Breeding for abiotic stresses for sustainable agriculture

Growth and antioxidant responses to water stress in eggplant MAGIC population parents, F1 hybrids and a subset of recombinant inbred lines

BACKGROUND

The generation of new eggplant (Solanum melongena L.) cultivars with drought tolerance is a main challenge in the current context of climate change. In this study, the eight parents (seven of S. melongena and one of the wild relative S. incanum L.) of the first eggplant MAGIC (Multiparent Advanced Generation Intercrossing) population, together with four F1 hybrids amongst them, five S5 MAGIC recombinant inbred lines selected for their genetic diversity, and one commercial hybrid were evaluated in young plant stage under water stress conditions (30% field capacity; FC) and control conditions (100% FC). After a 21-day treatment period, growth and biomass traits, photosynthetic pigments, oxidative stress markers, antioxidant compounds, and proline content were evaluated.

RESULTS

Significant effects (p < 0.05) were observed for genotype, water treatments and their interaction in most of the traits analyzed. The eight MAGIC population parental genotypes displayed a wide variation in their responses to water stress, with some of them exhibiting enhanced root development and reduced foliar biomass. The commercial hybrid had greater aerial growth compared to root growth. The four F1 hybrids among MAGIC parents differed in their performance, with some having significant positive or negative heterosis in several traits. The subset of five MAGIC lines displayed a wide diversity in their response to water stress.

CONCLUSION

The results show that a large diversity for tolerance to drought is available among the eggplant MAGIC materials, which can contribute to developing drought-tolerant eggplant cultivars.

Meta-QTL and Candidate Gene Analyses of Agronomic Salt Tolerance and Related Traits in an RIL Population Derived from Solanum pimpinellifolium

Breeding salt-tolerant crops is necessary to reduce food insecurity. Prebreeding populations are fundamental for uncovering tolerance alleles from wild germplasm. To obtain a physiological interpretation of the agronomic salt tolerance and better criteria to identify candidate genes, quantitative trait loci (QTLs) governing productivity-related traits in a population of recombinant inbred lines (RIL) derived from S. pimpinellifolium were reanalyzed using an SNP-saturated linkage map and clustered using QTL meta-analysis to synthesize QTL information. A total of 60 out of 85 QTLs were grouped into 12 productivity MQTLs. Ten of them were found to overlap with other tomato yield QTLs that were found using various mapping populations and cultivation conditions. The MQTL compositions showed that fruit yield was genetically associated with leaf water content. Additionally, leaf Cl- and K+ contents were related to tomato productivity under control and salinity conditions, respectively. More than one functional candidate was frequently found, explaining most productivity MQTLs, indicating that the co-regulation of more than one gene within those MQTLs might explain the clustering of agronomic and physiological QTLs. Moreover, MQTL1.2, MQTL3 and MQTL6 point to the root as the main organ involved in increasing productivity under salinity through the wild allele, suggesting that adequate rootstock/scion combinations could have a clear agronomic advantage under salinity.

Promising physiological traits associated with nitrogen use efficiency in rice under reduced N application

Higher grain yield in high-yielding rice varieties is mostly driven by nitrogen (N) fertilizer applied in abundant amounts leading to increased production cost and environmental pollution. This has fueled the studies on nitrogen use efficiency (NUE) to decrease the N fertilizer application in rice to the possible extent. NUE is a complex physiological trait controlled by multiple genes, but yet to be completely deciphered in rice. With an objective of identifying the promising physiological traits associated with NUE in rice, the performance of 14 rice genotypes was assessed at N0, N50, N100, and N150 for four (two wet and two dry) seasons using agro-morphological, grain yield, flag leaf traits, photosynthetic pigment content, flag leaf gas exchange traits, and chlorophyll fluorescence traits. Furthermore, the data were used to derive various NUE indices to identify the most appropriate indices useful to screen rice genotypes at N50. Results indicate that with the increase in N application, cumulative grain yield increased significantly up to N100 (5.02 t ha-1); however, the increment in grain yield was marginal at N150 (5.09 t ha-1). The mean reduction of grain yield was only 26.66% at N50 ranging from 15.0% to 34.2%. The significant finding of the study is the identification of flag leaf chlorophyll fluorescence traits (Fv/Fm, ΦPSII, ETR, and qP) and Ci associated with grain yield under N50, which can be used to screen N use efficient genotypes in rice under reduced N application. Out of nine NUE indices assessed, NUpE, NUtE, and NUEyield were able to delineate the high-yielding genotypes at N50 and were useful to screen rice under reduced N conditions. Birupa emerged as one of the high yielders under N50, even though it is a moderate yielder at N100 and infers the possibility of cultivating some of the released rice varieties under reduced N inputs. The study indicates the possibility of the existence of promising genetic variability for grain yield under reduced N, the potential of flag leaf chlorophyll fluorescence, and gas exchange traits as physiological markers and best suitable NUE indices to be deployed in rice breeding programs.

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.

