Marker-assisted breeding comes of age

Charles Pick
Business Development Manager
DNA LandMarks Inc.
August 2006

An article* posted here on SeedQuest last year declared the 10th anniversary for marker-assisted selection.  In the article, scientists from Pioneer Hi-Bred described how, in the early days, they were quite happy to screen 10,000 plants a year with DNA markers.  Today they routinely screen over 1 million plants annually.  Furthermore, they felt they had only seen the tip of the iceberg in terms of this technology’s potential.

In fact genetic markers go back further than 10 years.  In plants the technology started to develop in the 1980’s.  Even in those seminal days, scientists understood the tremendous potential that existed in mapping the genomes of living organisms.  Primarily they were excited about the possibility to find genes of interest and then track them reliably through generations of crosses.

Over the past two decades, there have been many advances and applications of markers in plant breeding.  There are countless markers that have been found closely linked to traits of interest and these are now used to screen plants for disease resistance, quality characteristics, etc.  Markers are also routinely used for fingerprinting lines both as part of breeding work and for variety protection once material is commercially released.

Yet for all of the work that has been done, marker technology has remained relatively obscure to the general public.  Ask someone on the street what they think of GMOs and not only will they know what you are talking about but they will probably have a strong opinion either pro or con on the technology.  Ask the same person what they think of marker-assisted breeding and they will just look at you quizzically.

However, a revolution seems to be in progress.  These days genetic markers are receiving considerably more attention.  Recent presentations by both Monsanto and Dupont/Pioneer have trumpeted marker-assisted breeding as a key plank in their R&D strategy.  Some of these presentations even refer to it as a “new technology”.  In a July article** in the Washington Post, long time GMO foe Jeremy Rifkin wrote with cautious optimism about the “new frontier” of genomics and how it will render genetic engineering “obsolete”.

So why are people only now discovering the importance of a technology that has been with us for about 20 years?  The two main reasons are the cost of the technology and the complexity of the traits being sought.

In some ways genetic marker technology has mirrored computer technology in its development arc.  Each development cycle reduces costs dramatically while at the same time increasing the power of the technology.  Isolating DNA from plant tissue was once a cumbersome affair and seemed as much alchemy as true science.  Likewise, early DNA markers were mostly based on RFLP (restriction fragment length polymorphism) technology which was slow and expensive to run.

Today tiny leaf disks can be clipped from breeding nurseries scattered around the globe, dried and shipped to a high-throughput lab for DNA robotic extraction and analysis.  Detection methods have evolved to the point where only very small amounts of template DNA are required and changes as small as a single nucleotide can be detected.  Furthermore, thousands of these reactions can be run in parallel.  All of these changes have resulted in the reaction costs dropping from several dollars to several cents each.  Such dramatic cost reductions have not only made marker-assisted breeding economically feasible, it has become strategically imperative to keep companies competitive.

The second factor in marker technology’s rise in prominence has to do with trait complexity.  To understand why this is important, we first need to look at genetic engineering.  This technology is very effective at moving single gene traits from one organism to another.  Today it is also routine to “stack” a number of these traits into a single variety.  Despite Jeremy Rifkin’s predictions, genetic engineering is still an important tool in agricultural biotechnology and will likely remain so for the foreseeable future.

However, most important agronomic traits (e.g. yield, drought tolerance, nitrogen use efficiency) are not controlled by a single gene.  Instead they are run by complex interactions amongst numerous genes.  Not only are these traits dependent on the presence of the right alleles of these genes, but in most cases the levels of expression of the genes are also key to obtaining the best possible performance.

Genetic engineering technology has not evolved to the point where these complex, multigenic traits can be reliably spliced from one organism to another.  However by using genetic markers it is possible to analyze the various genetic components that contribute to a complex trait.  These components are unique loci in the genome and analyzing their individual contribution to a trait is known as quantitative trait loci or QTL analysis.

* Key agricultural productivity technology arrives at 10-year milestone: marker-assisted selection has revolutionized how scientists increase crop performance with native crop genes
** Beyond genetically modified crops, Jeremy Rifkin, July 4, 2006

A world leader in DNA marker development and applications, DNA LandMarks Inc. offers a full array of marker technologies to the agricultural sector from development to mapping to high-throughput application.

Charles Pick can be reached at pickc@dnalandmarks.ca

World leader in genetic markers & mapping, DNA LandMarks can turbo charge your breeding program