Improving the Capacity of Pea Cover Crops to Enhance Soil Health

Final report for LNE21-428R

Project Type: Research Only
Funds awarded in 2021: $196,658.00
Projected End Date: 08/31/2023
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 strove to 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 screened 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 were 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 screening allowed us to identify traits that we hope will have the broadest on-farm impact. We then evaluated a subset of lines with high cover cropping potential on two on-farm sites that vary in soil type for beneficial-microbe recruitment, soil health improvement, and increasing subsequent crop yields. Additionally, we performed a cost-benefit analysis to quantify the economic effect these varieties have on farm profitability, and key informant interviews to understand constraints on cover crop adoption. Lastly, farmer engagement is critical for the success of our project and farmers have been substantially involved during the entirety of the project to the extent the pandemic has allowed. 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 have been 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 has benefited the Northeast farming community by clarifying hurdles to cover cropping and identifying some ways to lower these hurdles.

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.


Cover crop use has been rapidly increasing in the United States in recent years. In the 2019-2020 SARE national cover crop survey with 1,172 respondents, it was reported that the average acreage of planted cover crops increased by 40% from 2015 to 2019 [1]. Moreover, peas were listed as the second-highest planted legume cover crop by respondents [1]. The popularity of pea cover cropping is primarily due to it being a sustainable agronomic practice that helps promote soil health and farm profitability [2]. Despite these benefits and pea's popularity, minimal effort has gone into improving field pea as a cover crop or rotational partner [3, 4]. The majority of cover cropping research has been focused on comparing cover cropping traits between field pea and other species or species mixtures. In contrast, few studies have investigated differences in cover cropping traits between field pea varieties, such as yield increase in a subsequent crop, nutrient mobilization, beneficial microbe recruitment, or disease suppression. This reflects a larger gap in the crop breeding literature, where the "rotational value" of crops, their impact on subsequent crops, is rarely measured, let alone made the target of breeding [4].  Minimal effort to identify variation between field pea varieties is problematic because some pea varieties may potentially be more effective cover crops. Therefore, to make pea cover cropping more lucrative and advantageous for farmers, we need to first determine if differences in cover cropping traits exist and then identify novel pea varieties that are more effective at cover cropping and increasing farm profitability.

Our preliminary research has shown that pea varieties have highly variable effects on the yield of subsequently planted corn, with a wild pea variety increasing yields the most. This difference was potentially due to increased nutrient mobilization and beneficial microbe recruitment by the wild pea variety. Specifically, this variety increased soil carbon and recruited a higher amount of the beneficial bacteria BRC1, a microbe shown to suppress diseases in crops [5,6]. Furthermore, our results suggest that pea varieties differed in their ability to mobilize soil micro- and macronutrients, with Nepali varieties increasing carbon, nitrogen, manganese, and calcium more effectively than modern pea cultivars. Collectively, our preliminary research highlights that field pea varieties not currently readily available may be more beneficial to farmers because they can increase subsequent crop yields, recruit beneficial microbes, and mobilize nutrients better than commonly used cultivars. Therefore, to breed field pea as a cover crop and rotational partner, we need to further investigate intraspecific variation for cover cropping traits to identify novel field pea varieties that increase farm productivity, sustainability, and profitability. Lastly, this novel sustainable approach can be widely implemented on farms in the Northeast, from large conventional dairies to small diversified vegetable farms and even to home gardens.


Click linked name(s) to expand/collapse or show everyone's info
  • Dr. Rebecca McGee (Researcher)
  • Dr. Edward Marques (Researcher)
  • Bailey Kretzler
  • Heather Hassett
  • Justin Rich
  • Emmanuel Brefo (Researcher)
  • Niloo Nikravesh (Researcher)
  • Dr. Melike Bakir (Researcher)
  • Katherine Morrissey (Researcher)



Do novel pea cover crop varieties improve farm profitability and sustainability in the Northeast? We hypothesized that pea cover crop varieties not readily available, such as wild and landrace varieties; would be more effective at enhancing farm profitability and sustainability in the Northeast than commonly used modern cultivars.

Do novel pea cover crop varieties differ in cover cropping traits, such as beneficial microbe recruitment, soil health improvement, and increasing yields of subsequent crops? We hypothesized that wild and landrace pea varieties would recruit beneficial microbes, increase soil micro- and macronutrients, and increase subsequent crop yields compared to modern cultivars.