Harboured cation/proton antiporters modulate stress response to integrated heat and salt via up-regulating KIN1 and GOLS1 in double transgenic Arabidopsis

Recent research has pointed to improved salt tolerance by co-overexpression of Arabidopsis thaliana NHX1 (Na+ /H+ antiporter) and SOS1 (Salt Overly Sensitive1). However, functionality under salt stress accompanying heat is less understood in double transgenics. To further advance possible co-operational interactions of AtNHX1 (N) and AtSOS1 (S) under combined stress, modulation of osmolyte, redox, energy, and abscisic acid metabolism genes was analysed. The expression of the target BIP3 , KIN1 , GOLS1 , OHP2 , and CYCA3;2 in transgenic Arabidopsis seedlings were significantly regulated towards a dramatic suppression by ionic, osmotic, and heat stresses. AtNHX1 and AtSOS1 co-overexpression (NS) outpaced the single transgenics and control in terms of membrane disorganisation and the electrolyte leakage of the cell damage caused by heat and salt stress in seedlings. While NaCl slightly induced CYCA3;2 in transgenics, combined stress up-regulated KIN1 and GOLS1 , not other genes. Single N and S transgenics overexpressing AtNHX1 and AtSOS1 only appeared similar in their growth and development; however, different to WT and NS dual transgenics under heat+salt stress. Seed germination, cotyledon survival, and hypocotyl length were less influenced by combined stress in NS double transgenic lines than in single N and S and wild type. Stress combination caused significant reprogramming of gene expression profiles, mainly towards downregulation, possibly as a trade-off strategy. Analysing phenotypic, cellular, and transcriptional responses regulating growth facets of tolerant transgenic genotypes may support the ongoing efforts to achieve combined salt and heat tolerance.

Enhancement of nitrogen use efficiency through agronomic and molecular based approaches in cotton

Cotton is a major fiber crop grown worldwide. Nitrogen (N) is an essential nutrient for cotton production and supports efficient crop production. It is a crucial nutrient that is required more than any other. Nitrogen management is a daunting task for plants; thus, various strategies, individually and collectively, have been adopted to improve its efficacy. The negative environmental impacts of excessive N application on cotton production have become harmful to consumers and growers. The 4R's of nutrient stewardship (right product, right rate, right time, and right place) is a newly developed agronomic practice that provides a solid foundation for achieving nitrogen use efficiency (NUE) in cotton production. Cropping systems are equally crucial for increasing production, profitability, environmental growth protection, and sustainability. This concept incorporates the right fertilizer source at the right rate, time, and place. In addition to agronomic practices, molecular approaches are equally important for improving cotton NUE. This could be achieved by increasing the efficacy of metabolic pathways at the cellular, organ, and structural levels and NUE-regulating enzymes and genes. This is a potential method to improve the role of N transporters in plants, resulting in better utilization and remobilization of N in cotton plants. Therefore, we suggest effective methods for accelerating NUE in cotton. This review aims to provide a detailed overview of agronomic and molecular approaches for improving NUE in cotton production, which benefits both the environment and growers.

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

DUF966 genes are widely found in monocotyledons, dicotyledons, mosses, and other species. Current evidence strongly suggests that they are involved in growth regulation and stress tolerance in crops. However, their functions in cucumbers remain unexplored. Here, cucumber CsDUF966 was systemically identified and characterized using bioinformatics. Eight CsDUF966 genes were identified in the cucumber genome. These were phylogenetically separated into three groups. All CsDUF966 proteins were hydrophilic and localized to the nucleus. Moreover, three acidic and five basic proteins were identified. Evolutionary analysis of DUF966 between cucumber and 33 other Cucurbitaceae species/cultivars revealed that most CsDUF966 genes were conserved, whereas CsDUF966_4.c and CsDUF966_7.c were positively selected among the five cucumber cultivars. Expression profiling analysis showed that CsDUF966 had variable expression patterns, and that miRNA164, miRNA166, and Csa-novel-35 were involved in the post-transcriptional regulation of CsDUF966_4.c and CsDUF966_7.c. The expression of CsDUF966_4.c and CsDUF966_7.c, which were under strong neofunctionalization selection, was strictly regulated in fruit and tissues, including seeds, pericarps, peels, and spines, suggesting that these genes are fruit growth regulators and were strongly selected during the cucumber breeding program. In conclusion, the results reveal the roles of CsDUF966s in regulating cucumber fruit development and lay the foundation for further functional studies.

Genotypic differences in the synergistic effect of nitrogen and boron on the seed yield and nitrogen use efficiency of Brassica napus

BACKGROUND

Rapeseed (Brassica napus) is highly sensitive to nitrogen (N) and boron (B) deficiency; however, the synergistic effects of these elements on rapeseed production are poorly understood. The aim of this study was to investigate the effects of co-application of N and B on seed yield, N uptake and N use efficiency (NUE) of rapeseed. Three rapeseed cultivars (W10, ZS11 and HG) were treated with different N and B application rates, and the seed yield, N uptake and NUE were examined in 2-year field experiments.

