Population development

Although QTLs can be detected both in natural populations and in populations developed from controlled crosses, we will deal only with the latter, because these are most relevant to crop improvement programs. Developing a population for QTL mapping involves selecting the parents, crossing them with each other, then advancing the progeny in an appropriate manner to obtain a set of individual plants or lines segregating for the traits of interest.

Most commonly, a QTL mapping population is derived from the cross of two parental lines that show marked differences for the trait of interest, e.g., the cross of a disease-resistant line by a disease susceptible line, or the cross of a high-protein by a low-protein line. A typical QTL population consists of 100 to 300 lines or individuals, each of which is evaluated both for phenotypic traits and for molecular markers. However, when resources are available, larger population sizes are recommended and are sometimes used (Beavis, 1994, 1998). The accompanying animation demonstrates the development of three common types of QTL mapping population: F2, recombinant inbred line, and backcross populations.

*This animation has no audio.*

An F2 population is quickly and easily developed by self-pollinating the F1 hybrid between two parents. However, only a single plant represents each genotype, so replications over time or space cannot be carried out. Also, for some traits like yield, evaluations on single plants are usually not considered reliable. This limitation of F2 populations can be overcome in species that are easily cloned, such as some turfgrass and horticultural crops. In these cases, the cloned F2 plants can be used in replicated trials. Another possibility is to self-pollinate F2 plants to produce F3 families, each consisting of multiple plants, which are used for phenotypic evaluation.

recombinant inbred line (RIL) population is developed through single seed descent from the F2 generation. The result is a set of homogeneous, homozygous lines for which large amounts of seed can be produced for replicated trials. However, advancing the population for six or more generations is expensive in time and labor. For more information on RIL populations, see Burr and Burr, 1991.

The backcross population is easily developed by crossing an F1 plant to one of its parents. Like the F2 population, each primary backcross genotype is represented by a single plant. However, each backross-derived plant can be self-pollinated or cloned to obtain multiple plants for evaluation. Compared to an F2 population, a backcross population is less informative for linkage mapping because recombination among markers occurs in only one set of gametes (either male or female) (Lander et al., 1987). An adaptation of backcross QTL mapping is called the Advanced Backcross method (Tanksley and Nelson, 1996). It is especially useful for identifying beneficial QTL alleles in wild germplasm.

Doubled haploid populations are also used for QTL mapping. This type of population is described in detail at the Oregon Wolfe Barley site, http://barleyworld.org/oregonwolfe.

Fig. 3 Conditions for detecting QTLs. The Parent A genotype is shown on the left side of the chromosome, with the Parent B genotype on the right. M1 and M2 are marker loci and Q denotes a QTL. Polymorphisms are indicated by different subscripts at each locus.

Besides differing for phenotypic traits, the parents of a mapping population must also be sufficiently polymorphic at the genotypic (molecular marker) level so that chromosome recombination events can be tracked. In some cultivated crops, relatively little genetic polymorphism exists. In these cases, a cultivated variety might be crossed to a wild relative to increase the level of polymorphism.

A QTL in a particular region of the genome can be detected only if

  • the parents are polymorphic at the QTL, i.e., they have two different alleles that result in phenotypic differences;
  • the parents are polymorphic at a marker in the chromosome region containing the QTL;
  • there is linkage disequilibrium between the marker and the QTL, i.e., the marker allele and QTL allele from the same parental source tend to be inherited together.

Points one and two from the previous list, are illustrated in Figure 3.

This concludes the population development section.