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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Research Project #434691

Research Project: Combining Phenotype, Genetics, and Genomics to Develop Common Beans with Resistance to Highly Variable Pathogens

Location: Soybean Genomics & Improvement Laboratory

2020 Annual Report

Objective 1: Evaluate diverse common bean accessions, especially in the Andean gene pool, to discover genes and markers linked to these genes that confer resistance to the hyper-variable pathogens that cause rust, anthracnose, angular leaf spot, and other diseases of common bean. [NP301, C1, PS1A and PS1B] Objective 2: Use phenotypic approaches and molecular markers to develop common beans combining Andean and Mesoamerican gene pools to confer broad resistance to highly variable pathogens of common bean. [NP301, C1, PS1A and PS1B] Objective 3: Improve knowledge of virulence, genetic, and genomic diversity of the hyper-variable pathogens that cause common bean diseases. [NP301, C1, PS1A and PS1B; C3, PS3A]

The major objective of this project is to concurrently broaden the genetic base of common bean to decrease the vulnerability of this crop to the highly variable pathogens that cause the rust, anthracnose, and angular leaf spot diseases. This project is based on genetic solutions that use conventional (phenotype and genetics) and new (genomics) technologies to develop common bean cultivars with broad and durable resistance to these three pathogens. In objective 1, to discover new disease resistance genes, Andean and Mesoamerican common bean accessions will be inoculated under greenhouse conditions with numerous races of the three pathogens. Races known for their virulence will be used in these inoculations. Bean accessions with resistance to most races of three pathogens will be crossed with susceptible cultivars to characterize the new disease resistance genes. To develop DNA markers tagging the newly discovered resistance genes, DNA from the parents used in crosses and from segregating populations will genotyped with the BARCBEAD6K BeadChip. To validate the usefulness of the newly developed molecular markers, phenotypic and molecular approaches will be used. In objective 2, molecular methodologies will be used to accelerate the development of cultivars from various common bean market classes that combine sets of Andean and Mesoamerican genes and broad resistance. Multiple crosses will be performed and multiple races of these pathogens will be used to confirm the spectrum of resistance of the cultivars. In objective 3, to broaden the existing knowledge of the virulence, genetic, and genomic diversity of three mentioned pathogens, DNA from Mesoamerican and Andean strains with known virulence profiles will be used for sequencing and to obtain draft genomes of these pathogens. The sequences will be used to identify DNA markers that may tag specific strains of these pathogens. These markers can be used in genetic diversity studies, and can also be used to improve our understanding of the mechanisms that drive virulence changes in these pathogens.

