Research Project: Enhanced Agronomic Performance and Disease Resistance in Edible Legumes

Location: Grain Legume Genetics Physiology Research

2021 Annual Report

Objectives
Development and release of novel edible legume germplasm lines and cultivars with enhanced traits that benefit breeders, growers, consumers, and the environment, represent the long-term goals for this project. Given favorable outcomes, breeders will benefit from germplasm releases, growers from increased yield potential and nitrogen fixation, consumers from healthy low cost food with improved quality, and the environment from reduced pesticide use. Germplasm lines which incorporate novel traits from exotic sources into near-commercial seed market types will provide public and private breeders with useful traits for cultivar development. Moving traits from exotic sources into adapted commercial cultivars is an otherwise arduous task for most breeding programs. Thus, these germplasm releases will facilitate adoption of new traits by breeders and increase genetic diversity in their programs which is crucial for advancing yield potential and for sustainability in the long term. It is expected that some breeding lines with exceptional performance generated by this project will be released as cultivars. Another long-term goal is to better understand the genetics underpinning complex traits and leverage this knowledge to improve breeding strategies. High-throughput next generation sequencing combined with optical mapping and updated reference genomes will significantly facilitate genetic studies geared toward advancing our breeding efforts. We will seek better markers for indirect selection of economically important traits in pea and common bean and examine new marker-assisted breeding strategies. Populations generated for genetic analyses will be used for breeding and vice versa. Such dual purpose populations facilitate simultaneous advancement toward our long-term goals (germplasm development and genetic knowledge from genomic analyses). For the next five years this project will focus on the following objectives. Objective 1: Develop genomic analysis populations, and use them to improve genetic understanding of complex traits as well as to accelerate breeding for improved agronomic traits, including biological nitrogen fixation, drought tolerance, tolerance to low soil fertility, and resistance to problematic bacterial, fungal, and viral diseases. Objective 2: Develop, evaluate, and release fresh green pea and dry bean (kidney, pinto, black) germplasm with improved agronomic performance combined with durable disease resistance.

Approach
1. Research Goal: Genetic factors which condition complex stress resistance traits will be positioned on physical maps, with associated genomic sequences leveraged for marker-assisted breeding. Select populations will be evaluated for response to abiotic stresses (drought, low fertility) and diseases (Bean Common Mosaic Virus [BCMV], common bacterial blight [CBB], Fusarium root rot, Pea Seed-borne Mosaic Virus [PSbMV] and white mold) and genotyped with genomic markers (single-nucleotide polymorphisms [SNPs]). Linkage maps will be developed and quantitative trait loci (QTL) detected. SNPs with potential marker-assisted selection applications will be detected by melting temperature Tm-shift analysis. Reference genome data bases will be used for physical mapping, validating genetic map positions, and candidate gene discovery. If the BARCBean6K_3 BeadChip SNP array we intend to use for bean studies provides inadequate marker coverage then it may be necessary to generate additional SNPs through genotyping-by sequencing (GBS). 2. Research Goal: Combining independent QTL and major resistant genes will improve genetic resistance to abiotic stresses and contribute to durable disease resistance in pea and dry bean, and be combinable with quality attributes and enhanced agronomic performance. Bean improvement efforts will be based on the use of F4 bulk breeding populations. These populations derive from Andean Diversity Panel accessions selected to combine resistance to both biotic and abiotic stresses. All materials in the F4 generation and later must perform well under multiple stresses in the white mold nursery, terminal drought trial, low nitrogen (N)trial, purgatory plot (drought, soil compaction, low fertility, and root rots), and in the non-stress trial used to determine maximum yield potential, in order to be advanced for subsequent testing. Measured traits recorded for each plot in each trial will include grain yield, seed weight, early plant vigor, plant height, growth habit, flowering date and maturity, days to seed fill, biomass, pod wall ratio, Normalized Difference Vegetation Index (NDVI), and canopy temperature. Individual populations will be chosen for use in the Genome Wide Association Study (GWAS) to detect genomic regions under selection in different stress environments. Resistance to halo blight in beans will be improved by combining HB4.2 and HB5.1 QTL with major genes Pse-2 and Pse-3, which can produce lines that have durable resistance to all nine differential races of the pathogen Pseudomonas syringae. Seed quality and yield potential will be improved in pinto beans by developing lines through crosses between the new pinto germplasm releases USPT-WM-12 and PRP 153 and commercial pinto varieties. If no useful QTLs for abiotic stress resistance in beans are detected then these traits will be improved by phenotypic selection. Pea germplasm from the NPGS Pea Core Collection, commercial pea cultivars and advanced breeding lines will be screened for resistance to Bean Leaf Roll Virus (BLRV). Germplasm with resistance to BLRV will be identified that can be used in breeding programs to develop resistant cultivars.

