Early Prediction of Soybean Traits through Color and Texture Features of Canopy RGB Imagery

Global crop production is facing the challenge of a high projected demand, while the yields of major crops are not increasing at sufficient speeds. Crop breeding is an important way to boost crop productivity, however its improvement rate is partially hindered by the long crop generation cycles. If end-season crop traits such as yield can be predicted through early-season phenotypic measurements, crop selection can potentially be made before a full crop generation cycle finishes. This study explored the possibility of predicting soybean end-season traits through the color and texture features of early-season canopy images. Six thousand three hundred and eighty-three images were captured at V4/V5 growth stage over 6039 soybean plots growing at four locations. One hundred and forty color features and 315 gray-level co-occurrence matrix-based texture features were derived from each image. Another two variables were also introduced to account for location and timing differences between the images. Five regression and five classification techniques were explored. Best results were obtained using all 457 predictor variables, with Cubist as the regression technique and Random Forests as the classification technique. Yield (RMSE = 9.82, R2 = 0.68), Maturity (RMSE = 3.70, R2 = 0.76) and Seed Size (RMSE = 1.63, R2 = 0.53) were identified as potential soybean traits that might be early predictable.

Phosphorus use efficiency and crop production: Patterns of regional variation in the United States, 1987-2012

Crop N use efficiency (NUE) and P use efficiency (PUE) might be expected to exhibit different patterns across agricultural regions due to their very different environmental dynamics and management strategies. Here, following our previous work on regional patterns of NUE, we review patterns of PUE and related variables, including major inputs of P to US crops over 1987-2012, based on the Farm Resource Regions developed by the Economic Research Service (USDA-ERS). Unlike N, P inputs to cropland only occur in the forms of P fertilizer, which has generally changed little over time relative to N fertilizer, and manure P, which has increased. Expressed as percentages of total P inputs, they necessarily have opposite impacts on PUE because of the stronger relationship of crop production to fertilizer compared to manure produced in a region. Across the US, PUE trends have varied significantly, increasing in some regions, in contrast to NUE which has generally remained constant or declined on decadal time scales. As with N, the Heartland region dominates national patterns due to the magnitude of crop production, showing a significant relationship with fertilizer P but none with manure P on a cropland area basis. Most other regions show similar responses, but the Northern Crescent, Eastern Uplands and Southern Seaboard regions shows a negative response to fertilizer on the same basis. The regional response of production to P inputs on a cropland area basis differs from that on a total area basis, suggesting that the type of scaling used is critical under changing cropland area. In the US, manure is still treated largely as a waste to be managed rather than a nutrient resource. Differences between P and N need to be considered in the context of management of environmental quality and food security.

Review: Endophytic microbes and their potential applications in crop management

Endophytes are microbes (mostly bacteria and fungi) present asymptomatically in plants. Endophytic microbes are often functional in that they may carry nutrients from the soil into plants, modulate plant development, increase stress tolerance of plants, suppress virulence in pathogens, increase disease resistance in plants, and suppress development of competitor plant species. Endophytic microbes have been shown to: (i) obtain nutrients in soils and transfer nutrients to plants in the rhizophagy cycle and other nutrient-transfer symbioses; (ii) increase plant growth and development; (iii) reduce oxidative stress of hosts; (iv) protect plants from disease; (v) deter feeding by herbivores; and (vi) suppress growth of competitor plant species. Because of the effective functions of endophytic microbes, we suggest that endophytic microbes may significantly reduce use of agrochemicals (fertilizers, fungicides, insecticides, and herbicides) in the cultivation of crop plants. The loss of endophytic microbes from crop plants during domestication and long-term cultivation could be remedied by transfer of endophytes from wild relatives of crops to crop species. Increasing atmospheric carbon dioxide levels could reduce the efficiency of the rhizophagy cycle due to repression of reactive oxygen used to extract nutrients from microbes in roots. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Adjusting cotton planting density under the climatic conditions of Henan Province, China

