Abstract Food security is a key pillar of environmental security yet remains one of the world’s greatest challenges. Its obverse, food insecurity, negatively impacts health and well-being, drives mass migration, and undermines national security and global sustainable development. Ensuring food security is a delicate balance of myriad concerns within the atmospheric and Earth sciences, agronomy and agriculture engineering, social sciences, economics, monitoring, and policymaking. A Food Security Presidential Session at the American Meteorological Society’s (AMS) 2022 Annual Meeting brought together experts across disciplines to tackle issues at the nexus of weather, climate, and food security. The starkest takeaway was the realization that, despite its importance and clear roles for the atmospheric and climate sciences, food security has not been a focus for the AMS community. The aim of this paper is to build on the perspectives shared by this expert panel and to identify overlapping issues and key points of intersection between the food-security community and AMS. We examine 1) the interactions between weather, climate, and the food system and how they influence food security; 2) the time and spatial scales of food security decision support that match weather and climate phenomena; 3) the role of both providers and users of information as well as decision-makers in improving research to operations for food security; and 4) the opportunities for the AMS community to address food security. We conclude that, moving forward, the AMS community is well-positioned to scale up its engagement across the global food system to address existing scientific needs and technology gaps to improve global food security.

Food security is a key pillar of environmental security yet remains one of the world's greatest challenges. Its obverse, food insecurity, negatively impacts health and well-being, drives mass migration, and undermines national security and global sustainable development. Ensuring food security is a delicate balance of myriad concerns within the atmospheric and Earth sciences, agronomy and agriculture engineering, social sciences, economics, monitoring, and policymaking. A Food Security Presidential Session at the American Meteorological Society's (AMS) 2022 Annual Meeting brought together experts across disciplines to tackle issues at the nexus of weather, climate, and food security. The starkest takeaway was the realization that, despite its importance and clear roles for the atmospheric and climate sciences, food security has not been a focus for the AMS community. The aim of this paper is to build on the perspectives shared by this expert panel and to identify overlapping issues and key points of intersection between the food -security community and AMS. We examine 1) the interactions between weather, climate, and the food system and how they influence food security; 2) the time and spatial scales of food security decision support that match weather and climate phenomena; 3) the role of both providers and users of information as well as decision -makers in improving research to operations for food security; and 4) the opportunities for the AMS community to address food security. We conclude that, moving forward, the AMS community is well -positioned to scale up its engagement across the global food system to address existing scientific needs and technology gaps to improve global food security.

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.

Agriculture contributes nearly a quarter of global greenhouse gas (GHG) emissions, which is motivating interest in certain farming practices that have the potential to reduce GHG emissions or sequester carbon in soil. The related GHG emission (including N2O and CH4) and changes in soil carbon stock are defined here as “agricultural carbon outcomes”. Accurate quantification of agricultural carbon outcomes is the basis for achieving emission reductions for agriculture, but existing approaches for measuring carbon outcomes (including direct measurements, emission factors, process-based modeling) fall short of achieving the required accuracy and scalability necessary to support credible, verifiable, and cost-effective measurement and improvement of these carbon outcomes. Here we propose a foundational and scalable framework to quantify field-level carbon outcomes for farmland, which is based on the holistic carbon balance of the agroecosystem: Agroecosystem Carbon Outcomes = Crops (C) × Management (M) × Environment (E). Following a comprehensive review of the scientific challenges associated with existing approaches, as well as their tradeoffs between cost and accuracy, we propose that the most viable path for the quantification of field-level carbon outcomes in agricultural land is through an effective integration of various approaches (e.g. diverse observations, sensor/in-situ data, modeling), defined as the “system- of-systems” solution. Such a “system-of-systems” solution should simultaneously comprise the following components: (1) scalable collection of ground truth data and cross-scale sensing of crop conditions (C), management practices (M), and environment (E) at the local field level; (2) advanced modeling with necessary processes to support the quantification of carbon outcomes; (3) systematic Model-Data Fusion (MDF), i.e. robust and efficient methods to integrate sensing data and models at each local farmland level; (4) high computation efficiency and artificial intelligence (AI) to scale to millions of individual fields with low cost; and (5) robust and multi-tier validation systems and infrastructures to ensure solution fidelity and true scalability, i.e. the ability of a solution to perform robustly with accepted accuracy on all targeted fields. In this regard, we provide here the detailed scientific rationale, current progress, and future R&D priorities to achieve different components of the “system-of-systems” solution, thus accomplishing the Crop×Management×Environment framework to quantify field-level agricultural carbon outcomes.

Crisis mappers secure satellite imagery, photos, video, event data, incident data, and other documentary evidence to create an operational picture of a disaster in order to facilitate improved humanitarian response and assistance in a crisis. The era of human-powered crisis mapping between 2009 and 2014 was a bootstrapped effort very much a function of the peculiar state of technological development at the time—available but not yet formalized, streamlined, and automated. Humans filled the gap until machine assistance could catch up. These efforts, often mundane (e.g., cut and paste over and over for hours), were more reflective of the state of technology at the time than anything else. Another precondition that enabled the field to grow is the often taken-for-granted public good provided by the GPS satellites maintained by the U.S. Air Force. Without this service, the project at the time would not have emerged where and when it did. The future will be shaped as a result of improvements in automated forms of data collection; improved machine learning techniques to help filter, identify, visualize, and analyze the data; and the proliferation of low-cost drones and other forms of sensors, to name a few.