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.  We just learned, after project completion, that the population was re-sequenced by Nanoy Bandilla at North Dakota State University to a deeper depth.  The resequencing will provide more markers, giving better resolution, but not changing the fundamental results.

  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 were 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 were watered every other day with no added fertilizer. Additionally, empty soil-filled pots were utilized as a control treatment.  Seedlings that failed to emerge were replaced within a week of initial sowing.


After 50 days (flowering stage), plants were uprooted, and rhizosphere soil samples were 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 allowed us to quantify how pea varieties directly impact subsequent crop yields. "Enchanted" was 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 if they were produced, but not yet analyzed, to quantify yields.  Most corn plants did not set cobs.


YEAR-2: After initial greenhouse screening, we decided to focus on overwintering types, as these have the potential for double cropping in Vermont, where they can overcome cost barriers to adoption better than all other types of peas. We did this in part due to pandemic shifts, but also due to emerging results of our key informant interviews.  Summer pea cover cropping is rare in Vermont.  Peas that are grown in the summer tend to be selected primarily based on agronomic traits (sweetness and appearance in snap and snow peas; protein content and establishment and disease resistance in rarely grown field peas).  Most pea covers are winter-grown, making these pea types more important for our aims.  We grew 17 selected winter types at  Philo Ridge Farm and the UVM horticulture farm.  We lacked sufficient seed to engage further sites, following conversations with farmer partner Justin Rich.  The 25lbs that would have been required for a larger trial at Burnt Rock farm could not be generated from seed stocks of ~100 seeds with which we started. The varieties were instead screened in fall 2022-2023 for beneficial microbe recruitment, soil health improvement, and increasing subsequent crop yields. Approximately 20 g of each variety were planted at a depth of ~2.54 cm in 2.8 m2 plots [15]. Plots were irrigated as needed, particularly on the sandy soil at the UVM horticulture research farm. Plants were grown over the winter, after which soil rhizosphere and soil core samples were collected in spring 2023. The Philo Ridge planting was lost, due to a farm need to use the beds earlier than expected.  However, dates of emergence, any flowering, leaf chlorophyll content (an estimate of nitrogen content), and above and belowground biomass were collected at the UVM hort farm in spring 2023. Soil core samples were used for testing soil health improvement, and soil rhizosphere samples were tested for beneficial microbe recruitment. The same quantification measurements were used as in the greenhouse experiment. After pea plants were harvested, a broader range of crops were planted instead of just corn, allowing us to track yield of others crops. We hope to submit the draft manuscript from this work in February 2024, after taking in updated genotype data from Dr. Nanoy Bandilla at North Dakota State University (Kretzler, Marques, et al. In preparation for Plants People Planet)

  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 were sent to The University of Vermont Agricultural and Environmental Testing Laboratory. The laboratory tested 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. 

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 were 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 was processed for amplicon sequence variants (ASVs) using the requisite quality assurances in the Qiime2 and Dada2 pipelines [20]. The taxonomy of the ASVs was characterized using the Ribosomal Database Project (RDP version 11.3), NCBI 16S Microbial Database, and the Greengenes databases. Importantly, these steps have allowed us to identify and quantify the beneficial microbes that the pea varieties recruit.  In particular, we have found members of the Gemmatimonadetes, Armatimonadetes, and Planctomycetes that we previously found to be associated with increased corn yields (Marques et al, in review).  This analysis is complete, and we are currently writing the manuscript from it (Kretzler, Marques, et al, expected February 2024).

Cost-Benefit Analysis: We determined 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, using existing cost calculators. USDA NASS custom rates for each field activity (provided by farmers, up to 60lb/acre, although lower if planted with a cereal) were applied to measure costs on a per-acre basis. Cover crop revenues were determined by factors such as nitrogen (supplied by the varieties) and the projected value of the pea varieties (i.e., sold as forage or harvested as a snap pea) [25]. Net revenues were calculated by subtracting costs from revenue, which then were compared among varieties.   We compared several cost calculators available on the web, finding the one from North Dakota easiest to use but likely inaccurate in the northeast, and those Penn State ( and Maine ( useful as background but not up to date for calculations.

