MAS in breeding

Marker-assisted selection in breeding programs

Introduction

Marker-assisted selection (MAS) uses the genotype of a marker instead of, or in combination with, the phenotype of a plant in selection during a breeding program. This is especially helpful for traits that are highly influenced by the environment (e.g. yield, protein contents of seeds), or that are expensive or difficult to test, for example drought tolerance, fruit characteristics in crops with a long juvenile phase such as apple or vine, malting quality in barley or the resistance to a quarantine organism. MAS has the additional advantage that it can be performed off-season and off-site and in the very early stages of plant development since only a small amount of DNA (usually from a leaf sample) is needed. However, MAS also has disadvantages and limitations. The efforts needed to find markers and to create linkage maps are large and not justified for each crop or trait, and many traits may be more easily or just as easily selected using conventional visual selection on the trait of interest. Moreover, the selection result by MAS may be less good than in conventional breeding. This has to be kept in mind when studying the contents of this chapter.

Advantages of MAS

• using larger numbers of individuals
• With high-throughput MAS many plants in segregating breeding populations can be scored already at a young plant stage to discard all plants that do not have the desired combination of marker alleles (and hence the desired gene combination). Only the desired plants are kept, and those can be judged for other traits that are relevant to the breeder, but not covered by the markers. This implies that more populations and much larger populations can be handled than in case of conventional breeding, so MAS allows selection between and within more crosses and between more individuals per cross.
• Favorable traits can be selected at seedling stage, for example phenotypic testing of flour color (white or yellow) in wheat requires grains formed by mature plants; associated markers can be observed in 10-day old plants. This is even more important in crops with a long juvenile period (e.g. tulip, apple).
• elimination of unreliable phenotypic evaluation in field trials due to unfavourable conditions for the trial, or maybe large environmental effects on the trait = selection for traits that have a low heritability (or that have a low heritability in a particular trial, location, year)
• For example, disease resistance: the disease might not be present at a certain location or in a certain year
• Some traits, such as yield can be (marker-assisted) selected for on individual plant basis. By visual selection, this is hardly possible in most crops and it might require some extra years of propagation before enough material for a trial (per genotype) would be available for effective selection on such traits.
• more efficient backcrossing, because by using markers, selection against donor "background" and positive selection for "foreground" (the target allele) fewer rounds of backcrossing are required to eliminate the possibly unfavorable donor alleles.
• combining multiple genes simultaneously (gene 'pyramiding'), even if each gene alone would result in the same phenotype (for example: if several resistance genes each result in complete resistance, the phenotype in a bioassay does not tell the breeder how many R genes, and which, are present). MAS could maximize the number of resistance genes or allow the selection of a specific set of resistance genes. For race-specific resistance genes, genes working against different races could be stacked without the need of performing disease resistance tests with all races.
• testing for specific traits where phenotypic evaluation is not feasible (e.g. quarantine restrictions may prevent exotic pathogens to be used for screening; for oil contents of fruits in male (dioecious) oil palms). In animal breeding, think of marker-selection among bulls for breeding values for milk yield of their daughters even before these are born.

 

Disadvantages and limitations of MAS

• high initial investments (lab facilities, know-how) are needed, or costs for outsourcing the marker development and analyses
• the search for markers is time consuming
• genetic maps are desired also for different exotic parents which act as donors for desirable genes
• markers and the genes to which they are linked may be not polymorphic in segregating populations derived from other parental pairs. A marker-linked QTL for high yield found in cross A x B may not segregate in cross C x D, since it is fixed there already (as either the homozygous – or the + allele, or some unknown allele).
• In material to which multiple parents contributed, the marker allele that indicates a relevant trait gene to select for or against, the marker allele(s) for selection should be diagnostic: they should not occur in the other contributing parents, since there they may not be linked with the same relevant trait allele. The marker allele should be uniquely indicative for either the positive or the negative allele of the gene of interest, not in some crosses associated with the positive allele and in other crosses with the negative allele.
• some markers are inconsistent in their behavior
• failure to amplify or cut or hybridize
• MAS allows selection on the basis of individual genes. However, genes may behave background and environment dependent, i.e. they may have a different effect in a different genetic background because of
• epistasis: the effect of one gene is decreased or overruled by the effect of another gene (increase would also be possible and an example of interaction, but not a disadvantage in that case). The effect of a gene may depend on the presence of some other gene(s) in the genetic background that occurred in the population in which the gene was mapped, but may fail to occur in other parental material. Epistasis may also show at the metabolic level: a gene product might biochemically interact with a product of another gene.

Next to selection purposes, genetic markers can also be used, e.g.:

• to test the purity of a variety
• to test the identity of a variety and its putative ancestry
• to quantify the genetic diversity between species

Summary

→    MAS has advantages but also important disadvantages and limitations

Towards the end of this chapter, use of MAS in specific steps in breeding programs will be treated, such as marker-assisted backcrossing and marker-assisted gene pyramiding. However, before markers can be used for MAS in practical breeding programs, often some work needs to be done first.