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United States Department of Agriculture

Agricultural Research Service

Marker-Assisted Selection
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Marker-Assisted Selection: Using New Tools in Biotechnology in an Applied Breeding Program

Throughout the life sciences, a tremendous research effort has been directed towards molecular biology and biotechnology. Using these tools, a better understanding of the genetic code in all living systems is being developed. The genetic code is the basis for expression of traits in organisms; for example, traits observed in rice may include height, yield potential, length of growth cycle, resistance to diseases, etc. Some traits are controlled by one or a few genes whereas other traits may involve many genes. The expression of any particular gene can be modified by the presence of other genes or by the environment that the organism is in. In rice, for example, the softness or firmness of cooked rice may depend upon whether the rice was produced in a warm or cool climate. The traits that breeders observe in the field are a result of gene combinations in the plant and the influence of the environment on the expression of those genes. Thus, breeders evaluate genetic lines in different locations and years to make sure that they have consistently out-perform commercial cultivars across a diversity of environments and growing conditions.

Over the last decade, relatively little of the public research effort in plant molecular biology has been directly applied towards crop improvement. The USDA-TAES rice breeding program has endeavored to bridge the gap between biotechnology and conventional plant breeding. In 1993, a research project was initiated with an industry partner to develop genetic markers associated with heritable factors that influenced rice cooking and processing quality. Collaborative research in Dr. W. D. Park's lab at Texas A&M University identified DNA (genetic) markers that were associated with various forms of the rice starch synthesis gene which controls amylose content of the grain. The amount of amylose in the grain is the predominant factor in determining the softness/firmness of cooked rice. This trait is usually not evaluated until after several generations of self-pollination in the breeding process when excess seed is available. Having a genetic marker associated with this gene allows one to identify the desired form of the gene (allele) from the onset of the selection process using DNA from most any tissue on the plant. This technology allowed us to rapidly identify genetic lines that had the desired amylose allele and discard those without. The outcome was the development of two new cultivars, Cadet and Jacinto, which have unique cooking and processing quality. Where it generally takes 7-10 years to develop a cultivar, marker assisted selection decreased the development time of these cultivars by several years.

double helix
The genetic markers associated with rice amylose content are now being used by the USDA Rice Quality lab in Beaumont which screens some 8-10,000 breeding lines each year for all U.S. public rice breeding programs. Marker technology will provide a more accurate assessment of amylose content than the analytical methods previously used.

Picture of blast resistant genes

We have also made progress in developing molecular markers associated with various genes which convey resistance to blast disease caused by Pyricularia grisea. These markers are being used to combine multiple blast resistance genes into new cultivars and provide resistance to a broader array of the many different races (biotypes) of blast that occur in the U.S. These markers have also been useful in verifying that we have been successful for the first time in incorporating a new gene (Pi-b) for blast resistance from a Chinese cultivar into adapted U.S. lines. This gene will be an important resource for breeders as they enhance the natural disease resistance of rice cultivars and reduce the need for some agricultural pesticides.


Last Modified: 2/23/2005