RESULTS

The application of B fertilizer (4.5, 9 kg borax ha^-1 ) improved N uptake, NUE and seed yield. However, the magnitude of increase in seed yield by B fertilization was dependent upon the rate of N supply and genotype. The benefit of B was much greater at 180 kg N ha^-1 than at 0 or 60 kg N ha^-1 . The combination of N and B also improved N remobilization from sources (stems and husks) to sinks (seeds) and increased N recovery efficiency (NRE). Compared with the B-inefficient cultivar W10, the B-efficient cultivars ZS11 and HG were superior in growth, seed yield, N uptake and NUE on B deficient soils. Furthermore, B-efficient cultivars showed great potential in saving N input, and the yield increased by more than 40% under B deficiency conditions.

CONCLUSION

This study highlights a markedly synergistic effect of N and B nutrition on rapeseed NUE and yield production and shows that B-efficient genotypes can increase yield and reduce N inputs under B-deficient conditions. © 2021 Society of Chemical Industry.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

Genomics Enabled Breeding Strategies for Major Biotic Stresses in Pea (Pisum sativum L.)

Pea (Pisum sativum L.) is one of the most important and productive cool season pulse crops grown throughout the world. Biotic stresses are the crucial constraints in harnessing the potential productivity of pea and warrant dedicated research and developmental efforts to utilize omics resources and advanced breeding techniques to assist rapid and timely development of high-yielding multiple stress-tolerant-resistant varieties. Recently, the pea researcher's community has made notable achievements in conventional and molecular breeding to accelerate its genetic gain. Several quantitative trait loci (QTLs) or markers associated with genes controlling resistance for fusarium wilt, fusarium root rot, powdery mildew, ascochyta blight, rust, common root rot, broomrape, pea enation, and pea seed borne mosaic virus are available for the marker-assisted breeding. The advanced genomic tools such as the availability of comprehensive genetic maps and linked reliable DNA markers hold great promise toward the introgression of resistance genes from different sources to speed up the genetic gain in pea. This review provides a brief account of the achievements made in the recent past regarding genetic and genomic resources' development, inheritance of genes controlling various biotic stress responses and genes controlling pathogenesis in disease causing organisms, genes/QTLs mapping, and transcriptomic and proteomic advances. Moreover, the emerging new breeding approaches such as transgenics, genome editing, genomic selection, epigenetic breeding, and speed breeding hold great promise to transform pea breeding. Overall, the judicious amalgamation of conventional and modern omics-enabled breeding strategies will augment the genetic gain and could hasten the development of biotic stress-resistant cultivars to sustain pea production under changing climate. The present review encompasses at one platform the research accomplishment made so far in pea improvement with respect to major biotic stresses and the way forward to enhance pea productivity through advanced genomic tools and technologies.

Comparative genetic, biochemical and physiological analysis of sodium and chlorine in wheat

Plant with a great diversity shows several responses towards the biotic and abiotic stresses. Among these abiotic stresses, salinity is the main damaging factor as it reduces the yield of wheat plant with moderate salt tolerance. For its survival, plant undergoes through some genetic, biochemical and physiological changes to tackle the stress. This review mainly describes the conditions where various ions present in the soil, especially sodium and chlorine, enter into the plant and the genes or proteins involved with survival mechanism against the damage in plants. Salt stress causes alteration in enzymatic activity and Photosynthesis, oxidative stress, damage of cellular structure and components and ionic imbalance. Ion toxicity stress occur due to accumulation of excessive sodium ion and chloride ion. Transcriptional factors TaPIMP, TaSRG and TaMYBsdu 1 play key role in gene expression mechanism to overcome the stress. High affinity potassium transporter gene family is responsible for salt tolerance in wheat plant. HKT1;4 and HKT1;5 genes are responsible for Na exclusion in Triticum monococcum. Forty QTLs were found with the marker assisted selection in bread wheat for salinity tolerance and some morphological traits, 5 QTLs were related to sodium ion exclusion. In bread wheat, salt stress tolerance mechanism is mainly an exclusion of Na⁺ ions but also include K⁺ ion concentration. The salinity tolerant germplasm MW#293 provides an opportunity for the development of future salinity tolerant bread wheat.

Meta-QTL analysis and candidate genes identification for various abiotic stresses in maize (Zea mays L.) and their implications in breeding programs

Global climate change leads to the concurrence of a number of abiotic stresses including moisture stress (drought, waterlogging), temperature stress (heat, cold), and salinity stress, which are the major factors affecting maize production. To develop abiotic stress tolerance in maize, many quantitative trait loci (QTL) have been identified, but very few of them have been utilized successfully in breeding programs. In this context, the meta-QTL analysis of the reported QTL will enable the identification of stable/real QTL which will pave a reliable way to introgress these QTL into elite cultivars through marker-assisted selection. In this study, a total of 542 QTL were summarized from 33 published studies for tolerance to different abiotic stresses in maize to conduct meta-QTL analysis using BiomercatorV4.2.3. Among those, only 244 major QTL with more than 10% phenotypic variance were preferably utilised to carry out meta-QTL analysis. In total, 32 meta-QTL possessing 1907 candidate genes were detected for different abiotic stresses over diverse genetic and environmental backgrounds. The MQTL2.1, 5.1, 5.2, 5.6, 7.1, 9.1, and 9.2 control different stress-related traits for combined abiotic stress tolerance. The candidate genes for important transcription factor families such as ERF, MYB, bZIP, bHLH, NAC, LRR, ZF, MAPK, HSP, peroxidase, and WRKY have been detected for different stress tolerances. The identified meta-QTL are valuable for future climate-resilient maize breeding programs and functional validation of candidate genes studies, which will help to deepen our understanding of the complexity of these abiotic stresses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01294-9.