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.

The importance of allopolyploidy in plant evolution has been widely recognized. The genetic changes triggered by allopolyploidy, however, are not yet fully understood due to inconsistent phenomena reported across diverse species. The construction of synthetic polyploids offers a controlled approach to systematically reveal genomic changes that occur during the process of polyploidy. This study reports the first fully sequenced synthetic allopolyploid constructed from a cross between Cucumis sativus and C. hystrix, with high-quality assembly. The two subgenomes are confidently partitioned and the C. sativus-originated subgenome predominates over the C. hystrix-originated subgenome, retaining more sequences and showing higher homeologous gene expression. Most of the genomic changes emerge immediately after interspecific hybridization. Analysis of a series of genome sequences from several generations (S0, S4-S13) of C. ×hytivus confirms that genomic changes occurred in the very first generations, subsequently slowing down as the process of diploidization is initiated. The duplicated genome of the allopolyploid with double genes from both parents broadens the genetic base of C. ×hytivus, resulting in enhanced phenotypic plasticity. This study provides novel insights into plant polyploid genome evolution and demonstrates a promising strategy for the development of a wide array of novel plant species and varieties through artificial polyploidization.

Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan), is a botanical variety of cucumber cultivars native to southwest China that possesses excellent agronomic traits for cucumber improvement. However, breeding utilization of XIS cucumber is limited due to the current poor understanding of its photoperiod-sensitive flowering characteristics. In this study, genetic and transcriptomic analysis were conducted to reveal the molecular basis of photoperiod-regulated flowering in XIS cucumber. A major-effect QTL locus DFF1.1 was identified that controls the days to first flowering (DFF) of XIS cucumbers with a span of 1.38 Mb. Whole-genome re-sequencing data of 9 cucumber varieties with different flowering characteristics in response to photoperiod suggested that CsaNFYA1 was the candidate gene of DFF1.1, which harbored a single non-synonymous mutation in its fifth exon. Transcriptomic analysis revealed the positive roles of auxin and ethylene in accelerating flowering under short-day (SD) light-dark cycles when compared with equal-day/night treatment. Carbohydrate storage and high expression levels of related genes were important reasons explaining early flowering of XIS cucumber under SD conditions. By combining with the RNA-Seq data, the co-expression network suggested that CsaNFYA1 integrated multiple types of genes to regulate the flowering of XIS cucumber. Our findings explain the internal regulatory mechanisms of a photoperiodic flowering pathway. These findings may guide the use of photoperiod shifts to promote flowering of photoperiod-sensitive crops.

Karyotype dynamics driven by complex chromosome rearrangements constitute a fundamental issue in evolutionary genetics. The evolutionary events underlying karyotype diversity within plant genera, however, have rarely been reconstructed from a computed ancestral progenitor. Here, we developed a method to rapidly and accurately represent extant karyotypes with the genus, Cucumis, using highly customizable comparative oligo-painting (COP) allowing visualization of fine-scale genome structures of eight Cucumis species from both African-origin and Asian-origin clades. Based on COP data, an evolutionary framework containing a genus-level ancestral karyotype was reconstructed, allowing elucidation of the evolutionary events that account for the origin of these diverse genomes within Cucumis. Our results characterize the cryptic rearrangement hotspots on ancestral chromosomes, and demonstrate that the ancestral Cucumis karyotype (n = 12) evolved to extant Cucumis genomes by hybridizations and frequent lineage- and species-specific genome reshuffling. Relative to the African species, the Asian species, including melon (Cucumis melo, n = 12), Cucumis hystrix (n = 12) and cucumber (Cucumis sativus, n = 7), had highly shuffled genomes caused by large-scale inversions, centromere repositioning and chromothripsis-like rearrangement. The deduced reconstructed ancestral karyotype for the genus allowed us to propose evolutionary trajectories and specific events underlying the origin of these Cucumis species. Our findings highlight that the partitioned evolutionary plasticity of Cucumis karyotype is primarily located in the centromere-proximal regions marked by rearrangement hotspots, which can potentially serve as a reservoir for chromosome evolution due to their fragility.