The growth and development of cotton are closely related to climatic variables such as temperature and solar radiation. Adjusting planting density is one of the most effective measures for maximizing cotton yield under certain climatic conditions. The objectives of this study were (1) to determine the optimum planting density and the corresponding leaf area index (LAI) and yield under the climatic conditions of Henan Province, China, and (2) to learn how climatic conditions influence cotton growth, yield, and yield components. A three-year (2013-2015) field experiment was conducted in Anyang, Henan Province, using cultivar SCRC28 across six planting density treatments: 15,000, 33,000, 51,000, 69,000, 87,000, and 105,000 plants ha-1. The data showed that the yield attributes, including seed cotton yield, lint yield, dry matter accumulation, and the LAI, increased as planting density increased. Consequently, the treatment of the maximum density with 105,000 plants ha-1 was the highest-yielding over three years, with the LAIs averaged across the three years being 0.37 at the bud stage, 2.36 at the flower and boll-forming stage, and 1.37 at the boll-opening stage. Furthermore, the correlation between the cotton yield attributes and meteorological conditions indicated that light interception (LI) and the diurnal temperature range were the climatic factors that most strongly influenced cotton seed yield. Moreover, the influence of the number of growing degree days (GDD) on cotton was different at different growth stages. These observations will be useful for determining best management practices for cotton production under the climatic conditions of Henan Province, China.

Optimum plant density for crowding stress tolerant processing sweet corn

Globally, gains in sweet corn [Zea mays L.var. rugosa (or saccharata)] are a fraction of the yield advances made in field corn (Zea mays L.) in the last half-century. Grain yield improvement of field corn is associated with increased tolerance to higher plant densities (i.e., crowding stress). Processing sweet corn hybrids that tolerate crowding stress have been identified; however, such hybrids appear to be under-planted in the processing sweet corn. Using crowding stress tolerant (CST) hybrids, the objectives of this study were to: (1) identify optimum plant densities for a range of growing conditions; (2) quantify gaps in production between current and optimum plant densities; and (3) enumerate changes in yield and ear traits when shifting from current to optimum plant densities. Using a CST shrunken-2 (sh2) processing sweet corn hybrid, on-farm plant density trials were conducted in thirty fields across the states of Illinois, Minnesota and Wisconsin, from 2013 to 2017 in order to capture a wide variety of growing conditions. Linear mixed-effects models were used to identify the optimum plant density corresponding to maximum ear mass (Mt ha^-1), case production (cases ha^-1), and profitability to the processor ($ ha^-1). Kernel moisture, indicative of plant development, was unaffected by plant density. Ear traits, such as ear number and ear mass per plant, average ear length, and filled ear length declined linearly with increasing plant density. Nonetheless, there was a large economic benefit to the grower and processor by shifting to higher plant densities in most environments. This research shows that increasing plant densities of CST hybrids from current (58,475 plants ha^-1) to optimum (73,075 plants ha^-1) could improve processing sweet corn green ear yield and processor profitability on average of 1.13 Mt ha^-1 and $525 ha^-1, respectively.

Overexpression of rice gene OsATG8b confers tolerance to nitrogen starvation and increases yield and nitrogen use efficiency (NUE) in Arabidopsis

Nitrogen (N) is an important element required for plant growth and development, which also affects plant yield and quality. Autophagy, a conserved pathway in eukaryotes, degrades and recycles cellular components, thus playing an important role in N remobilization. However, only a few autophagy genes related to N remobilization in rice (Oryza sativa) have been reported. Here, we identified a core autophagy gene in rice, OsATG8b, with increased expression levels under N starvation conditions. It was investigated the function of OsATG8b by generating three independent homozygous 35S-OsATG8b transgenic Arabidopsis thaliana lines. The overexpression of OsATG8b significantly enhanced autophagic flux in the transgenic Arabidopsis plants. It was also showed that over-expressing OsATG8b promoted growth and development of Arabidopsis, in which the rosette leaves were larger than those of the wild type (WT), and the yield increased significantly by 25.25%. In addition, the transgenic lines accumulated more N in seeds than in the rosette leaves. Further examination revealed that overexpression of OsATG8b could effectively alleviate the growth inhibition of transgenic Arabidopsis under nitrogen (N) stress. N partitioning studies revealed that nitrogen-harvest index (NHI) and nitrogen use efficiency (NUE) were significantly increased in the transgenic Arabidopsis, as well as the ¹⁵N-tracer experiments revealing that the remobilization of N to seeds in the OsATG8b-overexpressing transgenic Arabidopsis was high and more than WT. Based on our findings, we consider OsATG8b to be a great candidate gene to increase NUE and yield, especially under suboptimal field conditions.