Juvenile Heat Tolerance in Wheat for Attaining Higher Grain Yield by Shifting to Early Sowing in October in South Asia

Farmers in northwestern and central India have been exploring to sow their wheat much earlier (October) than normal (November) to sustain productivity by escaping terminal heat stress and to utilize the available soil moisture after the harvesting of rice crop. However, current popular varieties are poorly adapted to early sowing due to the exposure of juvenile plants to the warmer temperatures in the month of October and early November. Therefore, a study was undertaken to identify wheat genotypes suited to October sowing under warmer temperatures in India. A diverse collection of 3322 bread wheat varieties and elite lines was prepared in CIMMYT, Mexico, and planted in the 3rd week of October during the crop season 2012-2013 in six locations (Ludhiana, Karnal, New Delhi, Indore, Pune and Dharwad) spread over northwestern plains zone (NWPZ) and central and Peninsular zone (CZ and PZ; designated as CPZ) of India. Agronomic traits data from the seedling stage to maturity were recorded. Results indicated substantial diversity for yield and yield-associated traits, with some lines showing indications of higher yields under October sowing. Based on agronomic performance and disease resistance, the top 48 lines (and two local checks) were identified and planted in the next crop season (2013-2014) in a replicated trial in all six locations under October sowing (third week). High yielding lines that could tolerate higher temperature in October sowing were identified for both zones; however, performance for grain yield was more promising in the NWPZ. Hence, a new trial of 30 lines was planted only in NWPZ under October sowing. Lines showing significantly superior yield over the best check and the most popular cultivars in the zone were identified. The study suggested that agronomically superior wheat varieties with early heat tolerance can be obtained that can provide yield up to 8 t/ha by planting in the third to fourth week of October.

Water Use Efficiency in Popcorn (Zea mays L. var. everta): Which Physiological Traits Would Be Useful for Breeding?

To ensure genetic gains in popcorn breeding programs carried out under drought conditions knowledge about the response of morphophysiological traits of plants to water stress for the selection of key traits is required. Therefore, the objective was to evaluate popcorn inbred lines with agronomically efficient (P2 and P3) and inefficient (L61 and L63) water use and two hybrids (P2xL61 and P3xL63) derived from these contrasting parents, cultivated under two water regimes (WW watered-WW; and water-stressed-WS) in a greenhouse, replicated five times, where each experimental unit consisted of one plant in a PVC tube. Irrigation was applied until stage V6 and suspended thereafter. Individual and combined analyses of variance were performed and the genotypic correlations and relative heteroses estimated. The water use efficient inbred lines were superior in root length (RL), root dry weight (RDW), and net CO2 assimilation rate (A), which were the characteristics that differentiated the studied genotypes most clearly. High heterosis estimates were observed for RL, SDW, leaf width (LW), leaf midrib length (LL), and agronomic water use efficiency (AWUE). The existence of a synergistic association between root angle and length for the characteristics A, stomatal conductance (gs), and chlorophyll concentration (SPAD index) proved most important for the identification and phenotyping of superior genotypes. Based on the study of these characteristics, the higher AWUE of the previously selected inbred lines could be explained. The results reinforced the importance of root physiological and morphological traits to explain AWUE and the possibility of advances by exploiting heterosis, given the morphophysiological superiority of hybrids in relation to parents.

Breeding for drought and heat tolerance in wheat

Many approaches have been adopted to enhance the heat and drought tolerance of wheat with mixed success. An assessment of the relative merits of different strategies is presented. Wheat is the most widely grown crop globally and plays a key role in human nutrition. However, it is grown in environments that are prone to heat and drought stress, resulting in severely reduced yield in some seasons. Increased climate variability is expected to have a particularly adverse effect of wheat production. Breeding for stable yield across both good and bad seasons while maintaining high yield under optimal conditions is a high priority for most wheat breeding programs and has been a focus of research activities. Multiple strategies have been explored to enhance the heat and drought tolerance of wheat including extensive genetic analysis and modify the expression of genes involved in stress responses, targeting specific physiological traits and direct selection under a range of stress scenarios. These approaches have been combined with improvements in phenotyping, the development of genetic and genomic resources, and extended screening and analysis techniques. The results have greatly expanded our knowledge and understanding of the factors that influence yield under stress, but not all have delivered the hoped-for progress. Here, we provide an overview of the different strategies and an assessment of the most promising approaches.