Progress Report
In support of Objective 1, seed was increased for two inbred pinto bean populations (350 lines) for use in field experiments to study drought tolerance. Two different inbred pinto bean populations (340 lines) were characterized for resistance to white mold disease in the field. Genetic markers for a major gene controlling resistance to white mold were generated and are being used for breeding improved pinto bean germplasm lines. Genomic analyses of 600 bean lines and 1200 individual plants from segregating populations revealed a mutation that knocks out a gene (bZIP) involved in DNA transcription into RNA. Bean common mosaic necrosis virus (BCMNV) requires that beans have this gene in order for the virus to be able to fully infect plants. The bZIP mutation is now used as a marker to select beans that have the bc-u virus resistance gene. This is the first reported discovery of a bZIP gene in bean involved in disease resistance. The relationship between the geographic origin of pea samples (accessions) and their resistance to Pea seedborne mosaic virus (PSbMV) was determined. This knowledge helps identify additional pea samples that may be disease resistant based on their geographic origin. In support of Objective 2, dry bean breeding nurseries for disease, drought, and preliminary and advanced yield trials, comprising 270 lines and 1080 research plots were planted in 2021. Two new “environmentally friendly” pinto bean varieties “USDA-Diamondback” and “USDA-Basin” with resistance to Bean common mosaic virus (BCMV) and tolerance to drought and low soil fertility stresses were released by the Office of Technology Transfer and plant variety protection certificates were submitted for these varieties to the United States Patent and Trade Office (USPTO). The pea aphid, Acyrthosiphon pisum, was used to screen 279 pea lines from the Pisum core collection for resistance to Bean leafroll virus (BLRV) under greenhouse conditions. Four commercial pea varieties currently grown in the United States were also evaluated. Twenty-three samples from seventeen countries were identified that were totally resistant to BLRV. These sources of disease resistance are being used by breeders to develop new varieties that combine enhanced disease resistance with improved nutritional qualities.

Accomplishments
1. New environmentally friendly ‘slow darkening’ pinto bean cultivar released. Pinto beans are the most widely grown dry bean market class in the United States. ARS researchers in Prosser, Washington, released a new pinto bean cultivar “USDA-Diamondback”, which was developed for superior seed quality and performance under both low and high input production systems. USDA-Diamondback exhibits tolerance to drought and low soil fertility that allows it to be grown with less water and fertilizer. USDA-Diamondback has the new slow darkening seed coat trait that helps it maintain excellent seed quality despite adverse weather during harvest or prolonged storage. A major seed company is interested in licensing this versatile pinto bean cultivar with enhanced seed quality that has excellent yield potential under less favorable growing conditions.

2. Genetic resistance to Bean leafroll virus identified in pea genetic resources. Bean leafroll virus (BLRV) is a major pathogen impacting pea production in the United States and new pea varieties with improved resistance to this disease are needed. ARS researchers at Prosser, Washington, evaluated 279 different pea samples for resistance to BLRV. Twenty-three samples from 17 countries were identified that were totally resistant to BLRV. These sources of disease resistance are being used by breeders to develop new varieties that combine enhanced disease resistance with improved nutritional qualities.

