Location: Grain Legume Genetics Physiology Research
2023 Annual Report
Objectives
Objective 1: Determine yield response and identify yield limiting factors of edible legume germplasm when grown under abiotic stress and managed using different production systems.
Sub-objective 1A: Assess inoculant effects on winter survivability, root rhizobial biodiversity, nitrogen fixing capacities, and yield of direct-seeded advanced edible winter pea (Pisum sativum L.) cultivars in a winter wheat crop rotation.
Sub-objective 1B: Identify novel pea germplasm with cold and drought tolerance, in the presence or absence of Rhizobium, to improve food-grade winter pea production across different agro-ecological environments.
Objective 2: Enhance G x E x M to develop biotic stress-resilient edible legume cropping systems that improve sustainable production.
Sub-objective 2A: Assess the G x E x M interactions of multiple bean genotypes to white mold under different tillage, fertilization and irrigation practices.
Sub-objective 2B: Identify and determine Fusarium root rot genetic resistance and the effect of seed treatments on root rot severity, rhizobial formation and winter survival in winter pea under different agro-ecological environments.
Approach
Sub-objective 1A:
Hypothesis: Winter peas will interact favorably with Rhizobium inoculants to improve winter survival, seed nutritional qualities, yield, and soil health.
Approach: Ten food-grade, cold tolerant, winter peas will be grown at two locations. Presence of Rhizobium inoculant on emergence, root nodulation, chlorophyll content, plant height, root/shoot dry weight, root disease severity, rhizobial diversity, soil nitrogen, seed composition, and seed yield/quality over multiple years will be evaluated.
Sub-objective 1B:
Goal: Identify novel pea germplasm from worldwide collections useful for improving cold and drought tolerance in food-grade winter pea cultivars.
Approach: Pea lines evaluated will be screened for cold tolerance (CT) under natural conditions. Lines with CT will be evaluated for drought and disease tolerance in seven rainfall zones. The five highest yielding lines with the best cold and drought tolerance across rainfall zones will be grown at the three lowest rainfall zones and presence/absence of Rhizobium inoculant on these lines evaluated.
Sub-objective 2A:
Goal: Identify G x E x M interactions that improve control of white mold disease of bean.
Approach: Three tillage (conventional, minimum, and no-till) treatments will be evaluated in alternating strips across a field. Two irrigation treatments, 80 and 100 percent evapotranspiration, will be imposed at flowering through maturity. Eight lines will be assessed across tillage x irrigation combinations. Traits measured will include: emergence, stand vigor, flowering date, canopy porosity, lodging, canopy height, normalized difference vegetation index, canopy coverage, canopy temperature, disease incidence/severity, above ground biomass, yield, and seed weight.
Sub-objective 2B:
Goal: Identify genetic resistance and fungicidal seed treatment combinations effective against Fusarium root rot (FRR) species impacting winter pea across different precipitation zones.
Approach: Twelve winter pea fields from six precipitation zones in Washington will be assessed for FRR at four growth stages and species identified. Pea lines from the Pisum Core Collection and cold-tolerant lines identified in Sub-objective 1B will be screened for resistance to the two major FRR species and association and bi-parental mapping populations used to determine quantitative trait loci associated with the resistance. Four winter pea lines with the best CT, resistance to FRR, and yield will be planted in three precipitation zones in Washington and treated with four fungicidal seed treatments to determine best management practices for FRR.
Progress Report
This is the final report for project 2090-21000-003-000D, “Developing Abiotic and Biotic Stress-Resilient Edible Legume Production Systems through Directed G x E x M Research”, which has been replaced by new project, 2090-21000-039-000D, “Improving Resilience of Dryland Legume Cropping Systems through Enhancement of Beneficial Microbiomes”. This new project has been certified. The following progress report provides a summary of the progress that was made on all objectives and sub-objectives over the life of the project.