E3 Ubiquitin Ligase SPL2 Is a Lanthanide-Binding Protein

The SPL2 protein is an E3 ubiquitin ligase of unknown function. It is one of only three types of E3 ligases found in the outer membrane of plant chloroplasts. In this study, we show that the cytosolic fragment of SPL2 binds lanthanide ions, as evidenced by fluorescence measurements and circular dichroism spectroscopy. We also report that SPL2 undergoes conformational changes upon binding of both Ca2+ and La3+, as evidenced by its partial unfolding. However, these structural rearrangements do not interfere with SPL2 enzymatic activity, as the protein retains its ability to auto-ubiquitinate in vitro. The possible applications of lanthanide-based probes to identify protein interactions in vivo are also discussed. Taken together, the results of this study reveal that the SPL2 protein contains a lanthanide-binding site, showing for the first time that at least some E3 ubiquitin ligases are also capable of binding lanthanide ions.

Genetics and genomics of root system variation in adaptation to drought stress in cereal crops

Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.

Addition of Aegilops biuncialis chromosomes 2M or 3M improves the salt tolerance of wheat in different way

Aegilops biuncialis is a promising gene source to improve salt tolerance of wheat via interspecific hybridization. In the present work, the salt stress responses of wheat-Ae. biuncialis addition lines were investigated during germination and in young plants to identify which Aegilops chromosomes can improve the salt tolerance of wheat. After salt treatments, the Aegilops parent and the addition lines 2M, 3M and 3M.4BS showed higher germination potential, shoot and root growth, better CO₂ assimilation capacity and less chlorophyll degradation than the wheat parent. The Aegilops parent accumulated less Na in the roots due to an up-regulation of SOS1, SOS2 and HVP1 genes, while it contained higher amount of proline, fructose, glucose, galactose, maltose and raffinose. In the leaves, lower Na level was accompanied by high amount of proline and increased expression of NHX2 gene. The enhanced accumulation of sugars and proline was also observed in the roots of 3M and 3M.4BS addition lines. Typical mechanism of 2M addition line was the sequestration of Na into the vacuole due to the increased expression of HVP1 in the roots and NHX2 in the leaves. These results suggest the Aegilops chromosomes 2M and 3M can improve salt tolerance of wheat in different way.

Spatial Heterogeneity of Winter Wheat Yield and Its Determinants in the Yellow River Delta, China

Understanding spatial differences of crop yields and quantitatively exploring the relationship between crop yields and influencing factors are of great significance in increasing regional crop yields, promoting sustainable development of regional agriculture and ensuring regional food security. This study investigates spatial heterogeneity of winter wheat yield and its determinants in the Yellow River Delta (YRD) region. The spatial pattern of winter wheat in 2015 was mapped through time series similarity analysis. Winter wheat yield was estimated by integrating phenological information into yield model, and cross-validation was performed using actual yield data. The geographical detector method was used to analyze determinants influencing winter wheat yield. This study concluded that the overall classification accuracy for winter wheat is 88.09%. The estimated yield agreed with actual yield, with R2 value of 0.74 and root mean square error (RMSE) of 1.02 t ha−1. Cumulative temperature, soil salinity and their interactions were key determinants affecting winter wheat yield. Several measures are recommended to ensure sustainable crop production in the YRD region, including improving irrigation and drainage systems to reduce soil salinity, selecting salt-tolerant winter wheat varieties, and improving agronomy techniques to extend effective cumulative temperature.

Root diversity in sesame (Sesamum indicum L.): insights into the morphological, anatomical and gene expression profiles

Sesame harbors a large diversity in root morphological and anatomical traits and a high root biomass improves the plant aboveground biomass as well as the seed yield. Sesame provides one of the most nutritious and healthy vegetable oils, sparking an increasing demand of its seeds. However, with the low yield and productivity of sesame, there is still a huge gap between the seed demand and supply. Improving the root system has a high potential to increase crop productivity, but information on the diversity of the sesame root systems is still lacking. In this study, 40 diverse sesame varieties were grown in soil and hydroponics systems and the diversity of the root system was investigated. The results showed that sesame holds a large root morphological and anatomical diversity, which can be harnessed in breeding programmes. Based on the clustering of the genotypes in hydroponics and soil culture systems, we found that similar genotypes were commonly clustered either in the small-root or in the big-root group, indicating that the hydroponics system can be employed for a large-scale root phenotyping. Our results further revealed that the root biomass positively contributes to increased seed yield in sesame, based on multi-environmental trials. By comparing the root transcriptome of two contrasting genotypes, 2897 differentially expressed genes were detected and they were enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, stilbenoid, diarylheptanoid and gingerol biosynthesis, flavonoid biosynthesis, suggesting that these pathways are crucial for sesame root growth and development. Overall, this study sheds light on the diversity of sesame root system and offers the basis for improving root traits and increasing sesame seed yield.

