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. Visscher et al. Livestock Production Science 65 2000 57 –70
through generations and relationship between ani- mals can be estimated using identity-by-decent
IBD measures. The study of associations between these IBD measurements with phenotypic perform-
ance has allowed the detection of linkage between marker loci and a QTL, and thereby the identification
of genome regions with major effects in quantitative traits. In the pig genome, several regions affecting
quantitative traits have already been found, mainly in studies using crosses between divergent breeds see,
e.g. Rothschild, 1998; Walling et al., 1998. Given the trend in the discovery of molecular markers and
advances in the statistical techniques to map QTL, the list of known single genes and genome regions
affecting quantitative traits is expected to sharply increase.
What is the impact of this powerful technology on pig breeding programmes and, in particular, on the
use of crossbreeding? Previously we discussed ways in which genetic markers might be used in pig
breeding programmes Visscher and Haley, 1995, 1998. Markers may be used to combine alleles
Fig. 3. Possible future breeding pyramid based upon 10 million slaughter pig per year.
variants of a gene or QTL from different breeds or lines using gene introgression programmes or by
3. Molecular techniques creating synthetic lines or to improve the response
of selection with lines. In addition to these two main One of the aims in molecular genetics is to
uses, there is a variety of ways to use genetic identify and locate the genes involved in the expres-
markers. They include the control of heterozygosity sion of discrete or quantitative traits. The use of such
and inbreeding, control and identification of product information in breeding programmes would provide
and stock, and the prediction of dominance heterosis a measurement of the genetic value of individuals,
within and between lines. This list is by no mean without necessarily looking at their phenotype or of
exhaustive, and breeding companies will surely find their relatives’ phenotypes. Since DNA can be
other ways of utilising molecular marker techniques. sampled from individuals of any sex or age, it also
enables the evaluation of all individuals for traits that 3.1. Marker assisted introgression MAI
are difficult to measure, such as for sex-specific or carcass traits.
The aim of genome introgression is to introduce Currently, the knowledge of genes affecting quan-
favourable characteristics from a donor breed or line titative traits is rapidly increasing. In pigs, several
into a recipient breed line. This is done by breeding genes or chromosome regions with large effects have
an F1 population and crossing it with the recipient already been found e.g. halothane gene, the estrogen
line while selecting for the desirable characteristic of receptor gene and many more are likely to be found.
the donor line. After several generations of backcros- Additionally, the genome map of the pig has
sing, the genetic background of the resulting line is thousands of marker loci that provide an important
primary the same of the recipient but preserving the resource for quantitative trait locus QTL mapping.
favourable characteristic of the donor one. Hence, A QTL is a location in the genome which has an
when single genes or genome regions with large effect on a quantitative trait. Using marker in-
effect on the trait are identified, marker information formation, chromosome regions can be followed
may be used to unambiguously introgress the specific
P . Visscher et al. Livestock Production Science 65 2000 57 –70
63
genome region of the donor population, and to speed the QTL see, e.g. Smith, 1967; Fernando and
up the genome recovery of the recipient genotype. Grossman, 1989; Lande and Thompson, 1990; Larzul
Currently, there are several examples where MAI is et al., 1997; Henshall and Goddard, 1998; Pong-
already possible in commercial pig breeding. For Wong and Woolliams, 1998.