In support of Sub-objective 1A, ARS researchers in Pullman, Washington, conducted trials to determine the effect of a commercial rhizobial inoculant on winter survivability, root rhizobial diversity, nitrogen fixing capacities, and yield of ten edible winter pea cultivars were planted in the Fall of 2018 (Pullman, Washington), 2020 (Moscow, Idaho), 2021 and 2022 (two sites: Moscow, Idaho and Lind, Washington). The 2018 research trial was severely impacted by extremely dry fall conditions and data could not be obtained from the plots. The 2020, 2021 and 2022 research trials provided excellent results on winter survivability, nitrogen levels in soils before and after planting, yields and seed protein content associated with inoculated and non-inoculated seed. In the 2021 and 2022 trials in Idaho and Washington plant emergence, foliar frost damage, canopy cover, levels of root nodulation, root disease, plant height and dry shoot weights were measured for all treatments. Root nodules were harvested to characterize the nitrogen-fixing bacteria responsible for the observed nodules. Plant and soil DNA from 2021 Idaho location was sent for sequencing. The 2021 Lind, Washington trial was the only trial dramatically impacted by the use of a commercial inoculant that promoted nitrogen fixation in the plants. Inoculated plants in this trial were more robust and higher yielding. The Lind location had never had peas grown in the crop rotation previously, and this may account for the importance of commercial inoculant since native inoculant was present but likely not at sufficient levels to promote plant growth. Soil, root, and nodules samples from 2021 trials in Idaho and Washington and from 2022 trials in Idaho were collected and processed. In addition, the effect of the ten winter pea cultivars on the height, protein content and yield of winter wheat when wheat was planted in rotation with these cultivars was assessed in 2022 and 2023. The nodulation rate of winter pea varieties “USDA-MiCa”, “USDA-Dint”, and “USDA-Klondike” was assessed across 3 locations in Washington in December 2021 and June 2022, and 4 locations in June 2023. A significant variation in nodulation rate between locations was detected for both winter and summer testing. The soil and plant nodule and root tissue were collected for bacterial isolation and microbiome profiling. Plant and soil DNA from 2021-2022 survey was analyzed using 16S rRNA and ITS genes and whole genome sequencing. Several fungal genera, including Didymella and Funneliformis, were differentially represented between the root and nodule microbiomes or between cultivars. Rhizobium was the only genus significantly overrepresented in nodules compared to roots. We identified a single major Rhizobium leguminosarum strains occupying both roots and nodules of plants grown in all locations, and overrepresented in the nodules. A limited number (more than 10) of R. leguminosarum species were unique to nodule tissue and differed between locations. Additionally, two Acidiphilium species were uniquely identified in the nodules at one of the locations. This data indicates that while Washington soils share a common highly competitive winter pea rhizobial symbiont, they also contain symbionts unique to specific locations.
In support of Sub-objective 1B, pea germplasm with cold and drought tolerance were assessed in different environments. In the Fall of 2018, 3,400 pea lines from the Western Regional Plant Introduction Station were evaluated in single row plots for cold and drought tolerance in Prosser, Washington, where the annual rainfall is approximately eight inches. These lines were assessed for plant emergence, cold/drought tolerance, growth vigor and yield. From these lines, 735 lines were selected that demonstrated the best cold/drought tolerance and yield and were planted in the Fall of 2019 and re-evaluated for the same parameters as previously described. From these plants, 63 lines that demonstrated the overall best cold/drought tolerance, growth vigor and yield were selected and grown in three different agro-ecological sites (Othello, Prosser, and Lind, Washington) in the Fall of 2021 and again in 2022 and evaluated for the previously described parameters. Twelve of the 63 lines selected that had excellent cold tolerance (less than 5% frost damage) and high vigor (score of 4 or 5 on a scale from 1 to 5, with 5 being the best) were also evaluated at the Lind and Othello sites in 2021 and in Lind, Othello, and Prosser in 2022 for the impact of a commercial seed inoculant on cold tolerance and yield. The application of a rhizobial seed treatment at the trial sites did not significantly impact cold tolerance of lines.
In support of Sub-objective 2A, ARS researchers conducted field trials each year under severe disease pressure to evaluate dry bean cultivars, germplasm lines, and genetic populations for reaction to Sclerotinia white mold disease. Advanced pinto (five lines), red (three lines), and one great northern bean line were screened for disease resistance across multiple trials. These lines are useful as parents in white mold resistance breeding programs. Multiple genetic populations were screened for reaction to white mold in the greenhouse and field to detect major genes (WM2.2, WM3.1, WM5.4, and WM7.4) involved in resistance to white mold disease. Genetic markers linked with these genes were developed to validate the effectiveness of marker-assisted selection for these genes in a pinto bean breeding program.
