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For more than 300 years, thoroughbred horses have been raised for a single purposeto win at the racetrack. The origin of these horses can be traced to a small group that was imported to England from North Africa and the Middle East in the 1600s. The population of racing horses remained small until the 1800s, when horse racing became increasing popular; today there are approximately half a million thoroughbred horses worldwide. Breeding and racing thoroughbred horses is a multibillion-dollar industry that relies on the premise that a horses speed is inherited. Speed is not, however, a simple genetic characteristic such as seed shape in peas. Numerous genes and nongenetic factors such as diet, training, and the jockey who rides the horse all contribute to a horses success or failure in a race. The inheritance of racing speed in thoroughbreds is more complex than that of any of the characteristics that we have studied up to this point. Can the inheritance of a complex characteristic such as racing speed be studied? Is it possible to predict the speed of a horse on the basis of its pedigree? The answers are yesat least in partbut these questions cannot be addressed with the methods that we used for simple genetic characteristics. Instead, we must use statistical procedures that have been developed for analyzing complex characteristics. The genetic analysis of complex characteristics such as racing speed of thoroughbreds is known as quantitative genetics.

Although the mathematical methods for analyzing complex characteristics may seem to be imposing at first, most people can intuitively grasp the underlying logic of quantitative genetics. We all recognize family resemblance: we talk about inheriting our fathers height or our mothers intelligence. Family resemblance lies at the heart of the statistical methods used in quantitative genetics. When genes influence a characteristic, related individuals resemble one another more than unrelated individuals. Closely related individuals (such as siblings) should resemble one another more than distantly related individuals (such as cousins). Comparing individuals with different degrees of relatedness, then, provides information about the extent to which genes influence a characteristic. This type of analysis has been applied to the inheritance of racing speed in thoroughbreds. In 1988, Patrick Cunningham and his colleagues examined records of more than 30,000 3-year-old horses that raced between 1961 and 1985. They reasoned that, if genes influence racing success, a horses racing success should be more similar to that of its parents than to that of unrelated horses. Similarly, the racing speeds of half-brothers and half-sisters should be more similar than the speeds of unrelated horses are. When Cunningham and his colleagues statistically analyzed the racing records for thoroughbreds, they found that a considerable amount of variation in track performance was due to genetic differencesracing speed is heritable. With the use of statistics, it is possible to estimate, with some degree of accuracy, the track performance of a horse from the performance of its relatives.

This chapter is about the genetic analysis of complex characteristics such as racing speed. We begin by considering the differences between quantitative and qualitative characteristics and why the expression of some characteristics varies continuously. Well see how quantitative characteristics are often influenced by many genes, each of which has a small effect on the phenotype. Next, we will examine statistical procedures for describing and analyzing quantitative characteristics. We will consider the question of how much of phenotypic variation can be attributed to genetic and environmental influences and will conclude looking at the effects of selection on quantitative characteristics. Its important to recognize that the methods of quantitative genetics are not designed to identify individual genes and genotypes. Rather, the focus is on statistical predictions based on groups of individuals.

The statistical methods described for use in analyzing quantitative characteristics can be used both to make predictions about the average phenotype expected in offspring and to estimate the overall contribution of genes to variation in the characteristic. These methods do not, however, allow us to identify and determine the influence of individual genes that affect quantitative characteristics. The genes that control polygenic characteristics are referred to as quantitative trait loci (QTLs). Although quantitative genetics has made important contributions to basic biology and to plant and animal breeding, the inability to identify QTLs and measure their individual effects has severely limited the application of quantitative genetic methods.

In recent years, numerous genetic markers have been identified and mapped with the use of recombinant DNA techniques, making it possible to identify QTLs by linkage analysis. The underlying idea is simple: if the inheritance of a genetic marker is associated consistently with the inheritance of a particular characteristic (such as increased height), then that marker must be linked to a QTL that affects height. The key is to have enough genetic markers so that QTLs can be detected throughout the genome. With the introduction of restriction fragment length polymorphisms and microsatellite variations, variable markers are now available for mapping QTLs in a number of different organisms. A common procedure for mapping QTLs is to cross two homozygous strains that differ in alleles at many loci. The resulting F1 progeny are then intercrossed or backcrossed to allow the genes to recombine through independent assortment and crossing over. Genes on different chromosomes and genes that are far apart on the same chromosome will recombine freely; genes that are closely linked will be inherited together. The offspring are measured for one or more quantitative characteristics; at the same time, they are genotyped for numerous genetic markers that span the genome. Any correlation between the inheritance of a particular marker allele and a quantitative phenotype indicates that a QTL is linked to that marker. If enough markers are used, it is theoretically possible to detect all the QTLs affecting a characteristic. This approach has been used to detect genes affecting various characteristics in several plant and animal species.

The number of genes affecting a quantitative characteristic can be estimated by locating QTLs with genetic markers and adding up the number of QTLs detected. This method will always be an underestimate, because QTLs that are located close together on the same chromosome will be counted together, and those with small effects are likely to be missed. QTL mapping also provides information about the magnitude of the effects that individual genes have on a quantitative characteristic. The polygenic model assumes that many genes affect a quantitative characteristic, that the effect of each gene is small, and that the effects of the genes are equal and additive. The results of studies of QTLs in a number of organisms now show that these assumptions are not always valid. Polygenes appear to vary widely in their effects. In many of the characteristics that have been studied, a few QTLs account for much of the phenotypic variation. In some instances, individual QTLs have been mapped that account for more than 20% of the variance in the characteristic.

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