example, the dominant white allele, which gives pigs What would be the impact of MAS in pig breed-
the white phenotype, has been identified Johansson ing? The results from several studies generally
et al., 1992 and can be introgressed into non-white associate MAS approaches with a greater short-term
lines to create homozygous white recipient lines. genetic gain than traditional methods using only
There have been several reports of a QTL allele from performance records. The magnitude of this extra
the Meishan on chromosome 7 which increases gain is dependent on the assumed genetic parameters
2
leanness in crosses with European pigs Rothschild, e.g. h of the trait, type and size of the QTL effect,
1998. Introgression of this favourable allele into frequency of the QTL, recombination rate between
commercial dam lines may be desirable, in particular marker and QTL. Conversely, a reduction in the
if it can be combined with introgressing additional long term cumulated gain when using genotype
QTL for reproductive performance. Studies assessing information has also been observed, specially with
the efficiency of MAI programmes suggest that a mass selection i.e. the individual’s breeding value is
successful introgression programme could result in a estimated using only information their own per-
new line which incorporates one or more genome formance and genotypic record or progeny test
regions from a donor line in 5–7 generations of selection programmes e.g. Gibson, 1994; Larzul et
selection e.g. Hospital et al., 1992; Visscher et al., al., 1997; Pong-Wong and Woolliams, 1998. How-
1996. The genetic cost of introgressing the desirable ever, this negative effect in the long term gain is
genome region would result in the new line having a limited to MAS schemes that only increase the
genetic lag from the recipient population. Assuming accuracy of the estimated breeding values, and also it
that MAI is carried out using the genotype of the may be controllable. For instance, under a BLUP
QTL itself, this genetic cost was equivalent to one to evaluation framework which is widely used in pig
two generations of selection in the nucleus popula- breeding, the long term loss is substantially mini-
tion Gama et al., 1992. mised Villanueva et al., 1998, and it may be
completely eliminated by optimising the relative 3.2. Marker assisted selection MAS
weight given to both the DNA and the phenotypic information across generations Dekkers and Van
The purpose of marker assisted selection is to use Arendonk, 1998; Manfredi et al. 1998.
the genotype of identified major genes or of linked A common characteristic from most of the MAS
markers to improve response to selection within line. approaches is that they target one area of the
In pig breeding programmes, the benefit of MAS genome, where only one QTL is segregating, at a
would be mostly from an increase in the accuracy of time. Segregation means that there are different
the estimated breeding values, but there may also be alleles in the population for a particular QTL, so that
benefit from an increase in intensity of selection e.g. some or all individuals are heterozygous. The
for sex-limited traits and a reduction of the genera- current status of the pig genetic map is sufficiently
tion interval e.g. for carcass traits. The use of MAS dense for it to appear inefficient to consider a MAS
has been widely discussed and several approaches programme targeting only a single area of the
adapted to different breeding structures in commer- genome. The next step would be the extension of
cial species, including pigs, have been proposed. The MAS to account for several QTL at the time. How
differences between approaches range from methods practical would it be to extend previous MAS
using only DNA information or to those that com- approaches to a genome-wide approach? In theory,
bine it with performance records, methods using the there should not be any complication in extending
genotype of a major gene itself or of linked markers most of the already proposed MAS schemes to
and methods using markers which are either in consider multiple QTL. For instance, when the QTL
linkage equilibrium or in linkage disequilibrium with is considered as a random effect in the method
64 P
. Visscher et al. Livestock Production Science 65 2000 57 –70
proposed by Fernando and Grossman 1989, the populations is a measure of the number of genera-
increased complexity from accounting for an extra tions they have diverged from a presumed common
QTL would be equivalent to add two more traits in ancestor, and is usually calculated from differences
the multivariate BLUP evaluation. Obviously, some in allele frequencies between the populations at a
consideration should be made of the size of the number of loci. Although the correlation between
computational problem, but this is unlikely to invali- genetic distance and heterosis is not always large,
date the use of MAS with multiple QTL. Perhaps the this method might target specific line combinations
most important concern about the Fernando and which are more likely to produce fit, high performing
Grossman 1989 approach is that the genetic model progeny. If this technique of combining lines for
used to describe the QTL is based on assumptions of crossbreeding works, it should also be possible to
normality so does not account for changes in allele use the same principles for mate selection. For
frequency and it cannot consider dominant QTL. The example, among a pool of selected males and
use of finite locus models, coupled with Monte Carlo females, mate allocation is performed based upon the
Markov chain MCMC computer methods, may be expected mean heterozygosity of the progeny. How
another viable alternative in the near future. Consid- can mate allocation be used in purebred lines? The
ering that this model can handle each locus in- benefit of maximising heterozygosity to exploit non
dependently, it is also straightforward to extend the additive variation is obvious at the multiplier and
model to assume some loci to be linked to a given commercial level. Favourable combinations of alleles
genetic marker. An additional advantage of such in the nucleus may result in a greater efficiency, for
models is the fact that they easily allow considera- example by increasing the fitness of animals at this
tion of QTL with dominance effects. However, level. To achieve a better commercial animal, the
before such models can be widely used, further exploitation of non-additive variation in purebred
studies are required to fully understand their be- lines should aim to produce the favourable allelic
haviour and properties. Early results show that a combinations in the crossbred generation. For in-
naive and simplistic implementation of a finite locus stance, if the cross of a pair of purebred lines is
model appears sensitive to the number of loci known to show appreciable heterosis, we may be
assumed in the model of analysis Pong-Wong et al., able to associate genetic markers with this effect and
1998. As our current state of knowledge does not within line MAS designed to fix the lines for
give us confidence in assumptions about the number alternative alleles would be expected to increase
of loci, we require analytical models that are robust performance in the crossbred.