Progress Report
This progress report relates to Goal 1A and to Milestone 1A of this project. To discover new disease resistance genes, particularly genes from common beans of the under-utilized Andean gene pool, we continued evaluating multiple sets of common beans. These included a collection of Andean and Middle American landraces from the germplasm bank of Maringa State University, Parana, Brazil. One of these landraces is the Andean common bean Beija Flor which is resistant to multiple Mesoamerican strains of the anthracnose pathogen. Beija Flor was crossed with susceptible Mesoamerican cultivars to produce the needed populations to identify the gene or genes conferring resistance in Beija Flor. To that end, we conducted an inheritance of resistance study in which we used the progeny of the crosses made between the resistant Beija flor with the susceptible cultivars Cornell 49242 and Crioulo 159. These parents and a large population (562 F2 progeny plants) were inoculated with several specific strains of the anthracnose pathogen. These results indicated that the resistance in Beija Flor is conferred by a single and dominant gene. This gene appears to be a new anthracnose resistance gene. This gene could protect the common bean crop from the highly virulent Mesoamerican strains of the anthracnose pathogen that exist in Mexico, Central America, Brazil, and other countries. We also have conducted similar studies to identify the genes in the Andean landraces G19883 and PI 260418 that confer broad resistance to the fungal pathogen that causes the widespread rust disease of common bean. The landrace G19833, originally from Peru, was used to sequence the reference genome of common bean. In our study, we found that G19833 was broadly resistant to many Mesoamerican and Andean strains of common bean rust. The resistant G19833 was crossed with the susceptible U.S. pinto bean Olathe. The inheritance of resistance study revealed the presence of a single and dominant rust resistance gene in G19833. We also used a population (274 F2 plants) from the cross between Pinto 114 (susceptible) x PI 260418 (resistant) to confirm the presence of a dominant gene in PI 260418, which is an Andean bean from Bolivia. So far, PI 260418 is the Andean bean with the broadest resistance to common bean rust strains. This progress report relates to Goal 1 B and Milestone 1B of this project. DNA molecular markers are essential tools that detect the presence of disease resistance genes. The markers can be used to breed common bean varieties with resistance to pathogens. Many existing molecular markers were developed with technologies from the late 1980s and 1990s. Several of these markers are not accurate and give false positive and negative results. With the objective of mapping disease resistance genes and developing accurate molecular markers, we are currently using modern DNA technologies. To accomplish this objective, multiple crosses were made to produce the needed populations. We developed two populations from crosses between the Andean bean Beija Flor (resistant) x Cornell 49241 (susceptible) and Beija Flor x Crioulo 159 (susceptible). A large population (562 F2 plants) was genotyped with the new BARCBEAN12K BeadChip with more than 11,000 single nucleotide polymorphism (SNP) DNA markers. The result of these studies indicated that the anthracnose resistance gene in Beija Flor was positioned on chromosome Pv04 of the genome of common bean. In addition, this gene was positioned between two KASP markers in a small genomic region of Pv04. Further work is needed to find additional markers in closer proximity to the anthracnose resistance gene. We also used a cross between Andean landrace G19833 that has broad resistance to the fungus that causes the rust disease of common bean. We genotyped 376 F2 plants from the G19833 (resistant) x Olathe (susceptible) cross with the BARCBEAN12K BeadChip. The results indicated that the rust resistance gene in G19833 was also positioned on the chromosome Pv04 flanked by two types of DNA markers. The same technologies were used to map a rust resistance gene present in the landrace PI 26048, a common bean collected in Bolivia. Using the BARCBEAN12K BeadChip, we found the resistance gene in PI 260428 was positioned on the upper arm of chromosome Pv04 of common bean. Although we have developed molecular markers tagging this resistance gene, more research is needed to develop tightly linked markers that could be very effective in marker-assisted selection. The same assays were also used to map the rust resistance gene in Mesoamerican landrace PI 18196, known to have the highly effective Ur-11 gene that confers extremely broad reistacne to the rust pathogen. This gene is resistant to all but one of the virulent strains of the rust pathogen. A population from the Pinto 114 susceptible x PI181996 resistant cross was genotyped and the Ur-11 gene was positioned on chromosome Pv11 between two new molecular markers. All of these markers are expected to accelerate breeding new common bean varieties with resistance to highly virulent pathogens of common bean. This progress report relates to Hypothesis 2 and Milestone 2. The products of multiple crosses between bean germplasm lines developed at USDA ARS, Beltsville, Maryland, with commercial bean cultivars from the University of Nebraska, the North Dakota State University, and Puerto Rico were evaluated. The lines from Beltsville have two to four Middle American and Andean rust resistance genes. The resulting lines from these crosses were evaluated for the presence of rust resistance genes using phenotypic and molecular markers. The phenotypic markers used are the visible, leaf reactions to races of common bean rust. The molecular markers used in these evaluations were recently developed at Beltsville using genomic technologies and sequencing technologies. These markers have been validated for accuracy on hundreds of cultivars with and without rust resistance genes. Two lines of pintos from Puerto Rico were identified as having the Ur-3 and Ur-11 rust resistance genes. This combination confers resistance to all known races of common bean rust. In addition, one pinto and two Great Northern lines from the University of Nebraska were identified to have Ur-3; Ur-3 and Ur-6; and Ur-11 genes, respectively. Additional lines from the University of Nebraska and North Dakota State University are in the process of evaluation. Some of these lines with rust resistance genes will be candidates for plant registration.

1. A new bean with broad resistance to rust. Pinto bean is the most important market class of common bean grown and consumed in the United States. North Dakota is the largest producer of dry beans in the United States and rust is a major disease of common bean that limits dry bean production in North Dakota, Michigan, Nebraska, Colorado and other states. The bean rust pathogen, a fungus, recurrently produces new virulent strains. A new strain, named race 20-3 that appeared in North Dakota, was virulent on previously resistant pinto bean varieties, exacerbating the need to develop resistant pinto varieties. Collaborative studies between USDA ARS scientists in Beltsville, Maryland, and scientists at North Dakota State University showed that the Ur-11 gene conferred resistance to race 20-3. Most importantly, Ur-11 conferred resistance to all known virulent strains of bean rust in the United States as well as to all known strains in the world, except for one strain from Honduras. The scientists then used this gene to breed a new pinto bean cultivar, named ND Falcon, and it is the first dry bean with Ur-11 in North Dakota. Given that ND Falcon has the Ur-11 rust resistance gene in addition to many other positive agronomic attributes, it is anticipated that ND Falcon will have a direct positive economic impact on pinto bean growers and processors and will contribute to the sustainable production of pinto beans in the United States.

Review Publications
Urrea, C.A., Hurtado-Gonzales, O.P., Pastor Corrales, M.A., Steadman, J.R. 2019. Registration of Great Northern common bean cultivar "Panhandle Pride" with enhanced disease resistance to bean rust and common bacterial blight. Journal of Plant Registrations.
Osorno, J.M., Vander Wal, A.J., Posch, J., Simons, K., Pasche, J.S., Nelson, B.D., Jain, S., Pastor Corrales, M.A. 2020. ‘ND Falcon’, a new pinto bean with combined resistance to rust and soybean cyst nematode. Journal of Plant Registrations. 14(2):117-125.