Global trends of cropland phosphorus use and sustainability challenges.

To meet the growing food demand while addressing the multiple challenges of exacerbating phosphorus (P) pollution and depleting P rock reserves1-15, P use efficiency (PUE, the ratio of productive P output to P input in a defined system) in crop production needs to be improved. Although many efforts have been devoted to improving nutrient management practices on farms, few studies have examined the historical trajectories of PUE and their socioeconomic and agronomic drivers on a national scale1,2,6,7,11,16,17. Here we present a database of the P budget (the input and output of the crop production system) and PUE by country and by crop type for 1961-2019, and examine the substantial contribution of several drivers for PUE, such as economic development stages and crop portfolios. To address the P management challenges, we found that global PUE in crop production must increase to 68-81%, and recent trends indicate some meaningful progress towards this goal. However, P management challenges and opportunities in croplands vary widely among countries.

Genomic insights into the evolution of Echinochloa species as weed and orphan crop.

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

Farm production diversity and women's dietary diversity: Evidence from central Tunisia.

In the context of studies on the effects of agricultural production diversity, there are debates in the scientific community as to the level of diversification appropriate for improving dietary diversity. In Tunisia, agriculture is a strategic sector for the economy and a critical pillar of its food sovereignty. Using instrumental variable methods to account for endogeneity, we have estimated the association between agricultural production diversity and women's dietary diversity among smallholder farming households in the Sidi Bouzid governorate (central Tunisia). Although we found a low level of agricultural production diversity and a fairly diversified diet among women, we observed a systematic weak positive association between five different indicators of agricultural production diversity and women's dietary diversity. We observed a stronger positive association between women's dietary diversity and women being more educated and households being wealthier. Neither diversity of food supplies in food markets nor market distance were associated with women's dietary diversity, whereas we observed a higher level of consumption of some products (dairy) when they were produced on the farm.

Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice.

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response.

Global cooling induced by biophysical effects of bioenergy crop cultivation.

Bioenergy crop with carbon capture and storage (BECCS) is a key negative emission technology to meet carbon neutrality. However, the biophysical effects of widespread bioenergy crop cultivation on temperature remain unclear. Here, using a coupled atmosphere-land model with an explicit representation of lignocellulosic bioenergy crops, we find that after 50 years of large-scale bioenergy crop cultivation following plausible scenarios, global air temperature decreases by 0.03~0.08 °C, with strong regional contrasts and interannual variability. Over the cultivated regions, woody crops induce stronger cooling effects than herbaceous crops due to larger evapotranspiration rates and smaller aerodynamic resistance. At the continental scale, air temperature changes are not linearly proportional to the cultivation area. Sensitivity tests show that the temperature change is robust for eucalypt but more uncertain for switchgrass among different cultivation maps. Our study calls for new metrics to take the biophysical effects into account when assessing the climate mitigation capacity of BECCS.

Growth and trend analysis of area, production and yield of rice: A scenario of rice security in Bangladesh.

Bangladesh positioned as third rice producing country in the world. In Bangladesh, regional growth and trend in rice production determinants, disparities and similarities of rice production environments are highly desirable. In this study, the secondary time series data of area, production, and yield of rice from 1969-70 to 2019-20 were used to investigate the growth and trend by periodic, regional, seasonal and total basis. Quality checking, trend fitting, and classification analysis were performed by the Durbin-Watson test, Exponential growth model, Cochrane-Orcutt iteration method and clustering method. The production contribution to the national rice production of Boro rice is increasing at 0.97% per year, where Aus and Aman season production contribution significantly decreased by 0.48% and 0.49% per year. Among the regions, Mymensingh, Rangpur, Bogura, Jashore, Rajshahi, and Chattogram contributed the most i.e., 13.9%, 9.8%, 8.6%, 8.6%, 8.2%, and 8.0%, respectively. Nationally, the area of Aus and Aman had a decreasing trend with a -3.63% and -0.16% per year, respectively. But, in the recent period (Period III) increasing trend was observed in the most regions. The Boro cultivation area is increasing with a rate of 3.57% per year during 1984-85 to 2019-20. High yielding variety adoption rate has increased over the period and in recent years it has found 72% for Aus, 73.5% for Aman, and 98.4% for Boro season. As a result, the yield of the Aus, Aman, and Boro seasons has been found increasing growth for most of the regions. We have identified different cluster regions in different seasons, indicating high dissimilarities among the rice production regions in Bangladesh. The region-wise actionable plan should be taken to rapidly adopt new varieties, management technologies and extension activities in lower contributor regions to improve productivity. Cluster-wise, policy strategies should be implemented for top and less contributor regions to ensure rice security of Bangladesh.