Along the way, our thinking on this aim however has changed with the emergence of winter-viable vegetable pea types.  Overwintering peas that can be harvested early in spring greatly change the economic dynamics of a cover crop.  When a cover crop is harvested, it becomes far more useful.  Even if it breaks even as a crop when labor and seeds and other inputs are tabulated, its environmental benefit is still there.  Consequently, we view this as an important step, as it creates a situation where cover cropping is not a loss, but a potential money maker.

We also performed a qualitative analysis with key informant interviews to identify barriers to using overwintering peas as dual-use cover crops, and other barriers to peas as a cover crop.  We interviewed 10 experts in a snowball fashion, based on an interview guide.  

Identification of Genetic Markers Associated with Cover Cropping Traits: To identify the genetic basis of cover cropping traits, we have conducted a genome-wide association study (GWAS) to identify single-nucleotide polymorphisms (SNPs) associated with cover cropping traits. Additionally, the analysis helps us to narrow the search for the underlying genes responsible for each trait by identifying associated regions of the chromosomes.  This analysis is complete, although in the past week we learned that it should be performed.  The initial genotyping done by Rebecca McGee, Michael Mazourek, and colleagues entailed a "genomic reduction" step to sequence only ~1% of the pea genome.  Since they performed this work in 2018, a complete genome sequence for pea has been completed by a French group in 2022.  Dr. Nanoy Bandilla at North Dakota State University has used that development to sequence a larger portion of the genome of each of the pea accessions in our study.  This updated data, to which we are arranging access, will give us better resolution.  We hope to be able to complete this reanalysis by February 2024, although we do not expect the general trends of our study to change.


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 was used to test for significant differences among varieties, effects on soil health measurements, net revenues, and corn yield for greenhouse and field trials. Significant differences were detected at an alpha level of 0.05, and a Tukey's post-hoc test was used to identify significant differences between varieties.

To test for differences in beneficial-microbe recruitment between varieties, alpha and beta diversity were calculated. ASVs were 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) were used to detect significant differences between varieties for alpha diversity. Additionally, beta diversity for varieties was calculated using the Bray-Curtis dissimilarity method. Beta diversity was 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 were used. Altogether, the results from each analysis 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 was conducted using the "SNPrelate" R package to identify associated SNPs for soil health improvement, beneficial-microbial recruitment, and increasing subsequent crop yields [21]. SNPs were considered significant at a Pvalue threshold of 5×10−8.  We are redoing the analysis because Nanoy Bandilla at NDSU has generated a new set of sequences at greater depth, allowing us to a analysis that can better narrow our resolution of particular genomic intervals.  This will slow publication but is unlikely to change any big-picture trends in our analysis.

Research results and discussion:

We have completed greenhouse work from our primary experiment, and extracted DNA and sent soil to the UVM agricultural lab for testing.  We have processed the sequencing results.  The pandemic has slowed the capacity of core facilities and laboratories to process samples. Based on sequencing of soil microbial communities, we found different microbial taxa associated with the roots of elite cultivars, landraces, and wild peas in the diversity panel.  This suggests that human selection, particularly modern breeding, has altered soil microbial associations in peas.  We are unable to paste in figures that better show this.  Our GWAS analysis shows that there are several chromosomal locations that underlie both the differences in soil microbe associations as well as leaf elemental profiles.  We hope to be able to update this result with more confidence after re-performing the analysis with updated marker data from Dr. Nanoy Bandilla.  We are hopeful that some of our results, which are more upstream than some SARE projects, will still prove useful for future breeding efforts in any type of pea.


In our work evaluating a subset of lines with the most potential as dual-use winter vegetable peas and cover crops, we have completed the collection and analysis. We expect to submit a second manuscript on this work (Brefo et al, to be submitted to Agrosystems, Geoscience, and Environment, hopefully by March 2024).  We think that overwintering vegetable types, which are dual-use (ie, harvestable) have the greatest potential to expand the use of pea cover crops in the far Northeast.  On small farms and gardens they are likely to give farmers an extra vegetable and protect and enrich the soil through the winter.