Combining Irrigation Scheme and Phosphorous Application Levels for Grain Yield and Their Impacts on Rhizosphere Microbial Communities of Two Rice Varieties in a Field Trial

Root and rhizosphere is important for phosphorus (P) uptake in rice plants. However, little is known about the detailed regulation of irrigation regimes, especially frequently alternate wetting and drying (FAWD), on P usage of rice plants. Here, we found that compared with normal water and P dose, FAWD with a reduced P dose maintained the grain yield in two rice varieties. Compared to rice variety Gaoshan1, rice variety WufengyouT025 displayed a higher grain yield, shoot P content, rhizosphere acid phosphatase activity, abundance of bacteria, and bacterial acid phosphatase gene of rhizosphere. Moreover, the FAWD regime may increase the abundance of bacteria with acid phosphatase activity to release available phosphorus in the rhizosphere, which is associated with rice varieties. Our results suggest that an optimized management of irrigation and phosphorous application can enhance both water and phosphorus use efficiency without sacrificing the yield, which may contribute significantly to sustainable agriculture production.

Enhanced nitrogen imbalances in agroecosystems driven by changing cropping systems in a coastal area of eastern China: from field to watershed scale

Agricultural activities exacerbate nitrogen (N) imbalances in the agroecosystem by disturbing the N inputs and outputs, yet the influence of changes in cropping systems on the N balance of agroecosystems remains unclear. In this study, at the field scale, we calculated the N balance of four cropping systems, (1) traditional crops with traditional crop rotation (G-G), (2) vegetables with traditional crop rotation (V-G), (3) vegetables with vegetable rotation (V-V), and (4) greenhouse vegetables (GHV); then analyzed the influence of changes in cropping systems from 1995 to 2015 on the N balances in the agroecosystems in sub-watersheds of the Dagu River. The results indicate that N balances were higher in GHV, V-V, and V-G than G-G, due to significantly higher inputs of N fertilizers and lower N use efficiency (NUE) in vegetable cultivation compared to traditional crops. Driven by economic benefits between 1995 and 2015, V-G, V-V, and GHV replaced G-G in a considerable number of cultivation areas in the sub-watersheds. These changes resulted in an increase of 109.9-170.1% in the N balance in the agroecosystem in the sub-watersheds between 1995 and 2015. In the entire watershed, the total N surplus contribution by V-V, V-G, and GHV increased from 39.3% to 79.1% between 1995 and 2015. These findings suggest that increased vegetable cultivation contributed to the increased risk of N pollution in agricultural production. Thus, there should be a focus on the management of cropping systems to control N loss from agricultural lands.

Maize leaf-removal: A new agronomic approach to increase dry matter, flower number and seed-yield of soybean in maize soybean relay intercropping system

Shading conditions adversely affect flower-number and pod-number of soybeans under maize-soybean relay-intercropping (MSR). Here we reveal that leaf-removal from maize-canopy improves the photosynthetically active radiation (PAR) transmittance and dry-matter production (DMP) of soybean (especially during the co-growth phase), and compensates the maize seed-yield loss by considerably increasing soybean seed-yield. In a two-year experiment with MSR, maize-plants were subjected to different leaf-removal treatments to increase the PAR-transmittance of soybean; removal of the topmost two-leaves (R2), four-leaves (R4), six-leaves (R6), with no-removal of leaves (R0). Leaf-removal treatments improved the PAR-transmittance, photosynthetic-rate, and morphological-characteristics of soybean under MSR. At 90 days after sowing, the dry-matter of pods, and seeds was increased by 25%, and 32%, respectively under R6 than R0. Importantly, enhanced PAR-transmittance and DMP under R6 enabled soybean to initiate a greater number of flowers 182.2 plant-1 compared to 142.7 plant-1 under R0, and it also decreased the flower-abscission (by 13%, from 54.9% under R0 to 47.6% under R6). These positive responses increased the pod-number by 49% and seed-number by 28% under R6 than R0. Overall, under R6, relay-intercropped soybean produced 78% of sole-soybean seed-yield, and relay-intercropped maize produced 81% of sole-maize seed-yield and achieved the land equivalent ratio of 1.59.

