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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

2021 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 for Goal 1A aims to discover new genes, especially of Andean origin, conferring resistance to highly variable common bean pathogens. Specifically, we emphasize conducting research to find new genes that confer resistance to a group of globally widespread and devastating diseases caused by pathogens with changing virulence; that is, pathogens that recurrently produce new virulent strains that invariably render susceptible varieties that previously were resistant. These include the pathogens that cause rust, anthracnose, and angular leaf spot diseases. The most effective two-prong genetic strategy to manage these pathogens is to 1. develop varieties combining two, but preferably more, disease resistance genes and 2. to broaden the genetic base of the common bean crop. To achieve this goal, it is necessary to have a diversity of disease resistance genes from the Andean and Middle American gene pools of common bean and genes from other species closely related to the common bean. We also search for disease resistance to other important diseases such as common bacterial blight. Recently, and in collaboration with a scientist from the University of Nebraska, we evaluated a large segregating population from a cross between two tepary beans known for their high levels of resistance to the rust and common bacterial blight pathogens at Beltsville. Tepary beans are also known for their tolerance to drought and high temperatures. The tepary population and the appropriate controls were evaluated for their resistance to two highly virulent strains (races) of the rust and two common bacterial blight pathogens strains. The resistance to rust revealed three different phenotypes, suggesting that the resistant tepary bean had a single gene or a pair of alleles where neither allele was dominant. This type of resistance is known as incomplete dominance. The resistance to the bacterial blight pathogen appeared to be controlled by two genes interacting with each other. This phenomenon is known as epistasis, and in this specific study, the epistasis is known as dominant epistasis. We also continue to use traditional and genomic technologies to discover and map other new disease resistance genes. In addition to the three resistance genes described above, we have found a new rust resistance gene in the Andean landrace PI 260418. We previously have reported that PI 260418 has a rust resistance gene on chromosome Pv04, provisionally named Ur-PI260A. The new gene, provisionally named Ur-PI260B, is located on chromosome 7. Our results suggested that the Ur-PI260A interacts with the Ur-PI260B, a phenomenon known as epistasis, where one gene (Ur-PI260A) hides the presence of the second gene (Ur-PI260B). We have also made advances in the further characterization of the rust resistance gene in the Andean bean G19833 and the anthracnose resistance gene in the Andean bean Beija Flor. This progress report for Goal 1 B endeavors to develop molecular markers linked with disease resistance genes in common bean. To this end, we have used traditional plant pathology and genetics methods as well as advanced procedures including bulk segregant analysis and high throughput genotyping using the Illumina single nucleotide polymorphisms (SNP) BARCBEAN12K Beadchip and KASP genotyping to map and fine map the resistance genes in the genome of common bean and to develop molecular markers that effectively tag the presence of the resistance genes. Among the multiple genes conferring rust resistance in common bean, the Ur-11 gene is one of the most important because this gene is resistant to all but one of the many known virulent strains (races) of the bean rust pathogen. This gene is resistant to all races of the rust pathogen collected from common bean varieties and cultivars of the Andean gene pool, and it is resistant to all but one of the known races collected from beans of the Middle American gene pool; thus, the great value of Ur-11 to common bean breeding programs. Despite the great importance of Ur-11, it has been very difficult to develop molecular markers that tag only Ur-11 and do not tag other rust resistance genes, such Ur-3, Ur-5, Ur-7 that are situated in the vicinity of Ur-11 that is present on chromosome Pv11 of common bean. We used 124 F2 plants and1639 F3 plants from a cross between PI 181996 x Pinto 114. The Middle American PI 181996 landrace is the principal source of Ur-11. Using the mentioned technologies, the Ur-11 gene was positioned on a small genomic region on the lower end of chromosome Pv11 of the common bean, flanked by two KASP markers. One of this KASP markers, known as SS322, effectively tagged the presence or absence of the Ur-11. To validate the observation, DNA from 152 common bean cultivars known to have or lack the Ur-11 gene was used to determine the accuracy of the SS322 marker. This marker was highly accurate in identifying the common bean cultivars with or without the Ur-11 rust resistance gene. These results indicate that the SS322 KASP marker could be used in marker assisted selection to identify common bean plants with the Ur -11 resistance gene. Using the same technologies, we have also recently mapped the Ur-4, a rust resistance gene present on Andean snap bean Early Gallatin. This gene has been mapped on chromosome Pv06. Although several KASP markers were found tagging the Ur-4 gene, the SS240 marker was highly accurate for the molecular identification of known common bean cultivars with and without the Ur-4 genes. Unlike a previously developed marker tagging, the SS240 marker was accurate regardless of the origin (Andean or Middle American) of the cultivar, a limitation previously encountered in older markers tagging Ur-4. In previous reports, we have reported using the same technologies to find accurate KASP markers tagging the Ur-3, and Ur -5 rust resistance genes. We are also pursuing the development of markers tagging anthracnose and angular leaf spot disease resistance genes. In summary, the results of this research will enable common bean breeders in the United States, other countries of the Americas, Africa, Europe, and other bean producing countries of the world to use these markers in marker-assisted selection for the development of dry and snap beans with resistance to multiple yield-reducing diseases of common bean. This progress report relates to Hypothesis 2 (Combining Mesoamerican and Andean resistance genes should result in broad disease resistance to the rust, ANT, and ALS pathogens) and Milestone 2 (Complete phenotypic evaluations of the first half of segregating populations). Bean germplasm lines developed at ARS-Beltsville, contain multiple genes conferring resistance to the rust, bean common mosaic, and bean common mosaic necrosis viruses. These lines have been used by our collaborators at the Universities of Nebraska, North Dakota State, and Puerto Rico to develop commercial common bean cultivars combining several disease resistance genes. The resulting bean lines are sent to ARS-Beltsville, for evaluations that determine the presence of various disease resistance genes. These lines are evaluated in the greenhouse with specific races of various pathogens, and the DNA from these plants are genotyped with markers obtained in our laboratory using genomic and high throughput sequencing technologies. We have developed markers mostly for genes conferring resistance to rust, anthracnose, and angular leaf spot diseases of common bean. In 2020, the evaluation of the black-seeded bean cultivar Twilight developed at the North Dakota State University was completed at ARS-Beltsville, and the registration of this cultivar was published in 2021. This is the first commercial black common bean with effective resistance to the new race 20-3 of the rust pathogen; however, the rust resistance of twilight is conferred by a gene that has not been yet mapped or named. The valuation of three cultivars was completed in 2021. TARS Tep 23, a tepary bean identified at the ARS-Puerto Rico, contains high resistance levels to multiple virulent races of the rust pathogen and resistance to the common bacterial blight pathogen. Our studies suggest that a single gene confers resistance to rust, and two different genes condition the resistance to the common bacterial blight. A manuscript of the registration of TARS-Tep 23 has been accepted. In addition, the evaluations of two cultivars developed at the University of Nebraska were also completed in 2021. One is a slow-darkening pinto cultivar named Wildcat, and the other is a great northern cultivar with upright architecture named White Pearl. Both were developed using bean germplasm lines from ARS-Beltsville as Parents that contain multiple genes for resistance to rust and two viral pathogens. Wildcat is the first slow-darkening pinto commercial cultivar in Nebraska. This is also the first cultivar from Nebraska with the Ur-11 rust resistance gene. White Pearl has the Ur-3 rust resistance gene. Both the pinto Wildcat and the great northern White Pearl also have resistance to the bean common bean mosaic virus and intermediate levels of resistance to common bacterial blight. The manuscripts describing the registrations of these two cultivars have been accepted.

