Finding the DNA segments associated with key traits for more efficient potato breeding.
Potato breeders select promising lines mainly based on the plants’ phenotypes – how the individual plants perform under greenhouse and field conditions; in other words, how each plant expresses its own specific DNA – its genotype – in a particular environmental situation.
But phenotypic selection can be time-consuming and imperfect. So Canadian researchers are matching key phenotypic traits with specific DNA segments to develop tools for quicker, more reliable identification of the best potato lines.
“This research on discovering associations between DNA and some key traits is to help us improve our efficiency in developing new varieties so they can meet the needs of the market and the environment,” says Benoit Bizimungu, a research scientist with Agriculture and Agri-Food Canada (AAFC) in Fredericton, N.B.
Bizimungu is leading this AAFC-funded research. The trait-associated DNA segments, known as molecular markers, can be used to screen breeding material in the lab, instead of having to grow thousands of seeds into plants and test them all for each desired trait.
Bizimungu’s research team is working on a comprehensive effort to develop markers for all the key traits in AAFC’s potato breeding program.
Molecular markers are useful for breeding any crop, but potato offers some special challenges for breeders. Bizimungu explains, “Potato is more genetically complex compared to some other common crops. Many crops have two sets of each chromosome, one from the male and another from the female parent. But potatoes have four sets of each chromosome, two from each parent, which complicates the transmission of traits, and perhaps more importantly, the prediction of the traits expressed by the progenies and the selection of lines combining the desirable traits.”
According to Bizimungu, this marker research is drawing on recent scientific and technological developments in genomics and DNA sequencing as well as in bioinformatics (analysis of complex biological data). One example of these advances is the sequencing of the potato genome in 2011, which showed that potato has over 39,000 genes spread across its genome. Also, researchers in many countries are continuing to learn more about the potato genome and its relationship with agronomic and end-use traits. In addition, advances in DNA sequencing technology are making sequencing faster and less expensive, so it has become practical to sequence the DNA of individual potato lines to determine their genotypes. And computers are getting better and better at handling the large amounts of data involved in comparing the DNA of multiple genotypes.
One of the processes that Bizimungu’s team is using is called Genome-Wide Association analysis to find the connections between phenotypic traits and particular DNA segments. AAFC’s potato breeding program has been collecting data on phenotypic traits in its advanced breeding lines over many years, including disease resistance, agronomic and quality traits. Recently, Bizimungu’s research team has started genotyping selected lines with traits of interest as well as some other potato lines that lack certain positive traits found in the advanced lines. Then the researchers look for statistical associations between the variations in the phenotypic properties and the variations in the DNA.
For instance, Bizimungu’s team analyzes the DNA of a group of potato lines that are resistant to a certain disease and a group of lines that are susceptible to the same disease. Then they look for DNA variations that occur in all the resistant lines but none of the susceptible lines. Such DNA variations can be used as diagnostic markers to screen for resistance to that disease.
The researchers are working step by step through the most important traits in AAFC’s breeding program. Bizimungu says, “We started with disease resistance traits because they are controlled by fewer genes, compared to more challenging traits which involve many genes. So we are starting with traits like late blight, scab and nematode resistance, and making our way to more complex ones.”
Bizimungu’s team is already achieving good progress in the search for disease resistance markers. “We have identified some key DNA variations associated with late blight, wart and scab. The next step is to use them in breeding on a routine basis. For that, we have recently acquired new high-throughput DNA screening equipment that allows us to test thousands of candidate lines early in the breeding cycle.”
Evaluating lines for disease resistance is a good example of how molecular markers can significantly benefit the breeding process, compared to phenotypic selection. Pathogens need specific environmental conditions to cause disease in a plant, but in the field those conditions may not always occur when breeders would like them to occur, which hampers the selection process. In some cases, breeding programs may even need to set up a disease nursery, spending time and effort to create the conditions necessary for the disease to occur, like adding inoculum to the plots or perhaps irrigating the plots to promote a disease that requires moist conditions. Also, assessing plants for the presence of a disease can be time consuming.
“For example, late blight is an important disease for potatoes, but it’s also difficult to select for resistance to late blight in the field because, while you need the presence of the disease, at the same time you do not want it in the field because it can spread into production areas. When using markers, we don’t need to have the disease present to know which lines are resistant because we can refer to the DNA segment,” says Bizimungu.
“So using markers really gives us some advantages in terms of improving efficiencies and speeding up the development of new varieties. For example, we could use the markers to screen for disease resistance and eliminate susceptible lines early in the selection process before we go to the field, and plant only resistant ones, which saves time and resources, and speeds up the whole process.”
Bizimungu believes the molecular markers coming from this research – and the improved varieties resulting from using the markers – will be very good news for potato growers, processors and consumers.
“These markers could have a major impact on improvement of the potato industry. We know the industry is facing some challenges that can be solved by adopting improved varieties. For example, having varieties with appropriate disease resistance helps in many regards. First of all it reduces the production risks associated with the disease and eliminates the need for chemicals to control the disease, which provides a cost reduction option. And it’s good for the environment as well,” he says.
“All the traits we’re working on are very important to industry, and we expect them to really make a difference in improving the economic and environmental sustainability of potato production.”