Reducing Nitrogen and Phosphorus Losses from Different Crop Types in the Water Source Area of the Danjiang River, China

Nitrogen and phosphorus are essential for plant growth and are the primary limiting nutrient elements. The loss of nitrogen and phosphorus in agricultural systems can cause the eutrophication of natural water bodies. In this paper, a field simulated rainfall experiment was conducted in a typical small watershed of the Danjiang River to study the nutrient loss process of nitrogen and phosphorus in slope croplands subjected to different crops and tillage measures. The characteristics of the runoff process and nutrient migration of different slope treatments were studied, which were the bare-land (BL, as the control), peanut monoculture (PL), corn monoculture (CL), bare land (upper slope) mixed with peanut monoculture (lower slope) (BP), corn and peanut intercropping (TCP), corn and soybean intercropping (TCS), downslope ridge cultivation (BS) slope, and straw-mulched (SC), respectively. The results showed that the runoff of CL, SC, TCS, BS, BP, PL and TCP slope types were 93%, 75%, 51%, 39%, 28%, 12%, and 6% of the those of the bare land, respectively. The total nitrogen concentration in runoff on different slope types decreased in the order of BP > PL > BS > SC > TCP > BL > CL > TCS. The BL was characterized with the highest NRL-TN (the loss of total nitrogen per unit area), with the value of 1.188 kg/hm2, while those of the TCP is the smallest with the value of 0.073 kg/hm2. The total phosphorus concentration in runoff decreasd in the order of BS > BP > PL > BL > TCP > SC > CL > TCS. The PRL-TP (the loss of total phosphorus per unit area) of BL is the largest (0.016 kg/hm2), while those of TCP is the smallest (0.001 kg/hm2). These indicate that the loss of nitrogen is much higer than that of phosphorus. The loss of nitrogen in runoff is dominated by nitrate nitrogen, which accounts for 54.4%-78.9% of TN. Slope croplands in the water source area should adopt the tillage measures of TCP and PL.These measures can reduce 85% of the runoff of nitrogen and phosphorus compared to the bare land. The results may assist in agricultural non-point source pollution control and help promote improved management of the water environment in the Danjiang River's water source area.

Inorganic and organic fertilizers application enhanced antibiotic resistome in greenhouse soils growing vegetables

Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in fertilizers pose risks to human health and their variation in soil after fertilization has been reported. However, some important questions, such as the origin of ARG and ARB observed in soil following fertilization, which are present in soil regardless of fertilizer type (i.e., core (shared) ARGs and ARB), and the contribution of various ARG subtypes to the soil antibiotic resistome, need to be addressed. In this study, the effects of a long-term (9-year) application of organic (manure) and inorganic (chemistry) fertilizers on ARGs in greenhouse soils growing vegetables were investigated using metagenomic sequencing. The results showed that both organic and inorganic fertilizers application increased the diversity and abundance of soil ARGs. The dominant ARG types in organic fertilizer (OF) were different from that in organic fertilizer treated soil (SO), inorganic fertilizer treated soil (SI) and no fertilizer control plots (SC). The difference of core ARGs abundance reflected the variation of ARG profiles among SC, SI and SO. The OF is likely a source of the elevated ARG subtypes in soil and almost all the soil core ARG subtypes can be detected in organic fertilizer. Fifteen ARG types were enriched in the soil with OF, and some ARG subtypes such as sul1, sul2, tetX and tetL might derived from OF while others including as vanR, tcmA, rosB, and mexF might be from indigenous microbes in soil. The nutrition factors were found to influence the ARG profiles in fertilized soil. In summary, this study revealed the possible reason for the soil total ARG numbers and their relative abundance increase after fertilization, which will facilitate the control of ARGs and ARB dissemination.

The potential of corn-soybean intercropping to improve the soil health status and biomass production in cool climate boreal ecosystems

Intercropping (IC) is a promising approach used to improve soil health and sustainable crop production. However, it is unknown whether IC improve the soil health status and biomass productivity of crops cultivated in podzols under cool climate in boreal ecosystems. Two silage corn and three forage soybean genotypes were cultivated either as inter or monocrop (MC) treatments in a randomized complete block design. IC resulted in 28% increase in total forage production (FP). A reduction in rhizosphere soil pH (RS-pH) was observed in the IC treatments. Conversely, the rhizosphere soil acid phosphatase (RS-APase) activity was significantly higher (26-46%) in the IC treatments and occurred concomitant with a significant increase in available phosphorus (RS-Pavailable) (26-74%) in the rhizosphere. Furthermore, IC enhanced the active microbial composition and strong positive correlations were observed between RS-Pavailable, RS-APase, microbial biomass and FP; while RS-pH was negatively correlated with FP, RS-APase and RS-Pavailable. These findings suggested silage corn intercropped with forage soybean could be a viable approach to enhance FP through improved active microbial community structure, RS-APase activity and RS-Pavailable when cultivated on podzols in cool climate boreal ecosystem.

