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

Location: Soybean Genomics & Improvement Laboratory

2019 Annual Report

Objectives
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]

Approach
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
Two research activities were performed that relate to Objective 1 that endeavors to discover new genes conferring resistance to major pathogens of common bean. In the first activity, a collection of 173 common bean landraces was obtained from the Bean Germplasm bank of the University of Maringá, Parana Brazil. This collection which included Andean and Mesoamerican landraces, was scheduled to be inoculated with multiple virulent strains of the bean rust pathogen under greenhouse conditions with the objective of finding new genes conferring rust resistance. A subgroup of entries was initially inoculated with four different virulent strains selected for their ability to detect rust resistance genes. So far, 20 landraces, 10 Andean and 10 Mesoamerican, were resistant to one or more races, and one entry was resistant to all four races. None of the current rust resistance genes used in this study as controls were resistant to all four races, suggesting that new rust resistance genes may be discovered in the Brazilian collection. In the second activity, 34 tepary bean accessions obtained from the University of Nebraska and USDA-ARS, Puerto Rico, have also been inoculated with multiple virulent strains of the rust pathogen. This trial included mostly cultivated but also some wild tepary bean accessions. The tepary bean, a related species from the tertiary gene pool of the common dry edible bean, is known to have high levels of tolerance to heat and drought and resistance to some common bean pathogens. Extremely high levels of resistance to multiple strains of the rust pathogen were observed in various tepary beans. These results suggested that some tepary beans contain new rust resistance genes. Because many of these tepary beans can be crossed with common bean, there is the possibility of using conventional hybridization methods to transfer the high levels of rust resistance from tepary bean to the common bean. In another activity related to Objective 2, phenotypic (conventional) and molecular markers obtained using genomic-based technologies were used to follow the movement of Ur-3 and Ur-5 rust resistance genes into one single common bean cultivar. The combination of these two genes is difficult due the interaction that occurs when these two genes are combined. In this interaction, called epistasis, one gene hides the presence of the other. Research performed this year led to the identification of two molecular markers that accurately tag each of these genes. The study was conducted by evaluating a segregating population obtained from the cross between common bean cultivars Aurora (with the Ur-3 gene) and Mexico 309 (with the Ur-5 gene). This population was first phenotyped with four selected races of the rust pathogen and genotyped with the two molecular markers. The phenotypic markers showed that Ur-3 masked the presence of Ur-5, but the molecular markers showed the presence of both genes. It took about four weeks of work to perform the less-accurate screen with the phenotypic markers whereas it took a few hours to perform the absolutely accurate screen with the molecular markers.

Accomplishments
1. Beans with resistance genes. Research conducted using genomics technologies at the USDA-ARS, Beltsville, Maryland, has enabled the development of two new molecular markers. Genes conferring resistance to the fungus that causes the destructive rust disease of common bean, dry and snap beans in the United States and other countries in South and Central America and in Africa. When combined in a bean plant, these two genes increase protection to rust. These two markers can be used by dry and snap bean breeders to develop rust resistant bean lines and varieties.

2. Beans of pride. A new, great northern common dry bean cultivar named “Panhandle Pride” was developed by scientists because Nebraska continues to lead all states in great northern common bean on production, Panhandle Pride was bred specifically for better adaptation to Nebraska growing conditions. Furthermore, Panhandle Pride combined genes for resistance to the fungus that causes rust disease, to common bacterial blight disease, and to the bean common mosaic virus. The yield of Panhandle Pride, tested in multiple locations in Nebraska, was higher than many of the popular great northern bean varieties planted in Nebraska. Panhandle Pride is being made available to farmers who want to grow great northern common dry beans.