Improving the Capacity of Pea Cover Crops to Enhance Soil Health

Progress report for LNE21-428R

Project Type: Research Only
Funds awarded in 2021: $196,658.00
Projected End Date: 02/28/2023
Grant Recipient: University of Vermont
Region: Northeast
State: Vermont
Project Leader:
Dr. Eric Bishop-von Wettberg
University of Vermont
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Project Information


Integrating peas into cropping systems is a sustainable farming practice that helps promote soil health and farm profitability. Despite these benefits, little research has gone into directly improving traits that make pea an effective cover crop. The majority of field pea research has focused on comparing field pea as a cover crop to other species, with little attention to assessing differences between field pea varieties in traits that affect the yield of subsequent crops such as soil nutrient accumulation. This is a shortcoming because some pea varieties are likely more effective cover crops than others. To make pea cover cropping more attractive for farmers, we need to identify superior pea cover crop varieties. As a result, our project will answer two plaguing questions in cover crop research:  1. Do novel pea cover crop varieties improve farm profitability and sustainability in the Northeast?  2. Do novel pea cover crop varieties differ in cover cropping traits, such as beneficial microbe recruitment, soil health improvement, and increasing subsequent crop yields? To address these questions, we will screen 108 novel pea varieties with genomic information. These varieties were strategically selected from wilds, landraces, and under-used modern pea varieties to capture a wide range of phenotypic diversity. The varieties will be initially screened in a greenhouse setting to look at the genetic basis of differences in microbe recruitment, soil health improvement, and increasing yields of a subsequently planted crop. This initial screening will allow us to identify a subset of varieties (~10) that will have the broadest on-farm impact. The selected varieties will then be screened in a randomized complete block design with three replicates per variety in a farm setting, for agronomic and economic performance. More specifically, they will be evaluated on three on-farm sites that vary in soil type for beneficial-microbe recruitment, soil health improvement, and increasing subsequent crop yields. Additionally, we will perform a cost-benefit analysis to quantify the economic effect these varieties have on farm profitability. Lastly, farmer engagement is critical for the success of our project, farmers will be substantially involved during the entirety of the project. For instance, during the conceptualization of this project, we had meetings and sent out surveys to farmers to gather their opinion on field pea cover crops. Their responses, such as, how they best gather new farming information and what traits they are looking for in a field pea have been incorporated into the project. Furthermore, farmers will be consulted throughout to make sure our research is applicable to the farming community and during the selection of varieties that make it to on-farm trials. Collectively, we believe our project can profoundly benefit the Northeast farming community by lowering hurdles to cover cropping.

Project Objective:

The project objective is to identify novel pea cover crop varieties that improve farm profitability and sustainability in the Northeast. To accomplish this goal, we will be screening novel pea varieties that are currently not readily available to farmers, such as wild, landraces, and underutilized-modern cultivars. We will screen varieties for the recruitment of beneficial microbes, soil health improvement, increasing yields of subsequent crops, and their impact on farm profitability through a cost-benefit analysis. The results from this project will promote cover cropping in the Northeast by increasing the productivity and profitability of pea cover crops.


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  • Dr. Rebecca McGee (Researcher)
  • Dr. Edward Marques (Researcher)
  • Bailey Kretzler
  • Heather hassett
  • Justin Rich


Materials and methods:

The USDA recently created the pea single seed descent population panel, PSPPMC to expedite pea improvement efforts. This collection contains 108 Pisum sativum varieties that are morphologically diverse to capture 97.4% of the genetic variation found in world germplasm collections. Included in this collection are wild peas, which are varieties that have not undergone the genetic bottleneck of domestication. Wild varieties tend to have more genetic and phenotypic diversity than domesticated varieties and have been identified as an integral resource for pea improvement. Lastly, each variety in the collection has already been sequenced, providing the ability to associate genetic markers with cover cropping traits. Therefore, this collection is the ideal resource to address our questions.


  1. Methods

YEAR-1: The research objective was to identify pea cover crop varieties that bolster agricultural production and profitability in the Northeast. To accomplish this goal, we screened 108 pea varieties. The varieties were screened at the UVM greenhouse for beneficial-microbe recruitment, soil health improvement, and increasing subsequent crop yields. Greenhouse screening was required because characterizing 108 varieties on working farms is unrealistic due to the associated high cost and the requirement of large plots of land. Four replicates of each variety will be grown in 2-gallon plastic pots at 21°C and 16/8 hour light/dark cycle in a randomized complete block design. The varieties were grown in soil from the UVM Horticulture Research Farm, which allowed for the presence of agricultural microbes [11]. Plants wer watered every other day with no added fertilizer. Additionally, empty soil-filled pots were utilized as a control treatment.