to such assumptions. Selection methods such as recurrent reciprocal
selection RRS may be implemented to select the 3.3. Prediction of crossbreeding performance and
purebred lines at the nucleus level, with or without mate selection
the use of molecular markers. RSS is a traditional selection method in which purebred parents are
Until recently, the decision on which lines to cross selected for purebred breeding on the basis of their
for producing F1 parents or slaughter pigs have been predicted crossbred performance. RRS is theoret-
very much by trial-and-error. This is an expensive ically efficient in the presence of overdominance,
way of testing crossbreds, and in theory it is possible however, to our knowledge there is little evidence
that the best cross has not been carried out because for overdominant gene action in livestock and other
not all combinations of breeds and lines are tried. species. RRS used to be practised in poultry breed-
The use of molecular markers can help to solve the ing, but less so at present [A. Koerhuis, personal
problem of deciding which combination of lines to communication. Generally, the value of using
test. Studies from maize and chickens tend to suggest crossbred information to select animals at the nu-
that there is a positive relationship between the cleus level is not clear, because it depends on the
genetic distance between the lines, as estimated from relative amount of dominance variation and whether
molecular markers, and the amount of heterosis in alleles are partially dominant or overdominant
the crossbred progeny. Genetic distance between two Wei and Van der Werf, 1994. Uimari and Gibson
P . Visscher et al. Livestock Production Science 65 2000 57 –70
65
1998 concluded that using crossbred information in sequence. Driven by human medicine, these tech-
a poultry breeding programme was superior to using nologies are probably not far away, perhaps only 5
pureline information only if the ratio between domi- years or so. Surely the livestock industry will utilise
nance variance and total genetic variance was ap- advances in such technologies, and should be pre-
proximately 0.3 or higher. Note that the increasing pared to use the information which is generated by
spread of A.I. in the pig also means that elite boars them.
from the nucleus level would also have offspring at the commercial level, so their information would be
3.5. Genetic modification technologies available at the moment when their half sib groups in
the nucleus level are to be selected. Although In this review, we have concentrated on reproduc-
technology may already be available to implement tive and molecular technologies which do not alter
such a structure, it is likely to need a massive the genome other than through the standard pro-
investment in the infrastructure to allow data of cesses of selective breeding. The reason for not
guaranteed quality to be retrieved from all levels of discussing transgenic or genetic modification tech-
the breeding structure. nologies in great length is because it is unlikely, in
our opinion, that these technologies will be used for 3.4. Genetic marker technology
pig improvement in the next 5–10 years. This prediction is based both on technological and con-
For some of the schemes suggested above, cheap sumer attitude arguments. In our opinion, genetically
genomic information, for example in the form of a modified meat is not likely to be acceptable to the
dense marker map, would be advantageous. Is this a consumer in the near future. The technological
realistic scenario for the livestock industries? We problems and prospects were recently discussed by
think it is, for a number of reasons. Firstly, the Pursel 1998, and are related to which genes to
current marker technology of choice, i.e. microsatel- target, and how to control the expression of genes
lite markers i.e., markers based on genetic variation which have been introduced.
in the number of repeat sequences at a particular locus, is relative new since the late 1980s, and new
technologies which could overtake them have been
4. Combining several techniques: speed genetics
