Several missing
marker data patterns were considered. The genetic variability explained by marked quantitative
trait loci (MQTL) was modeled with one or two MQTL of equal effect. Response to selection
by MABLUP using Method A or Method B were compared with that obtained by MABLUP
using the exact genetic variance covariance matrix, which was estimated using 15 000 samples
from the conditional distribution of genotypic values given the observed marker data. For the
simulated conditions, the superiority of MABLUP over BLUP based only on pedigree relationships
and trait data varied between 0.1% and 13.5% for Method A, between 1.7% and 23.8%
for Method B, and between 7.6% and 28.9% for the exact method. The relative performance of
the methods under investigation was not affected by the number of MQTL in the model.
Description
Keywords
marker assisted selection, BLUP, gametic variance covariance matrix
Citation
Liviu R. Totir et al, "The effect of using approximate gametic variance covariance matrices on marker assisted selection by BLUP," Genetics Selection Evolution 36 (2004), doi:10.1186/1297-9686-36-1-29, http://www.gsejournal.org/content/36/1/29