Alexander E. Liu

Background and aims: Cover crops have the potential to aid in adapting agricultural systems to climate change impacts through their ecosystem services, such as preventing soil erosion, remediating soil structure, and storing carbon belowground. Though roots are integral to these processes, there is a lack of cover crop root trait data. This study aims to characterize rooting behavior of several commercially available cover crops and assess how differences in root system architecture potentially impact their selection for ecosystem services. Methods: Twenty-two cover crop cultivars across the grass, legume, and brassica families were grown in O’Fallon, Missouri, USA. Canopy cover was monitored throughout the growing season. Shoot and root biomass samples were collected and analyzed. Results: Cereal rye and winter triticale were the most winter hardy cultivars and provided the highest percent canopy cover. Cereal rye and winter triticale also generated the highest amount of shoot and root biomass among treatments but diverged in their root system architectures. Winter triticale forms coarser roots and exhibited deeper rooting, which may be better suited for carbon sequestration. Rapeseed and Siberian kale have favorable C:N ratios for nutrient recycling, but rapeseed may invest more into lateral root formation and have a higher potential to “catch” excess nutrients. Conclusion: Selection of cover crops for ecosystem services should account for root system architecture and their suitability for these ecosystem services. Differences in root traits among cultivars within the same family highlight the potential to breed cover crop root system architecture to further enhance ecosystem service efficacy.

1 Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress ( Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand adaptive responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Using a root imaging and analysis pipeline, 4D pennycress root system architecture was characterized under four nitrate regimes (from zero to high nitrate concentration) across four time points (days 5, 9, 13, and 17 after sowing). Significant nitrate condition response and genotype interactions were identified for many root traits with greatest impact on lateral root traits. In trace nitrate conditions a greater lateral root count, length, interbranch density, and a steeper lateral root angle was observed compared to high nitrate conditions. Genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density. These results illustrate root trait variance available in pennycress accessions that could be useful targets for breeding of improved nitrate responsive cover crops for greater productivity, resilience, and ecosystem service.

Small RNAs, including microRNAs (miRNAs), phased secondary small interfering RNAs (phasiRNA), and heterochromatic small interfering RNAs (hc‐siRNA) are an essential component of gene regulation. To establish a broad potato small RNA atlas, we constructed an expression atlas of leaves, flowers, roots, and tubers of Desiree and Eva, which are commercially important potato (Solanum tuberosum) cultivars. All small RNAs identified were observed to be conserved between both cultivars, supporting the hypothesis that small RNAs have a low evolutionary rate and are mostly conserved between lineages. However, we also found that a few miRNAs showed differential accumulation between the two potato cultivars, and that hc‐siRNAs have a tissue specific expression. We further identified dozens of reproductive and non‐reproductive phasiRNAs originating from coding and noncoding regions that appeared to exhibit tissue‐specific expression. Together, this study provides an extensive small RNA profiling of different potato tissues that might be used as a resource for future investigations.

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical, and biotic properties of soil. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. Here I will present root phenotyping approaches for assessing ecosystem service in a prospective cash cover crop; pennycress (Thlaspi arvense L.). In development is a large format mesocosm system that will allow 3D root system architecture analysis of multiple plants. Using this system, we will be assessing how variation in pennycress root system architecture can affect ecosystem service and abiotic stress tolerance with the plant to scale from single plant to canopy level traits.

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disru...

Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical, and biotic properties of soil. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. Here I will present root phenotyping approaches for assessing ecosystem service in a prospective cash cover crop; pennycress (Thlaspi arvense L.). In development is a large format mesocosm system that will allow 3D root system architecture analysis of multiple plants. Using this system, we will be assessing how variation in pennycress root system architecture can affect ecosystem service and abiotic stress tolerance with the plant to scale from single plant to canopy level traits.

Differences in outputs between Fls3 and Fls2immunity receptors suggest they use distinct mechanisms to activate immunity in tomato.

Plants mount defense responses by recognizing indications of pathogen invasion, including microbe-associated molecular patterns (MAMPs). Flagellin from the bacterial pathogenPseudomonas syringaepv. tomato (Pst) contains two MAMPs, flg22 and flgII-28, that are recognized by tomato receptors Flagellin sensing 2 (Fls2) and Flagellin sensing 3 (Fls3), respectively. It is unknown to what degree each receptor contributes to immunity and if they promote immune responses using the same molecular mechanisms. Characterization of CRISPR/Cas9-generatedFls2andFls3tomato mutants revealed that the two receptors contribute equally to disease resistance both on the leaf surface and in the apoplast. However, striking differences were observed in certain host responses mediated by the two receptors. Compared to Fls2, Fls3 mediated a more sustained production of reactive oxygen species (ROS) and an increase in transcript abundance of 44 tomato genes, with two genes serving as reporters for Fls3. Fls3 had greaterin vitrokinase activity and interacted differently with thePsteffector AvrPtoB as compared to Fls2. Using chimeric Fls2/Fls3 proteins, we found that no receptor domain was solely responsible for the Fls3 sustained ROS, suggesting involvement of multiple structural features. This work reveals differences in the immunity outputs between Fls2 and Fls3, suggesting they use distinct molecular mechanisms to activate pattern-triggered immunity in response to flagellin-derived MAMPs.

Summary: The interaction between tomato and Pseudomonas syringae pv tomato (Pst) is a well‐developed model for investigating the molecular basis of the plant immune system. There is extensive natural variation in Solanum lycopersicum (tomato) but it has not been fully leveraged to enhance our understanding of the tomato–Pst pathosystem. We screened 216 genetically diverse accessions of cultivated tomato and a wild tomato species for natural variation in their response to three strains of Pst. The host response to Pst was investigated using multiple Pst strains, tomato accessions with available genome sequences, reactive oxygen species (ROS) assays, reporter genes and bacterial population measurements. The screen uncovered a broad range of previously unseen host symptoms in response to Pst, and one of these, stem galls, was found to be simply inherited. The screen also identified tomato accessions that showed enhanced responses to flagellin in bacterial population assays and in ROS assays upon exposure to flagellin‐derived peptides, flg22 and flgII‐28. Reporter genes confirmed that the host responses were due primarily to pattern recognition receptor‐triggered immunity. This study revealed extensive natural variation in tomato for susceptibility and resistance to Pst and will enable elucidation of the molecular mechanisms underlying these host responses.

The interaction between tomato and Pseudomonas syringae pv. tomato ( Pst ) is a well-developed model for investigating the molecular basis of the plant immune system. There is extensive natural variation in Solanum lycopersicum (tomato) but it has not been fully leveraged to enhance our understanding of the tomato-Pst pathosystem. We screened 216 genetically diverse accessions of cultivated tomato and a wild tomato species for natural variation in their response to three strains of Pst . The screen uncovered a broad range of previously unseen host symptoms in response to Pst , and one of these, stem galls, was found to be simply inherited. The screen also identified tomato accessions that showed enhanced responses to flagellin in bacterial population assays and in reactive oxygen species assays upon exposure to flagellin-derived peptides, flg22 and flgII-28. Reporter genes confirmed that the host responses were due primarily to pattern recognition receptor-immunity. This study revealed extensive natural variation in tomato for susceptibility and resistance to Pst and will enable elucidation of the molecular mechanisms underlying these host responses.