In support of Sub-objective 2B, twelve commercial winter pea fields across Washington state representing a wide range of rainfall zones were evaluated in 2018 for Fusarium species causing root rot. Two hundred thirty-four isolations were made of root rot pathogens infecting peas. These pathogens were cultured to purity and characterized to the species level using two genes (internal transcribed spacer region and translation elongation factor 1-alpha). The later gene was successful in characterizing the Fusarium species infecting the roots as F. culmorum, F. flocciferum, F. nirenbergiae, F. oxysporum, F. redolens, F. solani and, F. tardicrescens. F. redolens made up 81.2% of the isolates infecting the peas and was determined to be the principal pathogen of concern. From 2018 to 2020, 444 pea lines and 28 commercial cultivars were screened in greenhouse trials for resistance to Fusarium avenaceum, a major root rot pathogen of dry pea in Montana, North Dakota and Canada. From these lines, the most Fusarium-resistant feed pea, PI 166159 with pigmented seed, and food-grade dry pea, PI 250441 with non-pigmented seed, were identified and crosses were made between these resistant lines and the dry pea cultivar Aragorn to create a population for genetic analysis of resistance to Fusarium root rot resistance. In 2022, 191 lines and in 2023 93 lines were screened in repeated greenhouse experiments for resistance to F. avenaceum. These lines have been genotyped and will be used to map genes associated with root rot resistance in pea. In addition, in the Fall of 2021, five winter pea lines treated with five different fungicide seed treatments used to manage Fusarium root rot were evaluated at two locations (Lind and Othello) and again in the Fall of 2022 at Lind, Othello and Prosser sites to determine the impact of these treatments on cold tolerance, emergence, and yield.
Accomplishments
1. Advanced methods for screening legumes for resistance to Fusarium root rots. Fusarium root rots (FRR) can cause major yield losses in cool season food legumes across the United States. The most economical and environmentally friendly way to manage FRR in legumes is to develop disease resistant varieties. ARS researchers in Pullman, Washington, developed a screening method using lentil and Fusarium avenaceum for effective seed-safe sterilization, optimal inoculation, and visual and automated disease scoring. This system can be used on other legumes to efficiently screen lines for resistance to Fusarium species. The methods developed will improve the ability of breeders and advance disease resistant legume varieties that will improve yeilds for cool season growers.
Review Publications
Ashtari Mahini, R., Kumar, A., Elias, E.M., Fiedler, J.D., Porter, L.D., McPhee, K.E. 2020. Analysis and identification of QTL for resistance to Sclerotinia sclerotiorum in pea (Pisum sativum L.). Frontiers in Genetics. 11. Article 587968. https://doi.org/10/3389/fgene.2020.567968.
Yurgel, S., Johnson, S.S., Rice, J., Sa, N., Baumgartner, J., Pitzer, J.E., Roop, R.M., Roje, S. 2022. A novel formamidase is required for riboflavin biosynthesis in invasive bacteria. Journal of Biological Chemistry. 298(9). Article 102377. https://doi.org/10.1016/j.jbc.2022.102377.
Yurgel, S., Ajeethan, N., Smertenko, A. 2022. Response of plant associated microbiome to plant-root colonization by exogenous bacterial endophyte in perennial crops. Frontiers in Microbiology. Volume 12, Article 863946. https://doi.org/10.3389/fmicb.2022.863946.
Yurgel, S., Sallato, B., Cheeke, T. 2023. Exploring microbial dysbiosis in orchards affected by little cherry disease. Phytobiomes Journal. https://doi.org/10.1094/PBIOMES-10-22-0072-R.
Ajeethan, N., Abbey, L., Ali, S., Fuller, K., Yurgel, S. 2023. Response of apple orchard microbiome to management and plant selective pressure. Microorganisms. 11(6). Article 1372. https://doi.org/10.3390/microorganisms11061372.
Das, S., Porter, L.D., Ma, Y., Coyne, C.J., Chaves-Cordoba, B., Naidu, R.A. 2022. Resistance in lentil (Lens culinaris) genetic resources to the pea aphid (Acyrthosiphon pisum). Entomologia Experimentalis et Applicata. 170(8):755-769. https://doi.org/10.1111/eea.13202.