Image processing techniques to estimate weight and morphological parameters for selected wheat refractions.

The geometric and color features of agricultural material along with related physical properties are critical to characterize and express its physical quality. The experiments were conducted to classify the physical characteristics like size, shape, color and texture and then workout the relationship between manual observations and using image processing techniques for weight and volume of the four wheat refractions i.e. sound, damaged, shriveled and broken grains of wheat variety PBW 725. A flatbed scanner was used to acquire the images and digital image processing method was used to process the images and output of image analysis was compared with the actual measurements data using digital vernier caliper. A linear relationship was observed between the axial dimensions of refractions between manual measurement and image processing method with R2 in the range of 0.798-0.947. The individual kernel weight and thousand grain weight of the refractions were observed to be in the range of 0.021-0.045 and 12.56-46.32 g respectively. Another linear relationship was found between individual kernel weight and projected area estimated using image processing methodology with R2 in the range of 0.841-0.920. The sphericity of the refractions varied in the range of 0.52-0.71. Analyses of the captured images suggest ellipsoid shape with convex geometry while the same observation was recorded by physical measurements also. A linear relationship was observed between the volume of refractions derived from measured dimensions and calculated from image with R2 in the range of 0.845-0.945. Various color and grey level co-variance matrix texture features were extracted from acquired images using the open-source Python programming language and OpenCV library which can exploit different machine and deep learning algorithms to properly classify these refractions.

Genotyping-By-Sequencing diversity analysis of international Vanilla collections uncovers hidden diversity and enables plant improvement.

Genomics-based diversity analysis of natural vanilla populations is important in order to guide conservation efforts and genetic improvement through plant breeding. Vanilla is a cultivated, undomesticated spice that originated in Mesoamerica prior to spreading globally through vegetative cuttings. Vanilla extract from the commercial species, mainly V. planifolia and V. × tahitensis, is used around the world as an ingredient in foods, beverages, cosmetics, and pharmaceuticals. The global reliance on descendants of a few foundational clones in commercial production has resulted in an industry at heightened risk of catastrophic failure due to extremely narrow genetic diversity. Conversely, national and institutional collections including those near the center of cultivation contain previously undiscovered diversity that could bolster the genetic improvement of vanilla and guide conservation efforts. Towards this goal, an international vanilla genotyping effort generated and analyzed 431,204 single nucleotide polymorphisms among 412 accessions and 27 species from eight collections. Phylogenetic and STRUCTURE analysis sorted vanilla by species and identified hybrid accessions. Principal Component Analysis and the Fixation Index (FST) were used to refine relationships among accessions and showed differentiation among species. Analysis of the commercial species split V. planifolia into three types with all V. × tahitensis accessions being most similar to V. planifolia type 2. Finally, an in-depth analysis of V. × tahitensis identified seven V. planifolia and six V. odorata accessions as most similar to the estimated parental genotypes providing additional data in support of the current hybrid theory. The prevalence of probable V. × tahitensis parental accessions from Belize suggests that V. × tahitensis could have originated from this area and highlights the need for vanilla conservation throughout Central and South America. The genetic groupings among accessions, particularly for V. planifolia, can now be used to focus breeding efforts on fewer accessions that capture the greatest diversity.