1. Pinto beans developed with effective protection against multiple pathogens. Diseases caused by fungal and viral pathogens are major threats to dry bean production. Common bean rust, Bean golden yellow mosaic virus, bean common mosaic virus and bean common mosaic necrosis virus are devastating diseases of dry beans in Central America and the Caribbean. These diseases also occur in the United States. ARS-Mayaguez, Puerto Rico, ARS-Beltsville, Maryland, collaborated with the Zamorano University of Honduras and the Dominican Republic National Research Institute to develop two high-yielding pinto common bean germplasm lines combining multiple genes that together confer resistance to the pathogens causing these four diseases. Both lines are resistant to rust under field conditions in Puerto Rico and the Dominican Republic and resistant to bean golden yellow mosaic virus in Honduras.

Review Publications
Osorno, J.M., Vander Wal, A.J., Posch, J., Simons, K., Grafton, K.F., Pasche, J.S., Valentini, G., Pastor Corrales, M.A. 2020. A black bean with resistance to bean rust: Registration of `ND Twilight'. Journal of Plant Registrations.
Costa, L.C., Nalin, R.S., Dias, M.A., Ferreira, M.E., Song, Q., Pastor Corrales, M.A., Hurtado-Gonzales, O.P., Souza, E.A. 2020. Different loci control resistance to different isolates of the same race of Colletotrichum lindemuthianum in common bean. Theoretical and Applied Genetics. 134:543-556.
Maldonado-Mota, C.R., Moghaddam, S.M., Schroder, S., Hurtado-Gonzales, O.P., Mcclean, P.E., Pasche, J., Lamppa, R., Pastor Corrales, M.A., Tobar-Pinon, M.G., Osorno, J.M. 2020. Genomic regions and novel sources associated with resistance to anthracnose in the Guatemalan climbing beans germplasm collection. Genetic Resources and Crop Evolution. 68:1073–1083.
Beaver, J.S., Gonzalez, A., Godoy De Luz, G., Rosas, J.C., Hurtado-Gonzales, O.P., Pastor Corrales, M.A., Porch, T.G. 2020. Registration of PR1572-19 and PR1572-26 Pinto Bean Germplasm Lines with broad resistance to rust, BGYMV, BCMV, and BCMNV. Journal of Plant Registrations.
Gilio, T., Hurtado-Gonzales, O.P., Goncalves-Vidigal, M.C., Valentini, G., Ferreira Elias, J.C., Song, Q., Pastor Corrales, M.A. 2020. Fine mapping of an anthracnose-resistance locus in Andean common bean cultivar Amendoim Cavalo. PLOS ONE. 15(10):0239763.
Vidigal Filho, P.S., Goncalves-Vidigal, M.C., Sousa, V.B., Bisneta, M.V., Pastor Corrales, M.A., Oblessuc, P.R., Melotto, M. 2020. Genome-wide association study of resistance to the anthracnose and angular leaf spot diseases in Brazilian Mesoamerican and Andean common bean cultivars. Crop Science.