Alexander E Liu's research while affiliated with Donald Danforth Plant Science Center and other places

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. 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. 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. 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.

Background: The use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of root structure, analyzing the resulting 3D volumes to obtain detailed architectural traits of the root system remains a challenging computational problem. Two types of root features that are notably missing from existing computational image-based phenotyping methods are the whorls of a nodal root system and soil line in an excavated root crown. Knowledge of these features would give biologists deeper insights into the structure of nodal roots and the below- and above-ground root properties. Results: We developed TopoRoot+, a computational pipeline that computes architectural traits from 3D X-ray CT volumes of excavated maize root crowns. TopoRoot+ builds upon the TopoRoot software [1], which computes a skeleton representation of the root system and produces a suite of fine-grained traits including the number, geometry, connectivity, and hierarchy level of individual roots. TopoRoot+ adds new algorithms on top of TopoRoot to detect whorls, their associated nodal roots, and the soil line location. These algorithms offer a new set of traits related to whorls and soil lines, such as internode distances, root traits at every hierarchy level associated with a whorl, and aggregate root traits above or below the ground. TopoRoot+ is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years, and it exhibits reasonable accuracy against manual measurements for both whorl and soil line detection. TopoRoot+ runs in minutes for a typical downsampled volume size of 400³ on a desktop workstation. Our software and test dataset are freely distributed on Github. Conclusions: TopoRoot+ advances the state-of-the-art in image-based root phenotyping by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot+ makes it well-suited for high-throughput image-based root phenotyping.

Introduction 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 plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Methods Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing). Results Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density. Discussion These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

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 their potential impact on soil carbon and nitrogen cycling. Methods Twenty-two cover crop cultivars across the grass, legume, and brassica families were grown in O’Fallon, Missouri. 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 provide the highest percent canopy cover. Cereal rye and winter triticale also generate the highest amount of shoot and root biomass among treatments but exhibit different rooting behavior. Winter triticale forms coarser roots and exhibits deeper rooting, which may be better suited for carbon sequestration. Similarly, 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 taxonomic family highlight the potential to engineer cover crop root system architecture to further enhance ecosystem service efficacy.

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.

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.