After 50 days (flowering stage), plants were uprooted, and rhizosphere soil samples was collected. In addition, dates of emergence, any flowering, leaf chlorophll content (an estimate of nitrogen content), and above and belowground biomass were collected. The rhizosphere, categorized as the soil clinging to the root once the plant, was uprooted. Rhizosphere samples are still being tested for beneficial-microbe recruitment and soil-health improvement (see below). Subsequently, the "Enchanted" corn variety was planted in the pea-primed soil; this allows us to quantify how pea varieties directly impact subsequent crop yields. "Enchanted" wwas used because it is a neonicotinoid-free and late-season maturing variety. Corn was grown to maturity under the same greenhouse conditions as peas, and dry cob weight has been measured, but not yet analyzed, to quantify yields.


YEAR-2: After initial greenhouse screening, a subset of varieties (~10) that will have the broadest on-farm impact will be chosen by farmers and researchers to continue to on-farm field trials. The varieties will be planted in a randomized complete block design with three replicates per variety and three unplanted control plots at four on-farm sites that vary in soil type. The varieties will be screened again for beneficial-microbe recruitment, soil health improvement, and increasing subsequent crop yields. Approximately 20 g of each variety will be planted at a depth of ~2.54 cm in 2.8 m2 plots [15]. Plots will be irrigated as needed. Plants will be grown for 50 days, after which soil rhizosphere and soil core samples will be collected. In addition, dates of emergence, any flowering, leaf chlorophll content (an estimate of nitrogen content), and above and belowground biomass will be collected. Soil core samples will be used for testing soil health improvement, and soil rhizosphere samples will be tested for beneficial microbe recruitment. The same quantification measurements will be used as in the greenhouse experiment. After pea plants are harvested, the "Enchanted" corn variety will be planted according to the manufacturer’s specification. Once again, the corn will be watered ad libitum and grown to maturity, and dry cob weight will be used to quantify yields.


  1. Data Collection

Soil Health Improvement: To test for soil-health improvement, a portion of the greenhouse soil rhizosphere samples and field soil core samples have been sent to The University of Vermont Agricultural and Environmental Testing Laboratory. The laboratory is testing for pH, % nitrogen, % carbon, % soil organic matter, phosphorus, potassium, aluminum, calcium, copper, iron, magnesium, manganese, sulfur, and zinc. All measurements are key parameters for healthy and productive soils [22]. For both the greenhouse and field studies aboveground biomass and flowering time have been recorded. For the greenhouse study, a subset of the accessions will be selected to undergo root architecture measurements such as specific root length, number of nodules, and belowground biomass.

Beneficial Microbe Recruitment: To test for beneficial-microbe recruitment, microbial DNA has been extracted from soil control pots/plots and pea rhizosphere samples using QIAGEN DNeasy PowerSoil kits. After extraction, DNA samples will be sent to LC Sciences for DNA library preparation, 16S rRNA (V3 and V4 regions), and Internal Transcribed Spacer sequencing (MiSeq sequencer) in the next few weeks. Sequencing data will be processed for amplicon sequence variants (ASVs) using the requisite quality assurances in the Qiime2 and Dada2 pipelines [20]. The taxonomy of the ASVs will be characterized using the Ribosomal Database Project (RDP version 11.3), NCBI 16S Microbial Database, and the Greengenes databases. Importantly, these steps will allow us to identify and quantify the beneficial microbes that the pea varieties recruit.

Cost-Benefit Analysis: We will determine the profitability of pea varieties as a cover crop based on a cost-benefit analysis of cost per acre versus revenue at the end of on-farm trials. USDA NASS custom rates for each field activity (provided by farmers) will be applied to measure costs on a per-acre basis. Cover crop revenue will be determined by factors such as nitrogen (supplied by the varieties) and the projected value of the pea varieties (i.e., sold as forage) [25]. Net revenues will be calculated by subtracting costs from revenue, which then will be compared among varieties.

Identification of Genetic Markers Associated with Cover Cropping Traits: To identify the genetic basis of cover cropping traits, we will conduct a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) associated with cover cropping traits. Additionally, the analysis will help us to narrow the search for the underlying genes responsible for each trait by identifying associated regions of the chromosomes.