Integration of advanced technologies for plant variety and cultivar identification.

Identification of plant variety and cultivar is pivotal in the agricultural sector due to the abundance of plant varieties and cultivars developed in many crop species. However, plant variety and cultivar identification via basic morphological features is problematic and challenging when differentiating closely related species not only due to their limited differences but also due to technical limitations of the process being time-consuming, labour-intensive and costly, and statistically imprecise information being available due to phenotypic plasticity. Therefore, it is imperative to have rapid and highly efficient techniques to mitigate these limitations. This review provides an overview and summarization of the development and application of molecular markers such as Random Amplified Polymorphic DNA (RAPD), Restriction Fragment Length Polymorphism (RFLP), Simple Sequence Repeats (SSR), Inter-simple sequence repeats (ISSR), Amplified Fragment Length Polymorphism (AFLP), Single nucleotide polymorphism (SNP) and DNA barcoding, High-resolution melting (HRM) and biosensor technology as potential tools in the identification of plant variety and cultivar.

A novel semi-supervised framework for UAV based crop/weed classification.

Excessive use of agrochemicals for weed controlling infestation has serious agronomic and environmental repercussions associated. An appropriate amount of pesticide/ chemicals is essential for achieving the desired smart farming and precision agriculture (PA). In this regard, targeted weed control will be a critical component significantly helping in achieving the goal. A prerequisite for such control is a robust classification system that could accurately identify weed crops in a field. In this regard, Unmanned Aerial Vehicles (UAVs) can acquire high-resolution images providing detailed information for the distribution of weeds and offers a cost-efficient solution. Most of the established classification systems deploying UAV imagery are supervised, relying on image labels. However, this is a time-consuming and tedious task. In this study, the development of an optimized semi-supervised learning approach is proposed, offering a semi-supervised generative adversarial network for crops and weeds classification at early growth stage. The proposed algorithm consists of a generator that provides extra training data for the discriminator, which distinguishes weeds and crops using a small number of image labels. The proposed system was evaluated extensively on the Red Green Blue (RGB) images obtained by a quadcopter in two different croplands (pea and strawberry). The method achieved an average accuracy of 90% when 80% of training data was unlabeled. The proposed system was compared with several standards supervised learning classifiers and the results demonstrated that this technique could be applied for challenging tasks of crops and weeds classification, mainly when the labeled samples are small at less training time.

A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era.

BACKGROUND: The identification of chromosomes among Avena species have been studied by C-banding and in situ hybridization. However, the complicated results from several cytogenetic nomenclatures for identifying oat chromosomes are often contradictory. A universal karyotyping nomenclature system for precise chromosome identification and comparative evolutionary studies would be essential for genus Avena based on the recently released genome sequences of hexaploid and diploid Avena species. RESULTS: Tandem repetitive sequences were predicted and physically located on chromosomal regions of the released Avena sativa OT3098 genome assembly v1. Eight new oligonucleotide (oligo) probes for sequential fluorescence in situ hybridization (FISH) were designed and then applied for chromosome karyotyping on mitotic metaphase spreads of A. brevis, A. nuda, A. wiestii, A. ventricosa, A. fatua, and A. sativa species. We established a high-resolution standard karyotype of A. sativa based on the distinct FISH signals of multiple oligo probes. FISH painting with bulked oligos, based on wheat-barley collinear regions, was used to validate the linkage group assignment for individual A. sativa chromosomes. We integrated our new Oligo-FISH based karyotype system with earlier karyotype nomenclatures through sequential C-banding and FISH methods, then subsequently determined the precise breakage points of some chromosome translocations in A. sativa. CONCLUSIONS: This new universal chromosome identification system will be a powerful tool for describing the genetic diversity, chromosomal rearrangements and evolutionary relationships among Avena species by comparative cytogenetic and genomic approaches.