Soil Amendment With Different Maize Biochars Improves Chickpea Growth Under Different Moisture Levels by Improving Symbiotic Performance With Mesorhizobium ciceri and Soil Biochemical Properties to Varying Degrees

Chickpea (Cicer arietinum L.) is an important legume originating in the Mediterranean and the Middle East and is now cultivated in several varieties throughout the world due to its high protein and fiber content as well as its potential health benefits. However, production is drastically affected by prevalent water stress in most soybean-growing regions. This study investigates the potential of biochar to affect chickpea-Rhizobium symbiotic performance and soil biological activity in a pot experiment. Two different biochar types were produced from maize using different pyrolysis techniques, i.e., by heating at 600°C (MBC) and by batch-wise hydrothermal carbonization at 210°C (HTC), and used as soil amendments. The plant biomass, plant nutrient concentration, nodule numbers, leghemoglobin (Lb) content, soil enzyme activities, and nutrient contents of the grown chickpeas were examined. Our results indicated that plant root and shoot biomass, the acquisition of N, P, K, and Mg, soil nutrient contents, soil alkaline and acid phosphomonoesterases, and proteases were significantly increased by HTC char application in comparison to MBC char under both well-watered and drought conditions. Furthermore, the application of both biochar types caused an increase in nodule number by 52% in well-watered and drought conditions by improving the symbiotic performance of chickpea with Mesorhizobium ciceri. Rhizobial inoculation combined with HTC char showed a positive effect on soil FDA activity, proteases and alkaline phosphomonoesterases under well-watered and drought conditions compared to the control or MBC char-amended soils. This concept, whereby the type of producing biochar plays a central role in the effect of the biochar, conforms to the fact that there is a link between biochar chemical and physical properties and enhanced plant nutrient acquisition, symbiotic performance and stress tolerance.

The genetic basis of drought tolerance in the high oil crop Sesamum indicum

Unlike most of the important food crops, sesame can survive drought but severe and repeated drought episodes, especially occurring during the reproductive stage, significantly curtail the productivity of this high oil crop. Genome-wide association study was conducted for traits related to drought tolerance using 400 diverse sesame accessions, including landraces and modern cultivars. Ten stable QTLs explaining more than 40% of the phenotypic variation and located on four linkage groups were significantly associated with drought tolerance related traits. Accessions from the tropical area harboured higher numbers of drought tolerance alleles at the peak loci and were found to be more tolerant than those from the northern area, indicating a long-term genetic adaptation to drought-prone environments. We found that sesame has already fixed important alleles conferring survival to drought which may explain its relative high drought tolerance. However, most of the alleles crucial for productivity and yield maintenance under drought conditions are far from been fixed. This study also revealed that pyramiding the favourable alleles observed at the peak loci is of high potential for enhancing drought tolerance in sesame. In addition, our results highlighted two important pleiotropic QTLs harbouring known and unreported drought tolerance genes such as SiABI4, SiTTM3, SiGOLS1, SiNIMIN1 and SiSAM. By integrating candidate gene association study, gene expression and transgenic experiments, we demonstrated that SiSAM confers drought tolerance by modulating polyamine levels and ROS homeostasis, and a missense mutation in the coding region partly contributes to the natural variation of drought tolerance in sesame.

Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.)

Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.

Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice

Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promises to be an effective breeding option for these complex traits. We evaluated the effectiveness of two rather new options in the implementation of GS: trait and environment-specific marker selection and the use of multi-environment prediction models. A reference population of 280 rainfed lowland accessions endowed with 215k SNP markers data was phenotyped under a favorable and two managed drought environments. Trait-specific SNP subsets (28k) were selected for each trait under each environment, using results of GWAS performed with the complete genotype dataset. Performances of single-environment and multi-environment genomic prediction models were compared using kernel regression based methods (GBLUP and RKHS) under two cross validation scenarios: availability (CV2) or not (CV1) of phenotypic data for the validation set, in one of the environments. Trait-specific marker selection strategy achieved predictive ability (PA) of genomic prediction up to 22% higher than markers selected on the bases of neutral linkage disequilibrium (LD). Tolerance to drought stress was up to 32% better predicted by multi-environment models (especially RKHS based models) under CV2 strategy. Under the less favorable CV1 strategy, the multi-environment models achieved similar PA than the single-environment predictions. We also showed that reasonable PA could be obtained with as few as 3,000 SNP markers, even in a population of low LD extent, provided marker selection is based on pairwise LD. The implications of these findings for breeding for drought tolerance are discussed. The most resource sparing option would be accurate phenotyping of the reference population in a favorable environment and under a managed drought, while the candidate population would be phenotyped only under one of those environments.

Climate change and abiotic stress mechanisms in plants

Predicted global climatic change will perturb the productivity of our most valuable crops as well as detrimentally impact ecological fitness. The most important aspects of climate change with respect to these effects relate to water availability and heat stress. Over multiple decades, the plant research community has amassed a highly comprehensive understanding of the physiological mechanisms that facilitate the maintenance of productivity in response to drought, flooding, and heat stress. Consequently, the foundations necessary to begin the development of elite crop varieties that are primed for climate change are in place. To meet the food and fuel security concerns of a growing population, it is vital that biotechnological and breeding efforts to harness these mechanisms are accelerated in the coming decade. Despite this, those concerned with crop improvement must approach such efforts with caution and ensure that potentially harnessed mechanisms are viable under the context of a dynamically changing environment.

