Research Objective
The goal of this project was to identify germplasm and develop molecular markers that could be used in the breeding program to introgress resistance to anthracnose into a broad range of market classes.
Where and how was the research conducted?
This work was carried out in Saskatchewan with germplasm chosen for adaptation to western Canadian growing conditions. Phenotyping was carried out in the greenhouse using standard screening protocols, and molecular work was carried out in the lab.
Why?
We knew that we had resistance to anthracnose floating around the breeding program, but did not have an inexpensive way to test for resistance, nor to track introgression of resistance genes from one market class to another.
How will this project benefit farmers and/or the agricultural industry?
This project will assist in the development of anthracnose-resistant dry bean varieties for long-day, short-season growing regions like Saskatchewan. Resistance to anthracnose will be pyramided with tolerance to common bacterial blight (CBB) in future cultivars. This will reduce risk and lower pesticide use.
Objective 1: Identify markers to facilitate marker-assisted selection for resistance to anthracnose for Western Canadian beans.
Markers were identified for multiple resistance genes for both race 73 and race 105 of Colletotrichum lindemuthianum, the causal organism of bean anthracnose. Combinations of markers were identified that could be used to pyramid genes for more durable resistance.
Objective 2: Identify suitable sources of Co-42 and develop a strategy to incorporate this gene into susceptible market classes.
Given the success of objective 1 and the broad access to other genes that would cover both races that are a problem in western Canada, we opted not to pursue this gene, as it appears to only be in unadapted germplasm.
What are the results of this project in more detail?
Two major genes were associated with resistance to anthracnose races 73 and 105 in a bi-parental mapping population. Lines carrying the resistance gene at both loci were more resistant than those with none and slightly more resistant than those carrying only one of the genes.
One of these regions was also identified in an association analysis using diverse germplasm that is adapted to a Saskatchewan growing region.
An additional 11 genes were tagged within the diversity panel. Different combinations of two or three of these genes would confer resistance to one or both races of anthracnose.
Many of the genes are in regions already associated with known resistance genes, but some were novel.
Table 1. Summary of high-confidence SNP associations with resistance to anthracnose race 73 (r73) or race 105 (r105) in a Northern-adapted bean diversity panel. Co-# – known loci associated with resistance to different races of Colletotrichum lindemuthianum.
| Hit | Race | SNP | Chr | Region | Germplasm Found |
|---|---|---|---|---|---|
| 1 | r105 | Pv2.1Ch01p45055690 | Ch01 | near Co-1 / novel | Mesoamerican only |
| 2 | r73 | Pv2.1Ch01p50012263 | Ch01 | Co-1 | Andean / a few Mesoamerican |
| 3 | r105 | Pv2.1Ch03p371586 | Ch03 | Co-17 | Mesoamerican / 1 Andean (Redhawk) |
| r73 | Pv2.1Ch03p371586 | Ch03 | |||
| 4 | r105 | Pv2.1Ch04p1396189 | Ch04 | Co-3/Co-15/Co-16/Co-y | Mesoamerican only |
| r73 | Pv2.1Ch04p1396189 | Ch04 | |||
| 5 | r105 | Pv2.1Ch04p2413674 | Ch04 | Co-3/Co-15/Co-16/Co-y | Mesoamerican only |
| 6 | r105 | Pv2.1Ch04p40883719 | Ch04 | Mesoamerican only | |
| 7 | r73 | Pv2.1Ch04p44561215 | Ch04 | Mesoamerican only | |
| 8 | r105 | Pv2.1Ch07p76005 | Ch07 | Co-5/Co-6 | Mesoamerican only |
| 9 | r73 | Pv2.1Ch08p1867221 | Ch08 | Co-4 | Mesoamerican only |
| 10 | r105 | Pv2.1Ch10p42902860 | Ch10 | novel | Mesoamerican / 1 Andean (Bola 60 Días) |
| 11 | r73 | Pv2.1Ch11p48976004 | Ch11 | near Co-2 / novel | Andean / 1 Mesoamerican (Morden003) |
| 12 | r105 | Pv2.1Ch11p51896851 | Ch11 | near Co-2 / novel | Mesoamerican only |
Figure 1 is an example of different combinations of genes being able to identify lines with increased tolerance to anthracnose race 73.
Molecular markers were designed to tag these different genes and were tested on entries from the last three years of Co-op testing for which we received anthracnose scores. Initial results suggest that at least seven of these need to be redesigned for technical reasons. These will be redesigned and retested. Four markers did not segregate, suggesting the Co-op material tested did not have the resistance alleles we were testing for. Two markers were able to predict resistance to races 73 and 105 without trouble.
The ability to pick and choose among resistance loci adds some flexibility to breeding efforts, allowing us to pick material that is already carrying other important characteristics, such as seed shape and colour. Doing this work on material already adapted to Saskatchewan means we do not need to pick sources of resistance from the literature, which are usually unadapted.
We are beginning to implement marker-assisted selection for anthracnose resistance in the breeding program based on the output from this project. Instead of hoping that we managed to keep resistance through the breeding process and finding out we lost it at the end stages of the breeding pipeline, we now have tools to examine early generation material and make selections earlier to ensure selection for resistant material. Where possible, we will be pyramiding anthracnose resistance with resistance genes for other diseases (Common blight and BCMV) for which we have markers, in all market classes.
Recommendations:
Marker-assisted selection (MAS): The identified resistance loci should be targeted for marker development and incorporated into routine MAS pipelines to accelerate the introgression of resistance to both races of anthracnose known to be in western Canada.
Pyramiding of resistance loci: Given the additive effects observed, breeding strategies should prioritize pyramiding multiple resistance loci to achieve enhanced resistance. This will also slow down the possibility of races evolving to evade specific resistance genes.
Germplasm utilization: This work identified the most suitable adapted starting material for breeding based on resistance profiles, with Mesoamerican and select Andean lines both contributing valuable resistance loci.
What benefit do these outcomes bring to farmers in Saskatchewan?
This project will assist in the development of anthracnose-resistant dry beans. Resistance to anthracnose will be pyramided with tolerance to common bacterial blight (CBB) in future cultivars. This will reduce risk and lower pesticide use