Location: Grain Legume Genetics Physiology Research
2022 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 recombinant inbred dry bean populations. One population with 200 inbred lines will be used to study the inheritance of genetic resistance to white mold disease in red beans. The other population of 90 inbred lines will be used to characterize an unknown gene influencing resistance to Bean common mosaic virus disease in common bean. Genomic analyses of 300 bean lines and 900 individual plants from segregating populations revealed mutations underlying the recessive genes bc-2 on chromosome 11 and newly discovered bc-4 on chromosome 5. These mutations knock out copies of the same gene (ESCRT) influencing protein transport located on different chromosomes. Bean common mosaic virus requires only one copy of this transport gene to fully infect plants. Thus, it was found that both bc-2 and bc-4 genes are necessary for resistance. The ESCRT mutations are used as markers to select beans with the bc-2 and bc-4 virus resistance gene combination. This is the first reported discovery of ESCRT genes in bean involved in disease resistance. We developed assays for 39 markers linked to 24 resistance genes influencing 7 traits: resistance to Bean common mosaic virus, Beet curly top virus, Bean golden yellow mosaic virus, anthracnose, common bacterial blight, rust, and white mold diseases. Several genes have multiple markers because the best marker has not been identified yet. Other genes have multiple markers listed because each marker detects a different causal mutation within the candidate gene, an approximate 10,000 bp deletion in pinto and point mutation in navy beans underlie the bc-2 gene. These marker assays were made publicly available on the Bean Improvement Cooperative website. Pea germplasm accessions (191 plant introductions) from the Pea Single-Plant-Derived Core Collection were screened in two separate experiments for resistance to Fusarium root rot caused by Fusarium avenaceum in a greenhouse. The results from these screenings will be used in a genome-wide association mapping study to identify quantitative trait loci associated with the resistance. In addition, the plant introductions PI 166159 and PI 250441 demonstrating the best root rot resistance in the Pisum Core Collection were crossed with commercial pea cultivars to generate segregating populations to further study the inheritance of resistance while simultaneously transferring the resistance into better adapted materials useful to breeders interested in improving resistance to this soilborne pathogen.
In support of Objective 2, dry bean breeding nurseries for disease, drought, and preliminary and advanced yield trials, comprising 405 lines and 2440 research plots were planted in 2022. Three new “environmentally friendly” dry bean varieties “USDA Cody” pinto, “USDA Lava” red, and “USDA Sunrise” pink beans 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 for these varieties will be submitted to the U.S. Patent and Trade Office (USPTO). Pisum abyssinicum lines (19) from the Western Regional Plant Introduction Station were screened using viruliferous pea aphids to determine resistance to the Bean leafroll virus. These lines can potentially be used in breeding programs to introduce better resistance to Bean leafroll virus in commercial pea cultivars.
Accomplishments
1. New environmentally friendly dry bean cultivars released. ARS researchers in Prosser, Washington, released new pinto “USDA Cody”, red “USDA Lava” and pink “USDA Sunrise” bean cultivars which were developed for superior seed quality and performance under both low and high input production systems. USDA Cody exhibits tolerance to low soil fertility which allows it to be grown with less fertilizer. USDA Lava has early maturity which benefits delayed plantings. USDA Sunrise is tolerant to drought which allows it to be grown with less water. A prominent seed company is interested in licensing these versatile dry bean cultivars because of their excellent yield potential under less favorable growing conditions.
2. 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 scientists in Prosser, Washington, developed DNA markers for two different resistance genes, bc-2 on chromosome 11 and the newly discovered bc-4 gene on chromosome 5, and determined that both genes need to be present in combination to condition resistance to BCMV. This new knowledge fills gaps 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.
3. Genetic resistance to Fusarium avenaceum identified in lentil can benefit identifying the same resistance in pea. Fusarium root rot caused by Fusarium avenaceum is a major root rot pathogen on pea and lentil in North Dakota, Montana, and Canada. ARS researchers at Prosser and Pullman, Washington, evaluated 181 lentil lines from the Lentil Single-Plant-Derived Core Collection for resistance to F. avenaceum. These lines were used to determine eleven quantitative trait loci across four chromosomes associated with the resistance. Two potential genes coding for a nonsymbiotic hemoglobin protein (MEDsa GLB1) and an ethylene response factor were identified as excellent candidate genes conferring resistance to the pathogen. These genes can be targeted for marker-assisted selection to rapidly identify breeding lines with genetic resistance in lentil to the pathogen and can be evaluated in pea to determine if these same genes correlate across closely related species.
Review Publications
Heineck, G.C., Altendorf, K.R., Coyne, C.J., Ma, Y., McGee, R.J., Porter, L.D. 2022. Phenotypic and genetic characterization of the lentil single plant-derived core collection for resistance to root rot caused by Fusarium avenaceum. Phytopathology. 112(9):1979-1987. https://doi.org/10.1094/PHYTO-12-21-0517-R.
Wang, M., Van Vleet, S., McGee, R.J., Paulitz, T.C., Porter, L.D., Schroeder, K., Vandemark, G.J., Chen, W. 2021. Chickpea seed rot and damping-off caused by metalaxyl-resistant Pythium ultimum and its management with ethaboxam. Plant Disease. 105(6):1728-1737. https://doi.org/10.1094/PDIS-08-20-1659-RE.
Viscarra-Torrico, R., Pajak, A., Garzon, A., Zhang, B., Pandurangan, S., Diapari, M., Song, Q., Conner, R.L., House, J.D., Miklas, P.N., Hou, A., Marsolais, F. 2021. Common bean (Phaseolus vulgaris L.) with increased cysteine and methionine concentration. Legume Science. https://doi.org/10.1002/leg3.103.
MacQueen, A.H., Khoury, C.K., Miklas, P.N., McClean, P.E., Osorno, J.M., Runck, B.C., White, J.W., Kantar, M.B., Ewing, P.M. 2022. Local to continental-scale variation in fitness and heritability in common bean. Crop Science. 62(2):767-779. https://doi.org/10.1002/csc2.20694.
Keller, B., Ariza-Suarez, D., Portilla-Benavides, A., Buendia, H., Aparicio, J., Amongi, W., Mbiu, J., Nchimbi-Msolla, S., Miklas, P.N., Porch, T.G., Burridge, J., Mukankusi, C., Studer, B., Raatz, B. 2022. Genomic predictions in climbing beans and their genetic associations with bush bean populations. Frontiers in Plant Science. 13. Article 830896. https://doi.org/10.3389/fpls.2022.830896.
