Introduction to Forward Selection (a.k.a. Foreground Selection)


Heather L. Merk, The Ohio State University

Deana Namuth-Covert, University of Nebraska-Lincoln

This module outlines the concept of forward selection (also sometimes called foreground selection) and the use of molecular markers to facilitate this process. In addition, this module outlines criteria to identify desirable markers for forward selection.


Forward selection is selection for a desired trait/gene; it is what people typically think of when they think of plant breeders making selections. This is in contrast to background selection, which focuses on eliminating unwanted contribution of genetic materials, typically from a donor parent during trait introgression. It has been theorized for several decades that molecular markers can be used to assist progress with forward selection. View an example where forward selection has been used in tomato to select for improved resistance to bacterial spot.

Using Molecular Markers to Assist with Forward Selection

The possibility of using molecular markers to assist with forward selection came about with the rapid increase in the number of available molecular markers, beginning with RFLP markers in the 1980s (Tanksley and Hewitt, 1988) and more recently with SSRs and SNPs. Before using molecular markers to conduct forward selection, suitable marker(s) must be identified. This raises a key question: what is a suitable marker for forward selection? A suitable marker can be defined based on three factors: (1) marker properties, (2) association with desired trait, and (3) genetic distance between marker and trait. These three factors are discussed below.

1. Marker Properties

See the molecular markers module for an introduction to molecular markers. Desirable characteristics of molecular markers to be used for marker-assisted selection include co-dominant inheritance, reproducibility, low cost of marker development and genotyping, and capacity to be run on a high-throughput scale. For these reasons, SNPs (and to some extent SSRs) are currently in wide-spread use in molecular marker applications. Learn more about the advantages and disadvantages of different molecular markers.

Khan et al. (2007) provide an example of developing suitable molecular markers for use in marker-assisted selection. Previous quantitative trait locus (QTL) mapping studies identified a major QTL associated with fireblight resistance in apple (Calenge et al., 2005; Khan et al., 2006). In this initial study, RAPD and AFLP markers were associated with this QTL. However, RAPD and AFLP markers are not suitable for marker-assisted selection due to their dominant nature and potential issues of reproducibility between laboratories. Therefore, Khan et al. (2007), developed SCAR markers from the RAPD and AFLP markers for use in marker-assisted selection for resistance to fire blight in apple. SCAR markers are co-dominant and can be reproduced between laboratories.

2. Marker Association with Desired Trait

After a source of a desired trait, often a wild accession, has been identified as possessing a trait of interest to a breeding program, a next logical question for plant breeders is, “How can this trait be best incorporated into valuable breeding material?” The answer depends largely on the genetic nature of the trait. To study the genetic nature of a trait, phenotypic data and genotypic data from molecular markers can help determine the number and nature of gene(s)/QTLs controlling a trait by detecting associations between markers and traits.

To identify markers associated with a trait, a variety of methods are available, including single marker trait analysis, simple interval mapping, multiple interval mapping, and composite interval mapping. All of these methods require development of mapping populations and some methods require development of a genetic map. Learn more about genetic mapping. Often, mapping populations developed by researchers are not the same populations that breeders want to use. It is important to confirm associations between markers in traits in breeding populations to make sure the association holds true in that population. Why wouldn’t an association hold true in other populations? Associations between marker and trait may not hold true in other populations due to undetected interactions with other genes (epistasis) (Tanksley and Hewitt, 1988). In the case of quantitative traits, there may be interactions between genes and environment, making the phenotype dependent on the environment (Knoll and Ejeta, 2008).

Consider the following example. Tanksley and Hewitt (1988) identified molecular markers associated with three regions of the tomato genome that increased soluble solids in one population. Although the association was present in two other populations, it was not present in another population. The verification process can be quite elaborate. To help mediate this process, breeders can use a technique known as selective genotyping, in which genetic analysis is performed on a portion of the individuals in a population.

