Page 172 - Linear Models for the Prediction of Animal Breeding Values 3rd Edition

10 Use of Genetic Markers in

Breeding Value Prediction

10.1 Introduction

A genetic marker is a fragment of DNA that is associated with a certain location
(chromosome) within the genome. In the 1990s, most genetic markers used in live-
stock studies were microsatellites. DNA microsatellites, also referred to as simple
sequence repeats (SSR), consist of a specific sequence of DNA bases or nucleotides
which contain mono, di, tri, or tetra tandem repeats; for example, AAAAAAAAAAA
or CTGCTGCTGCTG, which may be referred to as (A) or (CTG) , respectively.
11 4
Alleles at a specific location (locus) can differ in the number of repeats (polymorphic)
and hence they are used as genetic markers. Microsatellites are inherited in a
Mendelian fashion and are typically co-dominant, that is, the heterozygote genotype
could be distinguished from either homozygote.
Genetic markers are useful in identifying portions of the chromosomes that are
associated with particular quantitative traits. The incorporation of information on
marker loci that are linked to quantitative trait loci (QTL), together with phenotypic
information in a genetic evaluation procedure, would increase the accuracy of evalu-
ations and therefore of selection. The use of breeding values with marker information
incorporated in the selection of animals in a breeding programme is termed marker-
assisted selection (MAS). The gains from MAS depend on the amount of genetic vari-
ation explained by the marker information and are larger for traits with low
heritabilities, and therefore EBV from phenotype are of low accuracy (Goddard and
Hayes, 2002). Similarly, MAS should result in larger increases in accuracies for traits
that are sex-limited, such as milk yield, or measured in only in culled animals, for
instance, carcass traits.
Fernando and Grossman (1989) presented a methodology that incorporated
marker information into the BLUP procedure for the genetic evaluation of animals.
This method is discussed and illustrated in this chapter. The extension of the method
of Fernando and Grossman (1989) by Goddard (1992) to handle information on
QTL bracketed by two markers is examined. This chapter deals with linkage analysis,
i.e. the use of microsatellites as markers for the purpose of MAS.

10.2 Defining a Model with Marker Information

Consider a single polymorphic marker locus (ML), which is closely linked to a quanti-
p
m
tative trait locus (MQTL). Assume individual i inherited M and M at the ML from
i i

156 © R.A. Mrode 2014. Linear Models for the Prediction of Animal Breeding Values,
3rd Edition (R.A. Mrode)