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Vol. 7 | No. 2 | Fall 2008

Marker-Assisted Selection

With the global population continuing to grow, competition for finite water supplies intensifying, and rising temperatures increasing the risk of drought and weather-related crop damage, it is more important than ever to increase agricultural productivity in a way that preserves our natural resources. One such way is crop breeding, or mating plants with desirable traits.

In recent decades, a greater understanding of the genetic material, or genomes, of crops has led to new breeding methods with several advantages over previous methods. One of these new methods—marker-assisted selection (MAS), or marker-assisted breeding—offers the potential to breed for important traits such as resistance to drought and other environmental stresses without genetic engineering.

In this example, marker-assisted selection (MAS) has been used to identify two tomato plants
with genetic segments (called quantitative trait loci or QTL) that together will contribute to
greater crop yield (i.e., more tomatoes per plant). MAS may reduce the number of breeding
steps necessary to produce desired traits in crops.

Needles in the Genetic Haystack

Conventional crop breeding relies on mating plants (usually of the same species), called varieties, that differ in certain genetic characteristics that will confer desirable properties on the offspring plant. These properties must be easily observed, or it will be difficult to determine whether the breeding process was successful. Easily observed traits such as many types of disease resistance are typically produced by a small number of powerful genes.

Many important crop traits, however, are not easy to observe or are controlled by many genes called quantitative trait loci (QTL) that individually contribute only a small amount to the trait but collectively result in its full expression. Crop yield is one example of a QTL-controlled trait. Often, only a few crop varieties have a desired QTL, and these varieties each typically contain only one or a few QTL. Because the small effect of these individual genes is hard to observe, and because the traits expressed by these genes may be altered by environmental effects, tracking them and bringing them together in one plant using conventional breeding methods can be difficult or impractical.

MAS, in contrast, is not dependent on observation of the desired trait. Instead, MAS works like a genetic barcode scanner, analyzing the unique sequence of components in a plant’s DNA to identify the desired genes. The process begins by identifying several thousand short, unique stretches of DNA called “markers” that are distributed throughout the plant’s genome. Some of these markers are associated with genes that contribute to the desired traits.

During breeding, if a marker is consistently associated with the desired gene—because they are both present or both absent in offspring plants—the marker can be used to track the gene. Thus, once a plant’s genetic barcode has been scanned and specific markers identified, it becomes possible to screen thousands of seedling plants for the presence of the desired gene(s).

The Benefits of MAS

While there are some limitations to MAS that keep it from being implemented on a larger scale (see the sidebar), it offers several advantages over other breeding methods that are currently available—the most important being that it can save valuable time by reducing the number of breeding steps needed to produce a crop variety. Even easily observed traits can take a decade or more to develop in new varieties using conventional methods. MAS can often cut that time in half. And because only a small portion of a leaf is needed for testing, MAS can be done when a plant is small rather than having to wait to observe the desired traits in a mature plant; this is especially helpful for long-lived crops such as fruit or timber trees. Finally, it may allow breeding of some complex QTL that cannot be accomplished by conventional methods.

This technology is also seen as a promising alternative to genetic engineering (GE). Like MAS, GE aims to improve crops at the genetic level, but GE involves extracting the desired genes from various organisms such as unrelated plant species or even bacteria nd then inserting them into the crop’s genome. Because this approach carries certain risks such as increased toxicity, allergenicity, or harm to beneficial insects, GE requires a degree of regulatory oversight or infrastructure that MAS does not. This is another way in which MAS saves time in new crop development. (When MAS is used to breed related wild plant species with crops, rather than breeding two or more crop varieties, there may be a somewhat higher risk to human health or the environment.)

Also, the fact that the genes used in MAS are already serving their desired function in a crop or related species may suggest a higher likelihood that these genes will prove useful in crop breeding, while the more exotic genes used in GE (from a bacterium, for example) may not. There may be some occasions when the greater range of genes available for use in GE enables the development of traits not possible through MAS, though so far there has been little evidence to prove this. Finally, MAS has the current advantage of being able to manipulate groups of genes more easily than GE, which has not proven successful in routinely adding groups of interacting genes to a crop.

As a supplement to traditional crop breeding and an alternative to genetic engineering, MAS is likely to play an important role in agriculture during the coming years. Any expansion of interest in sustainable agriculture methods will only magnify that role.

Doug Gurian-Sherman is a senior scientist in the Food and Environment Program.