Neonicotinoid seed treatments of soybean provide negligible benefits to US farmers

Neonicotinoids are the most widely used insecticides worldwide and are typically deployed as seed treatments (hereafter NST) in many grain and oilseed crops, including soybeans. However, there is a surprising dearth of information regarding NST effectiveness in increasing soybean seed yield, and most published data suggest weak, or inconsistent yield benefit. The US is the key soybean-producing nation worldwide and this work includes soybean yield data from 194 randomized and replicated field studies conducted specifically to evaluate the effect of NSTs on soybean seed yield at sites within 14 states from 2006 through 2017. Here we show that across the principal soybean-growing region of the country, there are negligible and management-specific yield benefits attributed to NSTs. Across the entire region, the maximum observed yield benefits due to fungicide (FST = fungicide seed treatment) + neonicotinoid use (FST + NST) reached 0.13 Mg/ha. Across the entire region, combinations of management practices affected the effectiveness of FST + NST to increase yield but benefits were minimal ranging between 0.01 to 0.22 Mg/ha. Despite widespread use, this practice appears to have little benefit for most of soybean producers; across the entire region, a partial economic analysis further showed inconsistent evidence of a break-even cost of FST or FST + NST. These results demonstrate that the current widespread prophylactic use of NST in the key soybean-producing areas of the US should be re-evaluated by producers and regulators alike.

Root-associated microbes in sustainable agriculture: models, metabolites and mechanisms

Since the discovery of penicillin in 1928 and throughout the 'age of antibiotics' from the 1940s until the 1980s, the detection of novel antibiotics was restricted by lack of knowledge about the distribution and ecology of antibiotic producers in nature. The discovery that a phenazine compound produced by Pseudomonas bacteria could suppress soilborne plant pathogens, and its recovery from rhizosphere soil in 1990, provided the first incontrovertible evidence that natural metabolites could control plant pathogens in the environment and opened a new era in biological control by root-associated rhizobacteria. More recently, the advent of genomics, the availability of highly sensitive bioanalytical instrumentation, and the discovery of protective endophytes have accelerated progress toward overcoming many of the impediments that until now have limited the exploitation of beneficial plant-associated microbes to enhance agricultural sustainability. Here, we present key developments that have established the importance of these microbes in the control of pathogens, discuss concepts resulting from the exploration of classical model systems, and highlight advances emerging from ongoing investigations. © 2019 Society of Chemical Industry.

Removing constraints to sustainable food production: new ways to exploit secondary metabolism from companion planting and GM

The entire process of agricultural and horticultural food production is unsustainable as practiced by current highly intensive industrial systems. Energy consumption is particularly intensive for cultivation, and for fertilizer production and its incorporation into soil. Provision of nitrogen contributes a major source of the greenhouse gas, N₂ O. All losses due to pests, diseases and weeds are of food for which the carbon footprint has already been committed and so crop protection becomes an even greater concern. The rapidly increasing global need for food and the aggravation of associated problems by the effects of climate change create a need for new and sustainable crop protection. The overall requirement for sustainability is to remove seasonal inputs, and consequently all crop protection will need to be delivered via the seed or other planting material. Although genetic modification (GM) has transformed the prospects of sustainable crop protection, considerably more development is essential for the realisation of the full potential of GM and thereby consumer acceptability. Secondary plant metabolism offers wider and perhaps more robust new crop protection via GM and can be accomplished without associated yield loss because of the low level of photosynthate diverted for plant defence by secondary metabolism. Toxic mechanisms can continue to be targeted but exploiting non-toxic regulatory and signalling mechanisms should be the ultimate objective. There are many problems facing these proposals, both technical and social, and these are discussed but it is certainly not possible to stay where we are in terms of sustainability. The evidence for success is mounting and the technical opportunities from secondary plant metabolism are discussed here. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Rice bean: a lesser known pulse with well-recognized potential

Required genetic resources for the improvement of agronomic, nutritional and economic value of rice bean are available in the world collection. International cooperative effort is required to utilize and conserve them. Rice bean [Vigna umbellata (Thunb.) Ohwi and Ohashi], a lesser known pulse among the Asiatic Vigna, has long been considered as a food security crop of small and marginal farmers of Southeast Asia. Considered as a nutritionally rich food and fodder, it is also a source of genes for biotic and abiotic stress tolerance including drought, soil acidity and storage pest. Although it spread from its centre of domestication in the Indo-China region to other parts around the world, it never became an important crop anywhere probably because of agronomic disadvantages. Crop improvement for determinate nature, good yield, less variable seed colour, pleasant organoleptic properties and lower antinutrients is required. Scanning of scientific literature indicates that genetic resources with desirable agronomic and nutritional traits exist within the current collection but are spread across countries. Genomic studies in the species indicate that except for insect resistance and aluminium toxicity tolerance, not much attention has been paid to decipher and utilize other stress tolerance and nutritional quality traits. Collaborative efforts towards improving farming, food, trade value and off-farm conservation of rice bean would not only help marginal farmers but will also help to preserve the yet to be explored genomic resources available in this sturdy pulse.