Allelic Diversity at Abiotic Stress Responsive Genes in Relationship to Ecological Drought Indices for Cultivated Tepary Bean, Phaseolus acutifolius A. Gray, and Its Wild Relatives.

Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius or P. parvifolius are from arid areas between Mexico and the United States. Therefore, we hypothesize that these bean accessions have diversity signals indicative of adaptation to drought at key candidate genes such as: Asr2, Dreb2B, and ERECTA. By sequencing alleles of these genes and comparing to estimates of drought tolerance indices from climate data for the collection site of geo-referenced, tepary bean accessions, we determined the genotype x environmental association (GEA) of each gene. Diversity analysis found that cultivated and wild P. acutifolius were intermingled with var. tenuifolius and P. parvifolius, signifying that allele diversity was ample in the wild and cultivated clade over a broad sense (sensu lato) evaluation. Genes Dreb2B and ERECTA harbored signatures of directional selection, represented by six SNPs correlated with the environmental drought indices. This suggests that wild tepary bean is a reservoir of novel alleles at genes for drought tolerance, as expected for a species that originated in arid environments. Our study corroborated that candidate gene approach was effective for marker validation across a broad genetic base of wild tepary accessions.

Overcoming barriers to the registration of new plant varieties under the DUS system.

Distinctness, Uniformity and Stability (DUS) is an intellectual property system introduced in 1961 by the International Union for the Protection of New Varieties of Plants (UPOV) for safeguarding the investment and rewarding innovation in developing new plant varieties. Despite the rapid advancement in our understanding of crop biology over the past 60 years, the DUS system has changed little and is still largely dependent upon a set of morphological traits for testing candidate varieties. As the demand for more plant varieties increases, the barriers to registration of new varieties become more acute and thus require urgent review to the system. To highlight the challenges and remedies in the current system, we evaluated a comprehensive panel of 805 UK barley varieties that span the entire history of DUS testing. Our findings reveal the system deficiencies such as inconsistencies in DUS traits across environments, limitations in DUS trait combinatorial space, and inadequacies in currently available DUS markers. We advocate the concept of genomic DUS and provide evidence for a shift towards a robust genomics-enabled registration system for new crop varieties.

sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks.

KEY MESSAGE: We proposed an ensemble convolutional neural network model to identify sgRNA high on-target activity in four crops and we used one-hot encoding and k-mers for sequence encoding. As an important component of the CRISPR/Cas9 system, single-guide RNA (sgRNA) plays an important role in gene redirection and editing. sgRNA has played an important role in the improvement of agronomic species, but there is a lack of effective bioinformatics tools to identify the activity of sgRNA in agronomic species. Therefore, it is necessary to develop a method based on machine learning to identify sgRNA high on-target activity. In this work, we proposed a simple convolutional neural network method to identify sgRNA high on-target activity. Our study used one-hot encoding and k-mers for sequence data conversion and a voting algorithm for constructing the convolutional neural network ensemble model sgRNACNN for the prediction of sgRNA activity. The ensemble model sgRNACNN was used for predictions in four crops: Glycine max, Zea mays, Sorghum bicolor and Triticum aestivum. The accuracy rates of the four crops in the sgRNACNN model were 82.43%, 80.33%, 78.25% and 87.49%, respectively. The experimental results showed that sgRNACNN realizes the identification of high on-target activity sgRNA of agronomic data and can meet the demands of sgRNA activity prediction in agronomy to a certain extent. These results have certain significance for guiding crop gene editing and academic research. The source code and relevant dataset can be found in the following link: https://github.com/nmt315320/sgRNACNN.git .

Crop, genotype, and field environmental conditions shape bacterial and fungal seed epiphytic microbiomes.