Agri-food systems are besieged by malnutrition, yield gaps, and climate vulnerability, but integrated, research-based responses in public policy, agricultural, value chains, and finance are constrained by short-termism and zero sum thinking. As they respond to current and emerging agri-food system challenges, decision makers need new tools that steer toward multi-sector, evidence-based collaboration. To support national agri-food system policy processes, the Integrated Agri-food System Initiative (IASI) methodology was developed and validated through case studies in Mexico and Colombia. This holistic, multi-sector methodology builds on diverse existing data resources and leverages situation analysis, modeled predictions, and scenarios to synchronize public and private action at the national level toward sustainable, equitable, and inclusive agri-food systems. Culminating in collectively agreed strategies and multi-partner tactical plans, the IASI methodology enabled a multi-level systems approach by mobilizing design thinking to foster mindset shifts and stakeholder consensus on sustainable and scalable innovations that respond to real-time dynamics in complex agri-food systems. To build capacity for these types of integrated, context-specific approaches, greater investment is needed in supportive international institutions that function as trusted in-region 'innovation brokers.' This paper calls for a structured global network to advance adaptation and evolution of essential tools like the IASI methodology in support of the One CGIAR mandate and in service of positive agri-food systems transformation.

Capsicum species are of great economic, medicinal, culinary and cultural value worldwide, however their genetic potential is still underutilized. In this study, a set of 21 microsatellite markers showed utility for distinguishing a diverse group of 42 Capsicum genotypes representing 11 species. The level of polymorphism among these genotypes was evaluated by calculating the polymorphic information content (PIC) and discriminating power (D) for each locus. A total of 208 alleles were detected at the 21 loci evaluated. Markers detecting the highest number of alleles also exhibited the highest number of rare alleles. PIC values and D estimations showed a significant positive correlation (r = 0.98; P < 0.0000). PIC values ranged between 0.500 (marker NG20) and 0.899 (marker NG17), giving an average of 0.775. Genetic relationships among genotypes were evaluated using UPGMA clustering, Principal Coordinate Analysis (PCoA) and Bayesian model-based clustering, allowing genotypes to be discriminated into groups according to their degree of genetic similarity corresponding to distinct taxa. Based on these analyses, the 21 microsatellite included in this study now define a standard tool for efficient assessment of molecular variability of Capsicum germplasm collections conserved worldwide.

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.

MYB (myeloblastosis) transcription factors (TFs) play important roles in controlling various physiological processes in plants, such as responses to biotic and abiotic stress, metabolism, and defense. A previous study identified a gene, Csa6G410090, encoding a plant lipid transfer protein (LTP), as a possible regulator in cucumber (Cucumis sativus L.) of the resistance response to root-knot nematode (RKN) [Meloidogyne incognita Kofoid and White (Chitwood)]. Myb-type DNA-binding TFs were presumed to regulate downstream genes expression, including LTPs, however, the regulation mechanism remained unclear. To elucidate whether and which MYB TFs may be involved in regulation of the resistance response, this study identified 112 genes as candidate members of the CsMYB gene family by combining CDD and SMART databases, using the Hidden Markov Model (HMM) and manual calibration. Within this group, ten phylogenetic subgroups were resolved according to sequence-based classification, consistent with results from comprehensive investigation of gene structure, conserved motifs, chromosome locations, and cis-element analysis. Distribution and collinearity analysis indicated that amplification of the CsMYB gene family in cucumber has occurred mainly through tandem repeat events. Spatial gene expression analysis showed that 8 CsMYB genes were highly expressed at differing levels in ten different tissues or organs. The roots of RKN-resistant and susceptible cucumbers were inoculated with M. incognita, finding that CsMYB (Csa6G538700, Csa1G021940, and Csa5G641610) genes showed up-regulation coincident with upregulation of the "hub" gene LTP (Csa6G410090) previously implicated as a major gene in the resistance response to RKN in cucumber. Results of this study suggest hypotheses regarding the elements and regulation of the resistant response as well as possible RKN resistance-enhancing strategies in cucumber and perhaps more broadly in plants.

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.

The original version of this article, published in Current Sustainable Renewable Energy Reports , Volume 4, Issue 3, September 2017, inadvertently misspelled an author’s last name on the title page as Haimanote Baybil. The correct name is Haimanote Bayabil.

1. Department of Soil and Crop Science, Colorado State University, USA 2. Department of Agronomy, University of Wisconsin-Madison, USA 3. Commonwealth Scientific and Industrial Research Organisation, Australia 4. Australian Department of the Environment and Energy, Australia 5. The Carbon Cycle Institute; Marin Carbon Project, USA 6. Union of Concerned Scientists, USA 7. Sustainable Agriculture Sciences, Rothamsted Research, UK 8. Agriculture and Agri-Food Canada, Canada 9. International Institute for Applied Systems Analysis, Austria 10. Alberta Agriculture and Forestry, Canada 11. International Maize and Wheat Improvement Center, Mexico 12. Natural Resource Conservation Service, United States Department of Agriculture, USA 13. Department of Geographical Sciences, University of Maryland, USA 14. Crop Research Institute, Czech Republic 15. Point Blue Conservation Science, USA 16. Department of Agronomy, Kansas State University, USA 17. National Agricultural and Food Centre, Soil Science and Conservation Research Institute, Slovakia

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.

Environmental heterogeneity, emerging pathogens and limited access to financial and agricultural inputs prevent farmers from producing consistent crop yields in many developing countries. Yield instability impedes establishment of processing and export industries, thereby inhibiting economic development. Modern varieties offer significant increases in yield stability.