Location: Soybean Genomics & Improvement Laboratory
2023 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
For Objective 1A: Anthracnose, rust, and angular leaf spot are devastating and widespread diseases of common bean in many common bean producing countries of the world. Andean resistance genes often confer resistance to highly virulent Mesoamerican strains and races of the three mentioned pathognes. Conversely, resistance genes on common beans of the Middle American gene pool confer very effective resistance to Andean races of the three pathogens. By collaborating with scientists in the U.S. and Brazil, we have identified and mapped seven genes controlling the rust resistance genes Ur-3, Ur-4, Ur-5, Ur-11, Ur-14, Ur-PI260418 and Ur-G19833, where Ur-3, Ur-5, Ur-11, and Ur-14 were from the Mesoamerican gene pool, and the rest were from the Andean gene pool. We identified and mapped three genes (Co-AC, Co-PA, Co-BF) controlling anthracnose resistance from the Andean gene pool, and two genes Co-3/Phg-3 and Co-1/Phg-1 controlling angular leaf spot disease, which were from the Mesoamerican gene pool and the Andean Gene pool, respectively. Germplasm carrying these resistance genes can be directly used as resistance donors in breeding programs. The identified germplasm and resistance genes will also expand the genetic base of common bean that enables the management of the rust and anthracnose pathogens known to have extensive and recurrently changing virulence.
For Objective 1B: Based on the analyses of host-pathogen interaction phenotypes under greenhouse conditions as well as common bean genotypes generated from high-throughput genotyping assays, the Illumina BARCBEAN12K BeadChip with 11,292 SNPs, and from genotyping by sequencing platform, we identified genetic variants associated with the resistance to anthracnose, rust, and angular leaf spot diseases and developed KASP molecular markers tagging the following major common bean disease resistance genes: Ur-3, Ur-4, Ur-5, Ur-11, Ur-G19833, and Ur-PI 260418 for rust resistance, and Co-Paloma, Co-AC, Co-BF, and Co-34 for anthracnose resistance, and Phg-3 for angular leaf spot resistance. We have also developed single sequence repeats (SSR) markers linked to the Ur-14 rust resistance gene and sequence-tagged site (STS) markers linked to the Co-14 anthracnose and the Phg-2 ALS resistance genes. These markers facilitate and accelerate the development of disease resistant cultivars.
For Objective 2: Bean germplasm lines developed at USDA-ARS in Beltsville, Maryland, 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, high yield, and other desirable agronomic attributes. The resulting bean lines were sent to ARS-Beltsville for evaluations of the presence of various disease resistance genes. These lines were evaluated in the greenhouse with specific races of various pathogens and the DNA from these plants were genotyped with markers developed in our laboratory. The collaboration has resulted in the registration of the following nine bean lines/cultivars since 2019:The black bean ND Twilight developed by North Dakota State University. ND Twilight combines a new, still unnamed, rust resistance gene that confers resistance to all races of the rust pathogen under field conditions in North Dakota and resistance to the soybean cist nematode. The great northern White Pearl, developed from the University of Nebraska, with the Ur-3 rust resistance gene and the I gene conferring resistance to all non-necrotic strains of the bean common mosaic virus. The Wildcat pinto bean, also developed from the University of Nebraska, with the Ur-11 rust resistance gene and other genes conferring resistance to common bacterial blight and the I gene and the scar marker that together confer resistance to all known strains of the bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) pathogens. The PR1572-19 and PR1572-26 pinto bean germplasm lines, developed from USDA-ARS Tropical Agriculture Research Station in Mayaguez, Puerto Rico, have the Ur-3 and Ur-11 rust resistance genes and the I, bc-3, and bgm-1 genes for resistance to three viruses. These two lines were the progeny of the pinto BelDakMi-RMR-12, a bean germplasm line developed at Beltsville containing the Ur-6, Ur-11, I, bc-3 resistance genes. The tepary bean TARS-Tep 23, developed from the USDA-ARS Tropical Agriculture Research Station in Mayaguez, Puerto Rico, confers resistance to the rust pathogen. This resistance, found on a tepary bean cultivar, appears to be broader than the resistance spectrum of all known rust resistance genes in common bean. Tep 23 also exhibits wide adaptation to tropical and temperate regions and tolerance under heat and drought stress conditions. In addition, a new snap bean cultivar with the Ur-11 rust resistant gene from ARS-Beltsville has been developed in Sri Lanka. Jn addition, two other lines/varieties, the great northern (white-seeded) Panhandle Pride (Nebraska, 2019), Pinto North Dakota Falcon (North Dakota, 2020) were also registered in the journal of Plant Registrations.
For Objective 3: We have completed the sequence the complex genome of Uromyces appendiculatus. A total of 73.4 Gb and 69.6 Gb were generated for races 5-0 and 31-1, respectively. In addition, 320M and 307M reads for races 5-0 and 31-1 were processed. De novo assemblies resulted in genomes of 587.6 Mb and 546.7 Mb at a k-mer of 90 for races 5-0 and 31-1, respectively. The N50s values were ~78Kb and 50.5Kb and the number of contigs larger than 500bp were 95,581 and 106,558 for races 5-0 and 31-1, respectively.CEGMA analysis against a conserved set of 248 protein families that occur in eukaryotes determined the assemblies to be 95% and 97% completed for races 5-1 and 31-1 respectively. Out of 83 SSRs tested, 77 resulted in clear amplification pattern. A subset of 16 SSRs were tested across the 46 races of U. appendiculatus maintained at Beltsville. The 16 SSRs markers identified 76 alleles, which was equivalent to using 158 SNP markers. This accomplishment offers new opportunities to improve our understanding of the interaction between common bean and different strains of the rust pathogen.
The project has produced more than 20 scientific manuscripts published in peer-reviewed journals.
Accomplishments
1. Development of common bean cultivar “USDA Rattler”. Pinto bean is the most important dry bean market class grown in the U.S. where it represents 65% of all dry beans produced on an annual basis. New pinto bean cultivars with improved traits including higher yields, yield stability, disease resistance, tolerances to drought and low soil fertility, and upright architecture, are sought after by growers. USDA-ARS scientists at Prosser, Washington, and Beltsville, Maryland, developed a new pinto bean cultivar named USDA Rattler which has all the above listed traits desired by farmers. USDA Rattler was purposely bred to perform well under both ideal and stressful growing conditions. Many years of selection in a yield nursery with optimum water and fertilizer inputs and a contrasting purgatory plot with multiple stresses including drought, low soil fertility, and soil compaction, was used to develop USDA Rattler. This cultivar was released in 2021 and a commercial license was granted to a seed company in 2022. USDA-Rattler provides growers with a new pinto bean cultivar that yields well across diverse environments.