Finally, in parallel to the genetic work, we have planted a subset of varieties that are winter hardy.  Some of these are dry pea types used as cover crops.  But others are vegetable types with more edible pods and sweeter seeds, which may better serve in Vermont and northeastern diversified vegetable farms as dual use crops that can be harvested as an early spring vegetable, but serve the ecological functions of a cover crop.


  1. Data Analysis and Presentation of Results


A general linear mixed model with block as a random term will be used to test for significant differences among varieties, effects on soil health measurements, net revenues, and corn yield for greenhouse and field trials. If significant differences are detected at an alpha level of 0.05, a Tukey's post-hoc test will be used to identify significant differences between varieties.

To test for difference in beneficial-microbe recruitment between varieties, alpha and beta diversity will be calculated. ASVs will be used to calculate alpha diversity for varieties using richness, evenness, and Simpson's Diversity index. A one-way ANOVA and a Tukey's post-hoc test (alpha level of 0.05) will be used to detect significant differences between varieties for alpha diversity. Additionally, beta diversity for varieties will be calculated using the Bray-Curtis dissimilarity method. Beta diversity will be analyzed with non-metric multidimensional scaling, permutational multivariate analysis of variance, and an Adonis test (alpha level of 0.05). To test for differences in the abundance of beneficial-microbe recruitment between varieties, a one-way ANOVA and a Tukey's post-hoc test (alpha level of 0.05) with a negative-binomial distribution will be used. Altogether, the results from each analysis will allow us to determine if varieties differ in beneficial-microbe recruitment.

To identify genetic markers associated with cover cropping traits, a linear mixed model GWAS will be conducted using the "SNPrelate" R package to identify associated SNPs for soil health improvement, beneficial-microbial recruitment, and increasing subsequent crop yields [21]. SNPs will be considered significant at a Pvalue threshold of 5×10−8.  Data analysis is currently underway, as plants were harvested in late November.


Research results and discussion:

We have completed weighing plants from our primary experiment, and extracted DNA and sent soil to the UVM agricultural lab for testing.  We are still awaiting results, and consequently have little to report at this time.  We appreciate that the pandemic has slowed the capacity of core facilities and laboratories to process samples, and we are on our timeline.


In our parallel work evaluating a subset of lines with the most potential as dual-use winter vegetable peas and cover crops, we have plants in the ground.  Germination and establishment were good in the fall, but we will not have survival data or taste tests until spring 2022.

Research conclusions:

We have not yet drawn conclusions because we are still awaiting DNA sequence data clarifying levels of microbial diversity.

Participation Summary
3 Farmers participating in research

Education & Outreach Activities and Participation Summary

Educational activities:

10 Consultations
1 Curricula, factsheets or educational tools
1 On-farm demonstrations
1 Tours
3 Webinars / talks / presentations
1 Workshop field days
2 Other educational activities

Participation Summary:

12 Farmers participated
1 Number of agricultural educator or service providers reached through education and outreach activities
Outreach description:

Due to the pandemic, in-person outreach was limited.  We are hopeful this work will expand over the next year as the pandemic eases, and as we have more results to present.  However, we were able to do a tour, workshop, and demonstration as part of the UVM Farmer training program.  We hope for more participation next summer.

We have also set up a UVM Extension webpage with information for new crops for Vermont.  The section on peas is still under development, but we expect this to eventually include factsheets.

We consulted with half the farmers participating in a NRCS CIG project focused on grazing and cover crops.  Although our results are still preliminary, we talked through some of their options as part of our recruiting process.

We also led two 4H Teen Science Cafes, reaching 40 middle and high school students.

Learning Outcomes

Key areas in which farmers reported changes in knowledge, attitude, skills and/or awareness:

As our results come together next year, we expect to ramp up our efforts in this area.

Project Outcomes

5 Grants applied for that built upon this project
2 Grants received that built upon this project
$15,000.00 Dollar amount of grants received that built upon this project
3 New working collaborations
Assessment of Project Approach and Areas of Further Study:

The pandemic has made outreach difficult.  We hope this will ease.

More broadly, we do face the challenge that peas are not particularly prolific.  Consequently, we lack sufficient seeds to distribute them at the scale needed to farmers to plant.  Focusing on vegetable peas that may be planted at a smaller scale is part of our thinking on this.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.