2007 U of M Research Special Report

Mapping Leaf Disease Resistance in Barley

Our Small Grains Initiative grant is directed toward implementing marker-assisted selection (MAS) to improve disease resistance in barley. While Fusarium head blight (FHB) remains the highest priority in that effort, this year’s report will focus on progress toward MAS in two leaf diseases. 

After FHB, net blotch and Septoria speckled leaf blotch are the two most important diseases for barley in Minnesota.  Under conducive conditions, both diseases can cause substantial yield losses.  The UM Barley Breeding Program currently screens for resistance to these diseases using seedling assays in the greenhouse and field nurseries.  This work is done in collaboration with Ruth Dill-Macky, Brian Steffenson, and Charla Hollingsworth in the Department of Plant Pathology. 

In parallel with our breeding effort, we have conducted several genetic studies to map the position of resistance genes for these diseases.  Once we have mapped the position of resistance genes to particular segments of chromosomes, we can use DNA markers to select for the genes via MAS.

The advantages of using MAS to conduct selection is that it does not require field or greenhouse screening (which can sometimes fail), it can be done at a very early stage of the breeding program (saving time and resources), and we can select for resistance to several diseases in the same individual plant (multi-tasking).

Technician Charlie Gustus and undergraduate student Summer Kluck initiated this project to evaluate a population that was created from crossing one parent that was resistant to net blotch, and another parent that was resistant to Septoria speckled leaf blotch.  Each line of the population along with the parents was evaluated in three separate greenhouse experiments for each disease and also for set of molecular markers. 

Analysis of the disease and marker data revealed that there was a major gene for resistance to each disease. Interestingly, both of these genes were located in the same region of barley chromosome 6. When geneticists conduct mapping studies, it is not uncommon to identify genes that are close together or linked.  This case was problematic, because the genes are said to be linked in repulsion (see sidebar Repulsion Phase Linkage).

What this means is that the resistance gene for net blotch was very close to the susceptible gene for Septoria speckled leaf blotch in one parent, and that the reverse was true for the other parent. In order for these two linked genes to be separated so that the desirable resistance genes for each disease can be present in an individual, there would need to be a recombination event between the two genes. This event, called crossing over, is essentially a breakage, swapping, and reconnection of chromosome segments. These recombination events occur naturally, but the closer two genes are together, the less likely there will be a recombination event between them.

So why is this a problem?  If two resistance genes were not linked, then our friend Gregor Mendel would predict that half of the progeny in the population would be resistant to one disease and half resistant to the other.  That would mean that about 25% of the progeny would be resistant to both diseases, which is the objective of our breeding program.  Since these genes were linked in repulsion, less than 5% progeny were resistant to both diseases.  This creates a problem since we would like to select among dozens or even a hundred disease resistant lines to identify those that were also high yielding and have favorable malting quality.

This is where using marker-assisted selection comes in handy.  Screening hundreds of lines in the field or greenhouse for both diseases would be very laborious. Instead, we can isolate DNA from each line and screen them for two DNA markers (one on each side of the linked genes).  We can then use the marker data to identify plants where the rare recombination event has placed the two resistance genes in an individual.

Once we have identified individuals containing both resistance genes, there will be a low frequency that this linkage will be broken, making it easier to identify progeny of future crosses that contain both genes, and are agronomically acceptable.   

One thing that makes the DNA markers screening fast and inexpensive is the establishment of USDA Regional Genotyping Labs to help breeders implement MAS. We work with the lab in Fargo, N.D. under the direction of Shiaoman Chao.  We grow plants for about two weeks, snip off a half inch piece of leaf tissue from each plant, place it into a small plastic plate that can hold 96 leaf samples, and ship them to Fargo.  In about 6-8 weeks, Dr. Chao emails a spreadsheet with the results and we can select the individuals that we want to advance in the breeding program.

The identification of these two genes for resistance to net blotch and Septoria speckled leaf blotch should allow us to quickly move them into our breeding program.  Since all of our current barley varieties are susceptible to these diseases, this will be an important first step to improve resistance. 

Because the pathogen may overcome these resistance genes, it will be necessary to continue to identify new genes to combine with existing genes. Several breeding lines with both genes will be entered into our first year yield trials this year, and crosses made last fall will generate more lines to be screened using MAS this summer.  Our ultimate goal is to combine resistances for these two diseases with lines in our program that have improved resistance to FHB.

– Dr Kevin Smith, barley breeder, smith376@umn.edu

Separating Resistance Genes from Susceptible Genes

This graphic courtesy U of M barley breeder Dr Kevin Smith helps illustrate the challenge of breeding stronger disease tolerance in new lines, in this example, net blotch and Septoria in barley.  The two parents A and B are said to be in ‘repulsion phase linkage,’ because for parent A, the desirable gene for resistance to net blotch is linked to the susceptible gene for Septoria.  Likewise for Parent B, the desirable gene for resistance to Septoria is linked to the susceptible gene for net blotch. The vertical rectangles represent the pair of chromosomes of each individual, and the circles and squares represent the genes for the two diseases.  If these genes were unlinked (on different chromosomes), half of the progeny would be resistant to each disease and 25% of the progeny would be resistant to both diseases.  In this case, where the genes are linked or close together, only rare recombinants would result in linkage of the two resistance (or susceptible) genes together. In breeding for disease resistance we would select those individuals with resistance genes for both diseases (shown circled).