Seeds are reproductive structures able to carry and transfer microorganisms that play an important role in plant fitness. Genetic and external factors are reported to be partly responsible for the plant microbiome assemblage, but their contribution in seeds is poorly understood. In this study, wheat, canola, and lentil seeds were analyzed to characterize diversity, structure, and persistence of seed-associated microbial communities. Five lines and 2 generations of each crop were subjected to high-throughput amplicon sequencing of the 16S rRNA and internal transcribed spacer (ITS) regions. Bacterial and fungal communities differed most by crop type (30% and 47% of the variance), while generation explained an additional 10% and 15% of the variance. The offspring (i.e., generation harvested in 2016 at the same location) exhibited a higher number of common amplicon sequence variants (ASVs) and less variability in microbial composition. Additionally, in every sample analyzed, a "core microbiome" was detected consisting of 5 bacterial and 12 fungal ASVs. Our results suggest that crop, genotype, and field environmental conditions contributed to the seed-associated microbial assemblage. These findings not only expand our understanding of the factors influencing the seed microbiome but may also help us to manipulate and exploit the microbiota naturally carried by seeds.

Food Crop Diversity, Women's Income-Earning Activities, and Distance to Markets in Relation to Maternal Dietary Quality in Tanzania.

BACKGROUND: Women's dietary diversity and quality are limited in low- and middle-income countries (LMICs). Nutrition-sensitive interventions that promote food crop diversity and women's access to income could improve diets and address the double burden of malnutrition in LMICs. OBJECTIVES: We examined the associations among food crop diversity and women's income-earning activities with women's diet quality, as well as effect modification by access to markets, in the context of small-holder food production in rural Tanzania. METHODS: Data from a cross-sectional study of 880 women from Rufiji, Tanzania, were analyzed. Women's dietary intake was assessed using a food frequency questionnaire. The prime diet quality score (PDQS; 21 food groups; range, 0-42), a unique diet-quality metric for women that captures the healthy and unhealthy aspects of diet, was computed. Generalized estimating equation linear models were used to evaluate the associations of food crop diversity and women's income-earning activities with PDQS, while controlling for socio-economic factors. RESULTS: Maternal overweight (24.3%) and obesity (13.1%) were high. The median PDQS was 19 (IQR, 17-21). Households produced 2.0 food crops (SD ± 1.0) yearly. Food crop diversity was positively associated with PDQS (P < 0.001), but the association was strengthened by proximity to markets (P for interaction = 0.02). For women living close (<1.1 km) to markets, producing 1 additional food crop was associated with a 0.67 (95% CI, 0.22-1.12) increase in PDQS, versus a 0.40 (95% CI, 0.24-0.57) increase for women living farther away. The PDQS increased with women's salaried employment (estimate, 0.96; 95% CI, 0.26-1.67). CONCLUSIONS: Household food production may interact with access to markets for sales and purchases, while nonfarm income also improves women's diet quality in rural Tanzania. Programs to improve women's diet quality should consider improving market access and women's access to income (source of empowerment), in addition to diversifying production.

A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice.

Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.

Crop wild relatives of the United States require urgent conservation action.

The contributions of crop wild relatives (CWR) to food security depend on their conservation and accessibility for use. The United States contains a diverse native flora of CWR, including those of important cereal, fruit, nut, oil, pulse, root and tuber, and vegetable crops, which may be threatened in their natural habitats and underrepresented in plant conservation repositories. To determine conservation priorities for these plants, we developed a national inventory, compiled occurrence information, modeled potential distributions, and conducted threat assessments and conservation gap analyses for 600 native taxa. We found that 7.1% of the taxa may be critically endangered in their natural habitats, 50% may be endangered, and 28% may be vulnerable. We categorized 58.8% of the taxa as of urgent priority for further action, 37% as high priority, and 4.2% as medium priority. Major ex situ conservation gaps were identified for 93.3% of the wild relatives (categorized as urgent or high priority), with 83 taxa absent from conservation repositories, while 93.1% of the plants were equivalently prioritized for further habitat protection. Various taxonomic richness hotspots across the US represent focal regions for further conservation action. Related needs include facilitating greater access to and characterization of these cultural-genetic-natural resources and raising public awareness of their existence, value, and plight.