Bambara groundnut: an exemplar underutilised legume for resilience under climate change

Bambara groundnut has the potential to be used to contribute more the climate change ready agriculture. The requirement for nitrogen fixing, stress tolerant legumes is clear, particularly in low input agriculture. However, ensuring that existing negative traits are tackled and demand is stimulated through the development of markets and products still represents a challenge to making greater use of this legume. World agriculture is currently based on very limited numbers of crops, representing a significant risk to food supplies, particularly in the face of climate change which is expected to increase the frequency of extreme events. Minor and underutilised crops can help to develop a more resilient and nutritionally dense future agriculture. Bambara groundnut [Vigna subterranea (L.) Verdc.[, as a drought resistant, nitrogen-fixing, legume has a role to play. However, as with most underutilised crops, there are significant gaps in knowledge and also negative traits such as 'hard-to-cook' and 'photoperiod sensitivity to pod filling' associated with the crop which future breeding programmes and processing methods need to tackle, to allow it to make a significant contribution to the well-being of future generations. The current review assesses these factors and also considers what are the next steps towards realising the potential of this crop.

Modernising breeding for orphan crops: tools, methodologies, and beyond

In spite of the limited investment in orphan crops, access to new technologies such as bioinformatics and low-cost genotyping opens new doors to modernise their breeding effectively. Innovation in plant breeding is imperative to meet the world's growing demand for staple food and feed crops, and orphan crops can play a significant role in increasing productivity and quality, especially in developing countries. The short breeding history of most orphan crops implies that genetic gain should be achievable through easy-to-implement approaches such as forward breeding for simple traits or introgression of elite alleles at key target trait loci. However, limited financial support and access to sufficient, relevant and reliable phenotypic data continue to pose major challenges in terms of resources and capabilities. Digitalisation of orphan-crop breeding programmes can help not only to improve data quality and management, but also to mitigate data scarcity by allowing data to be accumulated and analysed over time and across teams. Bioinformatics tools and access to technologies such as molecular markers, some of them provided as services via specific platforms, allow breeders to implement modern strategies to improve breeding efficiency. In orphan crops, more marker-trait associations relevant to breeding germplasm are generally needed, but implementing digitalization, marker-based quality control or simple trait screening and introgression will help modernising breeding. Finally, the development of local capacities-of both people and infrastructure-remains a necessity to ensure the sustainable adoption of modern breeding approaches.

Orphan crops: their importance and the urgency of improvement

Due to significant contributions of orphan crops in the economy of the developing world, scientific studies need to be promoted on these little researched but vital crops of smallholder farmers and consumers. Food security is the main challenge in the developing world, particularly in the least developed countries. Orphan crops play a vital role in the food security and livelihood of resource-poor farmers and consumers in these countries. Like major crops, there are members of all food types-cereals, legumes, vegetables and root and tuber crops, that are considered to be orphan crops. Despite their huge importance for present and future agriculture, orphan crops have generally received little attention by the global scientific community. Due to this, they produce inferior yields in terms of both quantity and quality. The major bottlenecks affecting the productivity of these crops are little or no selection of improved genetic traits, extreme environmental conditions and unfavorable policy. However, some orphan crops have recently received the attention of the global and national scientific community where advanced research and development initiatives have been launched. These initiatives which implement a variety of genetic and genomic tools targeted major constraints affecting productivity and/or nutritional quality of orphan crops. In this paper, some of these initiatives are briefly described. Here, I provide key suggestions to relevant stakeholders regarding improvement of orphan crops. Concerted efforts are urgently needed to advance the research and development of both the major and orphan crops so that food security will be achieved and ultimately the livelihood of the population will be improved.