Compositional equivalence of event IND-ØØ412-7 to non-transgenic wheat

Wheat is the most widely grown cereal grain, occupying a significant portion of the total cultivated land. As drought is the major environmental stressor affecting crop production, yield maintenance under water deficit conditions appears as a highly desirable phenotype for crop improvement. The HaHB4 (Helianthus annuus homeobox 4) gene from sunflower encodes for a transcription factor involved in tolerance to environmental stress. The introduction of HaHB4 in wheat led to the development of event IND-ØØ412-7 (HB4^® wheat), which displayed higher yield in production environments of low productivity potential. Compositional analysis of IND-ØØ412-7 wheat, including 41 nutrients and 2 anti-nutrients for grain and 10 nutrients in forage, was performed. Results of these studies indicated that IND-ØØ412-7 is compositionally equivalent to non-transgenic wheat.

Genetic basis of drought tolerance during seed germination in barley

Drought is one of the harshest abiotic stresses hindering seed germination, plant growth, and crop productivity. A high rate and uniformity of germination under stressful conditions are vital for crop establishment and growth; thus, for productivity. A better understanding of the genetic architecture of seed germination under drought stress is a prerequisite for further increasing yield potential. Barley is considered one of the most abiotic stresses-tolerant cereals. Elucidating the drought tolerance of barley during seed germination would indeed pave the way towards improving the performance of all cereals. However, we still know relatively little about the genetic control of drought tolerance during the seed germination phase. In our study, 218 worldwide spring barley accessions were subjected to PEG-induced drought during seed germination. Induced drought stress "20% PEG" significantly reduced the seed germination parameters and seedling related traits. A genome-wide association scan (GWAS) was used to identify genomic regions associated with our trait of interest. In total, 338 single nucleotide polymorphisms (SNPs) were found to be associated with several traits distributed across seven barley chromosomes, of which 26 genomic regions were associated with candidate genes. The current study found some of the quantitative trait loci (QTL) that have previously been reported to be linked to seed germination-related traits under drought conditions, as well as some new associations. Noteworthy, the identified QTL colocalized with a number of genes (within interval ±0.5 Mbp) that are exclusively distributed on chromosomes 1H, 2H, and 5H. The annotation of these genes in barley shows their roles in drought tolerance through encoding different transcription factors. The function of the identified genes during seed germination was also confirmed by the annotation of their counterparts in Arabidopsis. The current analyses show the power of the GWAS both for identifying putative candidate genes and for improving plant adaptive traits in barley.

Transcriptomic analysis of Aegilops tauschii during long-term salinity stress

Aegilops tauschii is the diploid progenitor of the bread wheat D-genome. It originated from Iran and is a source of abiotic stress tolerance genes. However, little is known about the molecular events of salinity tolerance in Ae. tauschii. This study investigates the leaf transcriptional changes associated with long-term salt stress. Total RNA extracted from leaf tissues of control and salt-treated samples was sequenced using the Illumina technology, and more than 98 million high-quality reads were assembled into 255,446 unigenes with an average length of 1398 bp and an N50 of 2269 bp. Functional annotation of the unigenes showed that 93,742 (36.69%) had at least a significant BLAST hit in the SwissProt database, while 174,079 (68.14%) showed significant similarity to proteins in the NCBI nr database. Differential expression analysis identified 4506 salt stress-responsive unigenes. Bioinformatic analysis of the differentially expressed unigenes (DEUs) revealed a number of biological processes and pathways involved in the establishment of ion homeostasis, signaling processes, carbohydrate metabolism, and post-translational modifications. Fine regulation of starch and sucrose content may be important features involved in salt tolerance in Ae. tauschii. Moreover, 82% of DEUs mapped to the D-subgenome, including known QTL for salt tolerance, and these DEUs showed similar salt stress responses in other accessions of Ae. tauschii. These results could provide fundamental insight into the regulatory process underlying salt tolerance in Ae. tauschii and wheat and facilitate identification of genes involved in their salt tolerance mechanisms.

Association analysis of drought tolerance in cut chrysanthemum (Chrysanthemum morifolium Ramat.) at seedling stage

Understanding the genetic architecture is a prerequisite for crop improvement. The current research aimed to characterize the extent of genetic variation of drought tolerance harbored in a global collection of 159 chrysanthemum cultivars over 2 years. An average subordinate function value (ASFV), integrating the wilting index, the fresh weight retention rate, and the survival rate after re-watering under two drought-stressed trials, was used to quantify the level of drought tolerance. The performance of ASFV was generally correlated between the 2 years; and a high magnitude (0.95) of broad-sense heritability, coupled with the moderate genetic advance, was estimated for the ASFV. By applying MLM model with both population structure and kinship matrix as covariates association mapping identified 16 markers linked to drought tolerance, with the proportion of the phenotypic variation explained by an individual marker ranging from 4.4 to 7.6%. Of the eight markers predictive across the 2 years, four (E11M24-9, E3M2-8, E1M5-5, and EST-SSR34-3) were identified as favorable alleles for drought tolerance. Several cultivars that carry at least three of the four favorable alleles were identified as potential donor parents for future improvement of the drought tolerance. The findings provide an insight into the genetic basis of the drought tolerance in chrysanthemum and will, therefore, aid in developing new cultivars with enhanced tolerance against drought stress.