3. Genetic Distance Between Marker and Trait

To effectively use a molecular marker to conduct forward selection, the marker must be tightly linked with the associated trait. Ideally, the gene(s) conferring the trait were previously cloned and the molecular markers were developed within the gene sequences. This ensures that there are no recombination events between the marker and gene. Although this may be possible for some genes, such as the RB gene in potato that confers resistance to late blight, it is generally not the case (Colton et al., 2006; Song et al., 2003). Commonly, the molecular marker is located some distance from the gene. When selection is based on a single marker, there is a chance that genetic recombination will occur between the marker and gene, resulting in loss of the gene. The chance of recombination is related to the genetic distance between the marker and gene; the farther apart the marker and gene, the more likely a recombination event between them.

To circumvent the potential for recombination between a marker and gene, researchers have promoted selection based on markers that flank the gene (flanking markers) (Hospital and Charcosset, 1997; Soller and Plotkinhazan, 1977; Tanksley, 1983). By selecting based on the marker genotype of flanking markers, breeders can identify recombination events between one of the markers and the gene. If there was a cross-over between a marker and gene, the two markers, which are on either side of the gene, would have different genotypes. The chance that double crossovers occurred is small and related to the distance between flanking markers (distance between marker and gene and distance between gene and the second marker).

Selection based on flanking markers, however, may lead to keeping extra genes that are located between the molecular markers in addition to the desired gene. This can be problematic if desired and undesired traits are closely linked. This again reinforces the concept of identifying molecular markers as closely linked to the desired gene as possible.


Molecular markers can be useful to aid in forward selection. When breeders consider using markers for forward selection, it is important to consider properties of the molecular marker, the strength of association between the marker and trait, and the genetic distance between the marker and gene(s) of interest.

References Cited

  • Calenge, F., D. Drouet, C. Denancé, W. E. Van de Weg, M. N. Brisset, J. P. Paulin, and C. E. Durel. 2005. Identification of a major QTL together with several minor additive or epistatic QTLs for resistance to fire blight in apple in two related progenies. Theoretical and Applied Genetics 111: 128–135 (Available online at: (verified 1 Jan 2011).
  • Colton, L. M., H. I. Groza, S. M. Wielgus, and J. M. Jiang. 2006. Marker-assisted selection for the broad-spectrum potato late blight resistance conferred by gene RB derived from a wild potato species. Crop Science 46: 589–594 (Available online at: (verified 1 Jan 2011).
  • Hospital, F., and A. Charcosset. 1997. Marker-assisted introgression of quantitative trait loci. Genetics 147: 1469–1485. (Available online at: (verified 18 Oct 2010).
  • Khan, M. A., B. Duffy, C. Gessler, and A. Patocchi. 2006. QTL mapping of fire blight resistance in apple. Molecular Breeding 17: 299–306 (Available online at: (verified 1 Jan 2011).
  • Khan, M. A., C. E. Durel, B. Duffy, D. Drouet, M. Kellerhals, C. Gessier, and A. Patocchi. 2007. Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection. Genome 50: 568–577 (Available online at: (verified 1 Jan 2011).
  • Knoll, J., and G. Ejeta. 2008. Marker-assisted selection for early-season cold tolerance in sorghum: QTL validation across populations and environments. Theoretical and Applied Genetics 116: 541–553 (Available online at: (verified 1 Jan 2011).
  • Soller, M., and J. Plotkinhazan. 1977. Use of marker alleles for introgression of linked quantitative alleles. Theoretical and Applied Genetics 51: 133–137 (Available online at: (verified 1 Jan 2011).
  • Song, J. Q., J. M. Bradeen, S. K. Naess, J. A. Raasch, S. M. Wielgus, G. T. Haberlach, J. Liu, H. H. Kuang, S. Austin-Phillips, C. R. Buell, J. P. Helgeson, and J. M. Jiang. 2003. Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight. Proceedings of the National Academy of Sciences of the United States of America 100: 9128–9133. (Available online at: (verified 1 Jan 2011).
  • Tanksley, S. D., and J. Hewitt. 1988. Use of molecular markers in breeding for soluble solids content in tomato – a re-examination. Theoretical and Applied Genetics 75: 811–823 (Available online at: (verified 1 Jan 2011).
  • Tanksley, S. D. 1983. Molecular markers in plant breeding. Plant Molecular Biology Reporter 1: 3–8 (Available online at: (verified 1 Jan 2011).

External Links

Funding Statement

Development of this lesson was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

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