Prospects of orphan crops in climate change

MAIN CONCLUSION

Orphan crops can contribute to building resilience of marginal cropping systems as a climate chnage adaptation strategy. Orphan crops play an important role in global food and nutrition security, and may have potential to contribute to sustainable food systems under climate change. Owing to reports of their potential under water scarcity, there is an argument to promote them to sustainably address challenges such as increasing drought and water scarcity, food and nutrition insecurity, environmental degradation, and employment creation under climate change. We conducted a scoping review using online databases to identify the prospects of orphan crops to contribute to (1) sustainable and healthy food systems, (2) genetic resources for future crop improvement, and (3) improving agricultural sustainability under climate change. The review found that, as a product of generations of landrace agriculture, several orphan crops are nutritious, resilient, and adapted to niche marginal agricultural environments. Including such orphan crops in the existing monocultural cropping systems could support more sustainable, nutritious, and diverse food systems in marginalised agricultural environments. Orphan crops also represent a broad gene pool for future crop improvement. The reduction in arable land due to climate change offers opportunities to expand the area under their production. Their suitability to marginal niche and low-input environments offers opportunities for low greenhouse gas (GHG) emissions from an agro-ecosystems, production, and processing perspective. This, together with their status as a sub-set of agro-biodiversity, offers opportunities to address socio-economic and environmental challenges under climate change. With research and development, and policy to support them, orphan crops could play an important role in climate-change adaptation, especially in the global south.

Rational trade-offs between yield increase and fertilizer inputs are essential for sustainable intensification: A case study in wheat-maize cropping systems in China

In order to feed a population of nearly 1.4 billion people with limited arable land resources, China's high crop production has been maintained by an intensive cropping system with excessive inputs of chemical fertilizers, resulting in high environmental costs. This study attempted to explore the reasonable balance between yield increase and nitrogen (N) inputs in the intensive wheat-maize cropping system in the North China Plain, which is one of the most important grain production regions in China. Based on yield simulations with the DSSAT-CERES-Wheat and DSSAT-CERES-Maize models and a household survey of 241 farmers' fields, we conducted a coupled analysis of the regional crop yields, N fertilizer inputs, and farmers' technical conversion efficiency with respect to winter wheat and summer maize production in four representative study areas. We also conducted a quantitative analysis of the equilibrium relationship between fertilizer application rates and expected yields, and the optimum N fertilization amounts for wheat and maize were recommended. The results indicated that farmers' average yields had reached almost 80% of the attainable yields, which meant that there was little room for farmers to increase their yields. However, we found that the yield gaps among the different farmers were still large, and most farmers applied excessive amounts of N while obtaining unsatisfactory yields due to poor fertilizer management techniques. Only 15% of winter wheat and 4% of summer maize on farmers' fields had achieved the synergy of high crop yields and efficient fertilization, and farmers' technical conversion efficiency was still relatively low. Therefore, farmers should be guided to appropriately lower their yield expectations and reduce the overuse of N fertilizer. In the future, if farmers receive necessary education and training and adopt advanced fertilizer management techniques, sustainable intensification of agricultural production with lower environmental costs will be feasible in China.

Effect of native growth promoting bacteria and commercial biofertilizers on growth and yield of wheat (Triticum aestivum) and barley (Hordeum vulgare) under salinity stress conditions

Salinity is one of the main obstacles to the production of crops in dry regions of the world. This study focuses on the effects of different strains of plant growth promoting rhizobacteria (PGPR) isolated from native soils on the physiological responses of wheat and barley plants under normal and salt stress conditions. Soil samples were collected from a field in Ilam province, in Iran and bacterial isolates were isolated and screened for salt tolerance, included siderophore and ACC-deaminase production and phosphate solubilizing. Thereafter a two-years greenhouse experiment was conducted as a completely randomized block design with four replications. The applied treatments included bacterial inoculation at five levels (B0: non-inoculation, B1: Siderophore producing + salt-tolerant bacteria, B2: phosphate solubilizing + salt-tolerant bacteria, B3: ACC-deaminase producing + salt-tolerant bacteria, B4: Barvar-2 biological fertilizer, B5: Biofarm-2 biological fertilizer) and salt stress at three levels (S1: 0 dS/m, S2: 4 dS/m, S3: 8 dS/m). Results showed that phosphate solubilizing+ salt-tolerant bacteria resulted in the highest barley grain yield at 4 dS/m salinity level and had no significant difference with ACC-deaminase producing + salt-tolerant bacteria and Barvar-2 biological fertilizer and Biofarm-2 biological fertilizer. The highest proline content in wheat and barley observed in Siderophore producing+ salt-tolerant bacteria at 8 dS/m by 17.48 and 23.42, respectively, followed by phosphate solubilizing+ salt-tolerant bacteria by 16.53 and 19.78. Therefore, the application of isolated growth promoting bacteria can be recommended as an effective biofertilizer in Ilam province.

