Molly Miller Jahn

Knowledge is a critical enabling factor for healthy agri-food innovation systems (AIS). AIS and related knowledge management (KM) frameworks face significant implementation challenges. We review applications of KM to AIS, the current state of the art and shortcomings and present a new KM framework, Agricultural Knowledge Management for Innovation (AKM4I). Previous agricultural KM frameworks do not integrate innovation pragmatically, use linear, reductionist, top-down pathways to innovation, and do not explicitly incorporate issues of power, politics, ownership, and trust when combining scientific and local knowledge across multiple stakeholders. The AKM4I framework addresses systemic interactions favouring innovation outcomes by formalising flows and management of information and knowledge between diverse sets of stakeholders; and explicitly considering previously unresolved practical and relational barriers aiming to facilitate more equitable, rapidly evolving, and actionable knowledge generation and management for innovation and transformational change. An agricultural case study serves as an example of the implementation of AKM4I.

There are few reliable data sets to inspire confidence in policymakers that soil organic carbon (SOC) can be measured on farms. We worked with farmers in the Tamar Valley region of southwest England to select sampling sites under similar conditions (soil type, aspect and slope) and management types. Topsoils (2–15 cm) were sampled in autumn 2015, and percentage soil organic matter (%SOM) was determined by loss on ignition and used to calculate %SOC. We also used the stability of macroaggregates in cold water (WSA) (‘soil slaking’) as a measure of ‘soil health’ and investigated its relationship with SOC in the clay‐rich soils. %SOM was significantly different between management types in the order woodland (11.1%) = permanent pasture (9.5%) > ley‐arable rotation (7.7%) = arable (7.3%). This related directly to SOC stocks that were larger in fields under permanent pasture and woodland compared with those under arable or ley‐arable rotation whether corrected for clay content ( F = 8.500, p < .0001) or not ( F = 8.516, p < .0001). WSA scores were strongly correlated with SOC content whether corrected for clay content (SOC _adj R ² = .571, p < .0001) or not (SOC _unadj R ² = 0.490, p = .002). Time since tillage controlled SOC stocks and WSA scores, accounting for 75.5% and 51.3% of the total variation, respectively. We conclude that (1) SOC can be reliably measured in farmed soils using accepted protocols and related to land management and (2) WSA scores can be rapidly measured in clay soils and related to SOC stocks and soil management.

Background: Potato virus Y (PVY) is a major pathogen of potatoes with major impact on global agricultural production. Resistance to PVY can be achieved by engineering potatoes to express a recessive, resistant allele of eukaryotic translation initiation factor eIF4E, a host dependency factor essential to PVY replication. Here we analyzed transcriptome changes in eIF4E over-expressing potatoes to shed light on the mechanism underpinning eIF4E-mediated recessive PVY resistance. Results: As anticipated, modified eIF4E-expressing potatoes demonstrated a high level of resistance, eIF4E expression, and an unexpected suppression of the susceptible allele transcript, likely explaining the bulk of the potent antiviral phenotype. In resistant plants, we also detected marked upregulation of genes involved in cell stress responses. Conclusions: Our results reveal a previously unanticipated second layer of signaling attributable to eIF4E regulatory control, and potentially relevant to establishment of a broader, more systematic antiviral host defense.

The importance of building/maintaining soil carbon, for soil health and CO₂ mitigation, is of increasing interest to a wide audience, including policymakers, NGOs and land managers. Integral to any approaches to promote carbon sequestering practices in managed soils are reliable, accurate and cost-effective means to quantify soil C stock changes and forecast soil C responses to different management, climate and edaphic conditions. While technology to accurately measure soil C concentrations and stocks has been in use for decades, many challenges to routine, cost-effective soil C quantification remain, including large spatial variability, low signal-to-noise and often high cost and standardization issues for direct measurement with destructive sampling. Models, empirical and process-based, may provide a cost-effective and practical means for soil C quantification to support C sequestration policies. Examples are described of how soil science and soil C quantification methods are being used to support domestic climate change policies to promote soil C sequestration on agricultural lands (cropland and grazing land) at national and provincial levels in Australia and Canada. Finally, a quantification system is outlined – consisting of well-integrated data-model frameworks, supported by expanded measurement and monitoring networks, remote sensing and crowd-sourcing of management activity data – that could comprise the core of a new global soil information system.

Capsaicinoids are compounds synthesized exclusively in the genus Capsicum and are responsible for the burning sensation experienced when consuming hot pepper fruits. To date, only one gene, AT3, a member of the BAHD family of acyltransferases, is currently known to have a measurable quantitative effect on capsaicinoid biosynthesis. Multiple AT3 paralogs exist in the Capsicum genome, but their evolutionary relationships have not been characterized well. Recessive alleles at this locus result in absence of capsaicinoids in pepper fruit. To explore the evolution of AT3 in Capsicum and the Solanaceae, we sequenced this gene from diverse Capsicum genotypes and species, along with a number of representative solanaceous taxa. Our results revealed that the coding region of AT3 is highly conserved throughout the family. Further, we uncovered a tandem duplication that predates the diversification of the Solanaceae taxa sampled in this study. This pair of tandem duplications were designated AT3-1 and AT3-2. Sequence alignments showed that the AT3-2 locus, a pseudogene, retains regions of amino acid conservation relative to AT3-1. Gene tree estimation demonstrated that AT3-1 and AT3-2 form well supported, distinct clades. In C. rhomboideum, a non-pungent basal Capsicum species, we describe a recombination event between AT3-1 and AT3-2 that modified the putative active site of AT3-1, also resulting in a frame-shift mutation in the second exon. Our data suggest that duplication of the original AT3 representative, in combination with divergence and pseudogene degeneration, may account for the patterns of sequence divergence and punctuated amino acid conservation observed in this study. Further, an early rearrangement in C. rhomboidium could account for the absence of pungency in this Capsicum species.

Pepper mottle virus (PepMoV) is the most common potyvirus infection of pepper plants and causes significant yield losses. The Pvr7 gene from Capsicum chinense PI159236 and the Pvr4 gene from C. annuum CM334 both have been reported to confer dominant resistance to PepMoV. The Pvr7 locus conferring resistance to PepMoV in C. annuum ‘9093’ was previously mapped to chromosome 10. To develop a high-resolution map of the Pvr7 locus in 9093, we constructed an intraspecific F₂ mapping population consisting of 916 individuals by crossing PepMoV-resistant C. annuum ‘9093’ and the PepMoV-susceptible C. annuum ‘Jeju’. To delimit the Pvr7 target region, single-nucleotide polymorphism (SNP) markers derived from the Pvr4 region were used for genotyping the F₂ population. Molecular mapping delimited the Pvr7 locus to a physical interval of 258 kb, which was the same region as Pvr4 on chromosome 10. Three SNP markers derived from Pvr4 mapping perfectly cosegregated with PepMoV resistance. Sequencing analyses of the Pvr7 flanking markers and the Pvr4-specific gene indicated that Pvr7 and Pvr4 are the same gene. Resistance spectrum analysis of 9093 against pepper potyviruses showed that 9093 has a resistance spectrum similar to that of cultivar CM334. These combined results demonstrate that, unlike previously thought, the dominant PepMoV resistance in 9093 could be derived from C. annuum ‘CM334’, and that Pvr4 and Pvr7 should be considered as the same locus.