Breeding Success Series: PART 3, How DNA Markers are Helping Us to Help You!

Texas Peanut Producers Board is dedicated to spending 50 percent of our annual budget on research, approximately $350 thousand annually. In an effort to keep our farmers informed, our peanut research team got together and wrote a series of articles over successes in the industry. We will be featuring these articles in a three part blog series. “Thank you to our Texas Peanut Breeding Research Team Members, Drs. Mark Burow, Michael Baring, Charles Simpson and John Cason, for their contributions.” 

Read Part 1: The Past 15 Years HERE.

Read Part 2: Advanced Lines that are Near Release HERE.


Part III: How DNA Markers are Helping Us to Help You!


Dr. Mark Burow is the lead researcher for the TAMU molecular marker program for the peanut breeding team. His lab located at the TAMU AgriLife Research and Extension Center in Lubbock has developed markers for a number of different traits. All of the talk in today’s scientific world seems to be about GMO’s and Marker Assisted Selection. Our program does not develop GMO peanuts, but we are using marker assisted selection on a limited basis and this trend is going to grow exponentially in the upcoming years. We have markers for early and late leafspot resistance, Rootknot nematode resistance, the high oleic trait, seed size, and a number of different traits associated with drought and salt tolerance. We also expect to use markers for TSWV and Sclerotinia resistance in the near future.

The question is, how do these markers benefit the grower? Basically, the markers make the breeding program more effective and efficient by allowing us to know definitively what traits we have captured in each plant selection which will inevitably allow us to get more done in a shorter amount of time. First, being able to associate a trait such as nematode resistance to a certain DNA (or gene) marker allows us to test a plant and know without a doubt that it is carrying that trait. We use to have to take multiple root samples for hundreds of lines, wash them in solution and perform egg counts under a microscope which was tedious and time consuming and not always accurate if nematode populations were low. Also, plants typically carry two forms (alleles) of each gene, one obtained from each original parent. A plant that has one allele for nematode resistance and one for susceptibility will be resistant, but its offspring will include both resistant and susceptible plants. With markers, we can select plants that have both resistant alleles, so the next generation will not include susceptible plants.


Figure 1. Example of calling different marker scores. Each dot is the marker score for two alleles for a single peanut plant. YY (green) has two copies of the same allele for a trait. XX (red) has two copies of the other allele. XY (blue) has one copy of each form of the gene.

Secondly, one of our main goals is to provide the growers with a variety that has many different traits which could include multiple disease resistance, high yield and grade potential, high oleic, early maturity, and even drought tolerance. Every time we add a trait to the selection scheme the odds of our finding a single plant with every one of these traits goes down exponentially. If we could run DNA samples and test for all of these traits at one time it would simplify our selection process and make the program much more efficient. For traits such as drought tolerance, selection has traditionally been done at late stages in the breeding program, because it was considered that selection for complex traits cannot be done early in a breeding program. But we have identified markers that we can select early in the process.   This means that we will need to screen thousands of seeds early in the breeding program to make selections, but we would not be able to screen thousands of plot rows of a single population later in the breeding scheme to select for multiple traits. We expect that markers will allow us to select for the major genes early, but we will still need to test for yield and grade in the field, of course, to select the best materials for release.

We are not quite to the point of being able to test for several traits at one time using a single DNA sample, but we are getting close. A micro-chip has been designed which will allow us to test up to 92 individual plants for up to 90 different markers at one time (Fig 2).  This saves months of time each year in identifying markers to use. Once this process is complete it will streamline our marker assisted selection process. We are also hoping to purchase equipment that will allow us to screen hundreds or thousands of plant samples at a time for fewer markers, to make the process more efficient yet. This is why it is so important to develop good markers for our desired traits.


Figure 2: Example of a micro-chip for screening multiple traits simultaneously.

The third answer to how these markers benefit the growers and our program is that they allow us to screen for traits in years where we are unable to get good field screenings. For example, if we plant a group of materials to test for nematode resistance in a field that ends up not having nematode pressure. Another example would be trying to screen a large population for drought tolerance and having a wet year. In both cases we would have lost a year’s worth of selection because the environment was not right for screening purposes. The environment has no effect on our ability to test DNA for associated markers.      

So, to recap, with marker assisted selection we know without a doubt exactly what traits we have captured. We know that we will soon be able to screen for multiple traits simultaneously. We also realize that these markers will allow us to select even when Mother Nature doesn’t comply. All of these things combined will make the breeding program more efficient and more effective in terms of developing new varieties for the growers. So far, we have used DNA markers to select for resistance to Rootknot nematodes in our breeding populations and to develop NemaTAM and Webb. It is our hope that within the next couple of years we will be able to make crosses and screen the resulting progeny for many of the traits mentioned above at one time. This could help us to eliminate 50%+ materials that don’t have the desired traits which would save on money, labor, time, and land area for planting, and to focus the later stages of breeding on yield and grade after already selecting for other traits. Yield and grade are what growers need for improved profitability.

This concludes our three part series over research successes in the peanut industry. Thanks again to AgriLife researchers Michael R. Baring, Mark D. Burow, Charles E. Simpson, and John M. Cason for their hard work! 

Read Part 1, The last 15 Years HERE.

Read Part 2: Advanced Lines that are Near Release HERE.