3. Improved understanding of the genetic control of virus resistance in common bean. Bean common mosaic virus (BCMV) reduces yield and quality of common bean in the United States and worldwide. The best strategy to control the disease is to develop new varieties with improved resistance, which unfortunately is controlled by complex interactions between multiple resistance genes. ARS researchers in Prosser, Washington, developed DNA markers for two different resistance genes, bc-1 and bc-u, and determined that the bc-u gene alone delays symptoms and enhances resistance when combined with bc-1. This new knowledge solved a question that bean breeders have been asking for more than 40 years about the genetic control of resistance to BCMV, and the new DNA markers are being used to accelerate the development of new bean varieties with improved disease resistance.

Review Publications
Swisher Grimm, K.D., Porter, L.D. 2021. KASP markers reveal established and novel sources of resistance to Pea seed-borne mosaic virus in pea genetic resources. Plant Disease. https://doi.org/10.1094/PDIS-09-20-1917-RE.
Williamson-Benavides, B.A., Sharpe, R., Nelson, G., Bodah, E.T., Porter, L.D., Dhingra, A. 2020. Identification of Fusaruim solani f. sp. pisi (Fsp) responsive genes in Pisum sativum. Frontiers in Genetics. 11. Article 950. https://doi.org/10.3389/fgene.2020.00950.
Beaver, J., Estevez, C., Miklas, P.N., Porch, T.G. 2020. Contributions in Puerto Rico to Phaseolus spp. research. Journal of Agriculture of the University of Puerto Rico. 104(1):43-111. https://doi.org/10.46429/jaupr.v104i1.18287.
Miklas, P.N., Osorno, J., Cichy, K.A. 2020. Agronomic performance and cooking quality characteristics for slow darkening pinto beans. Crop Science. 60(5):2317-2327. https://doi.org/10.1002/csc2.20220.
Soltani, A., Walter, K.A., Wiersma, A., Santiago, J.P., Quiqley, M., Chitwood, D., Sharkey, T.D., Porch, T.G., Miklas, P.N., McClean, P.E., Osorno, J.M., Lowry, D.B. 2021. Loss of physical seed dormancy, a major domestication trait in common bean, is likely caused by a single loss-of-function mutation. Biomed Central (BMC) Plant Biology. 21, Article 58. https://doi.org/10.1186/s12870-021-02837-6.
Soler-Garzon, A., Oladzadabbasabadi, A., Beaver, J., Beebe, S., Lee, R., Lobaton, J., Macea, E., Mcclean, P., Raatz, B., Rosas, J.C., Song, Q., Miklas, P.N. 2021. NAC candidate gene marker for bgm-1 and interaction with QTL for resistance to Bean golden yellow mosaic virus in common bean. Frontiers in Plant Science. 12. Article 628443. https://doi.org/10.3389/fpls.2021.628443.
Richard, M., Gratias, A., Alvarez Diaz, J., Thareau, V., Pflieger, S., Meziadi, C., Blanchet, S., Miklas, P.N., Marande, W., Bitocchi, E., Papa, R., Geffroy, V. 2021. A common bean truncated CRINKLY4 kinase controls gene-for-gene resistance to the fungal pathogen Colletotrichum lindemuthianum. Journal of Experimental Biology. 72(10):3569-3581. https://doi.org/10.1093/jxb/erab082.
Garcia, C., Campa, A., Soler-Garzon, A., Miklas, P.N., Ferreira, J. 2021. GWAS of pod morphological and color characters in common bean. Biomed Central (BMC) Plant Biology. 21. Article 184. https://doi.org/10.1186/s12870-021-02967-x.
Soler-Garzon, A., McClean, P., Miklas, P.N. 2021. Genome-wide association mapping of bc-1 and bc-u reveals candidate genes and new adjustments to the host-pathogen interaction for resistance to Bean common mosaic necrosis virus in common bean. Frontiers in Plant Science. 12. Article 699569. https://doi.org/10.3389/fpls.2021.699569.