We still acknowledge that there are a high number of barriers to farmer adoption of winter peas.  Our key informant interviews were very persuasive in convincing us that major barriers remain.  Chief among these are seed cost and farm operations.  Austrian winter peas are expensive (approaching ~$50 for a 50lb bag).  By using the NDSU and Penn State Farm calculators it looks like the cost of seed could be offset by harvesting a pea crop (depending on labor costs) and nitrogen credits for the subsequent crop.   As overwintering vegetable peas are not widely available, the cost of this seed is not easy to estimate.  Yet, this cost could likely be recouped if Northern New England farmers were able to truly double crop by using overwintering peas.  However, farm labor is valuable, and finding time to plant in fall, and potential harvest in spring is just hard.  Furthermore, the value of spring fresh peas is relatively limited, as indicated by a few key informants who were not sure they could sell them.  Furthermore, peas have to be done by the end of May to be practical for double cropping in Vermont's Champlain Valley, and they tend to not be mature until June or even July.  Furthermore, even if peas can be harvested (for people or animals), many farms lack the labor to handle a pea harvest at a time when summer crops need to be planted.  So, although peas are a valuable cover crop due to their capacity to fix ~150 lbs/acre of nitrogen, and that harvesting them increases their value, logistics of farm operations pose significant hurdles.

Nevertheless, beyond this project, we are picking up discussions with regional seed companies to look at options for distributing more overwintering pea seeds, and hopefully lowering costs.  We are also distributing some of the seeds (which lack IP protection) to local seed savers through the UVM master gardener program.  We are hopeful that local seed saving will lead to the emergence of landraces with better adaptation to Northern New England. Although overwintering double cropped peas may have a narrow niche, we still hope they have a niche.

Research conclusions:

Our analysis of the pea diversity panels identified few candidate loci/chromosomal regions associated with increasing corn biomass in peas.  Our work does suggest that there are a number of beneficial microbes that can be identified, and some intriguing markers that will be useful for future breeding.

More broadly, we have come to conclude that the most viable cover crops are those that can be harvested.  Economic calculations become more positive when there is a harvest of the cover crop. Vegetable peas, which are harvested either as small shoots or immature pods (snap, snow peas) can be harvested from specific varieties.  These varieties have been crossed with winter-hardy Austrian field peas by the USDA pea breeding program.  We feel that these peas have the greatest potential to fill the need for overwintering peas for cover crops.  We hope that distributing these to regional seed companies and seed savers will bring these to fruition.

Participation Summary
10 Farmers participating in research

Education & Outreach Activities and Participation Summary

Educational activities:

10 Consultations
1 Curricula, factsheets or educational tools
1 Journal articles
1 On-farm demonstrations
1 Published press articles, newsletters
1 Tours
5 Webinars / talks / presentations
1 Workshop field days

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 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 expect to expand this to other legumes. The web page is found here:

We consulted with half the farmers participating in a NRCS CIG project focused on grazing and cover crops.  

We also led three 4H Teen Science Cafes, reaching 60 middle and high school students.  We also did two Science Cafes for the general public.

An article was produced for the Maine Organic Gardener association on using overwintering peas as a dual use cover crop and green vegetable. The Green Peas of Spring_ Overwintering Snap Peas as a Cover Crop and Early Season Vegetable - Maine Organic Farmers and Gardeners


Learning Outcomes

4 Farmers reported changes in knowledge, attitudes, skills and/or awareness as a result of their participation
3 Service providers reported changes in knowledge, attitudes, skills and/or awareness as a result of project outreach
3 Educators or agricultural service providers reported changes in knowledge, skills, and/or attitudes as a result of their project outreach
Key areas in which farmers reported changes in knowledge, attitude, skills and/or awareness:

Feedback on our MOFGA publication and conversations in our key informant interviews suggests that growers are intrigued by the idea of double cropping.  They are also generally impressed with the genetic gains being made in winter pea cold hardiness.  Some farmers, such as our advisor and partner Justin Rich, are interested in improvements in Nitrogen fixation that might allow a farmer to make better estimates of nitrogen credits from peas.

Project Outcomes

7 Grants applied for that built upon this project
4 Grants received that built upon this project
$75,000.00 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 made outreach difficult.  We hope that although this project is done, we can keep doing more in person outreach. This winter we will be at NOFA VT, as we have the last few years.  We were unable to get onto the VT and NE Veg and Berry growers schedules this winter, but hope our research is viewed more favorably next year.

We have also developed a new relationship with the UVM Master Gardener program, which we hope will allow us to more effectively engage stakeholders.  We think this is particularly effective for overwintering vegetable peas, which are suitable for smaller growers or even gardeners.  This relationship may be our greatest success in the long term.

More broadly, we do face the challenge that peas are not particularly prolific or valuable as a vegetable or forage.  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.