Chlorophyll fluorescence and carbohydrate concentration as field selection traits for heat tolerant chickpea genotypes

Chickpea (Cicer arietinum L.), a cool season crop is severely affected by heat stress, predicted to increase due to warming climates. Research for identifying heat tolerance markers for potential chickpea genotype selection is imperative. The study assessed the response of four chickpea genotypes to a natural temperature gradient in the field using chlorophyll fluorescence, non-structural carbohydrate, chlorophyll concentrations, gas exchange and grain yield. Field experiments were carried out in two winter seasons at three locations with known differences in temperature in NE South Africa. Results showed two genotypes were tolerant to heat stress with an F_v/F_m of 0.83-0.85 at the warmer site, while the two sensitive genotypes showed lower F_v/F_m of 0.78-0.80. Both dark-adapted F_v/F_m and F_q'/F_m' (where F_q' = F_m' -F) measured at comparable high light levels correlated positively with grain yield. The two tolerant genotypes also showed higher photosynthetic rates, starch, sucrose and grain yield than the sensitive genotypes at the warmer site. However, these parameters were consistently higher at the cooler sites than at the warmer. These results were further validated by a climate chamber experiment, where higher F_v/F_m decline in the sensitive compared to tolerant genotypes was observed when they were exposed to short-term heat treatments of 30/25 °C and 35/30 °C. Tolerant genotypes had higher F_v/F_m (0.78-0.81) and grain yield plant^-1(1.12-2.37g) compared to sensitive genotypes (0.74-0.75) and (0.32-0.89g plant^-1) respectively in the 35/30 °C. It is concluded that chlorophyll fluorescence and leaf carbohydrates are suitable tools for selection of heat tolerant chickpea genotypes under field conditions, while the coolest site showed favourable conditions for chickpea production.

Chinese chives and garlic in intercropping in strawberry high tunnels for Neopamera bilobata Say (Hemiptera: Rhyparochromidae) control

Strawberry is affected by several pests and diseases. Neopamera bilobata is an emerging pest that has been reported by several strawberry growers, usually associated with catfacing symptoms in fruits. We evaluated intercropping garlic or Chinese chives on N. bilobata populations on strawberry crops grown in high tunnels in two experiments. In the first experiment, we evaluated N. bilobata populations on strawberry intercropping with garlic plants (three densities: 8, 16, 24 GP - garlic plant per plot) on the bags by taking 12 samples from December 2015 to April 2017. N. bilobata populations on strawberry were also assessed when Chinese chives were grown under the suspended wooden structures in which strawberry plants are grown ('undercropping') (14 samples), in two high tunnels, from November 2016 to March 2017. The number of nymphs and adults on 14 randomly selected fruits per plot were assessed. During the garlic intercropping experiment, the treatments of three densities of garlic reduced N. bilobata populations; however, the 24 GP treatment caused a greater reduction than the 8 GP treatment. Garlic densities reduced N. bilobata populations by 35, 50, and 64% for the 8, 16, and 24 GP treatments, respectively. Chinese chives cultivated under the structures reduced N. bilobata populations by 47%. The results suggest that intercropping garlic or undercropping Chinese chives are suitable tools to be tested in integrated pest management in strawberry crops.

Microbial Enzymatic Activities and Community-Level Physiological Profiles (CLPP) in Subsoil Layers Are Altered by Harvest Residue Management Practices in a Tropical Eucalyptus grandis Plantation

Harvest residue management is a key issue for the sustainability of Eucalyptus plantations established on poor soils. Soil microbial communities contribute to soil fertility by the decomposition of the organic matter (OM), but little is known about the effect of whole-tree harvesting (WTH) in comparison to stem only harvesting (SOH) on soil microbial functional diversity in Eucalyptus plantations. We studied the effects of harvest residue management (branches, leaves, bark) of Eucalyptus grandis trees on soil enzymatic activities and community-level physiological profiles in a Brazilian plantation. We measured soil microbial enzymatic activities involved in OM decomposition and we compared the community level physiological profiles (CLPP) of the soil microbes in WTH and SOH plots. WTH decreased enzyme activities and catabolic potential of the soil microbial community. Furthermore, these negative effects on soil functional diversity were mainly observed below the 0-5 cm layer (5-10 and 10-20 cm), suggesting that WTH can be harmful to the soil health in these plantations.