Nitrogen nutrition in cotton and control strategies for greenhouse gas emissions: a review

Cotton (Gossypium hirustum L.) is grown globally as a major source of natural fiber. Nitrogen (N) management is cumbersome in cotton production systems; it has more impacts on yield, maturity, and lint quality of a cotton crop than other primary plant nutrient. Application and production of N fertilizers consume large amounts of energy, and excess application can cause environmental concerns, i.e., nitrate in ground water, and the production of nitrous oxide a highly potent greenhouse gas (GHG) to the atmosphere, which is a global concern. Therefore, improving nitrogen use efficiency (NUE) of cotton plant is critical in this context. Slow-release fertilizers (e.g., polymer-coated urea) have the potential to increase cotton yield and reduce environmental pollution due to more efficient use of nutrients. Limited literature is available on the mitigation of GHG emissions for cotton production. Therefore, this review focuses on the role of N fertilization, in cotton growth and GHG emission management strategies, and will assess, justify, and organize the researchable priorities. Nitrate and ammonium nitrogen are essential nutrients for successful crop production. Ammonia (NH₃) is a central intermediate in plant N metabolism. NH₃ is assimilated in cotton by the mediation of glutamine synthetase, glutamine (z-) oxoglutarate amino-transferase enzyme systems in two steps: the first step requires adenosine triphosphate (ATP) to add NH₃ to glutamate to form glutamine (Gln), and the second step transfers the NH₃ from glutamine (Gln) to α-ketoglutarate to form two glutamates. Once NH₃ has been incorporated into glutamate, it can be transferred to other carbon skeletons by various transaminases to form additional amino acids. The glutamate and glutamine formed can rapidly be used for the synthesis of low-molecular-weight organic N compounds (LMWONCs) such as amides, amino acids, ureides, amines, and peptides that are further synthesized into high-molecular-weight organic N compounds (HMWONCs) such as proteins and nucleic acids.

Stress-induced changes of growth, yield and bioactive compounds in lemon balm cultivars

The aim of the present study was to investigate the impact of water deficiency on five Melissa officinalis genotypes. For three months water supply of 70% (control) and 40% (stress) of soil water capacity treatments have been adjusted in a pot experiment. Considering the morphological data, the different genetic potentials of cultivars were manifested only under optimum water regimes while under drought they merged into one homogeneous basic population representing the species. The biomass data decreased for all cultivars under drought stress, but the degree of loss was genotype specific. Genotype dependence of the change in essential oil accumulation was clearly proved by the data. Three of the cultivars ('Gold Leaf', 'Lorelei' and 'Quedlinburger Niederliegende') showed the same essential oil content both in control and stress treatments. Under drought stress the cultivar 'Lemona' produced only 35% of its essential oil content, however cv. 'Soroksár' reacted with 58% increase of essential oil accumulation to drought treatment. Considering the non-volatile bioactive compounds a unique response of the investigated accessions to drought stress was demonstrated. Cultivar 'Lorelei' showed an increased accumulation of total hydroxicinnamic acid derivatives content while cv. 'Gold Leaf' and 'Soroksár' clearly reacted with higher accumulation of total flavonoid fraction. In the case of cv. 'Quedlinburger Niederliegende' the remarkable decline in total flavonoid content is the most obvious stress reaction. The rosmarinic acid content of all genotypes showed lower accumulation level in consequence of lower water supply.

Biochemical, physiological and molecular evaluation of rice cultivars differing in salt tolerance at the seedling stage

Changes in the antioxidant enzymes, lipid peroxidation, sodium and potassium, chlorophyll, H2O2 and proline content were monitored in the leaves of 42 rice varieties which were not yet well-documented for the salinity tolerance under different salinity levels. The tolerant varieties (FL478, Hassani, Shahpasand, Gharib and Nemat) showed signs of tolerance (lower Na+/K+ ratio, high proline accumulation, less membrane damage, lower H2O2 production, and higher superoxide dismutase and catalase activity) very well. The positive relationship between the level of salt tolerance and the amount of proline accumulation in the rice varieties support the important role of proline under the salt stress. The varieties were genotyped for 12 microsatellite markers that were closely linked to SalTol QTL. The results of association analysis indicated that RM1287, RM8094, RM3412 and AP3206 markers had the high value of R2 for the regression models of the studied traits. It shows the important role of SalTol in controlling physio-biochemical traits. The results can be used in the future marker assisted selection (MAS) directly, if the results are confirmed.

The Emerging Oilseed Crop Sesamum indicum Enters the "Omics" Era

Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and quantitative trait locis for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an "orphan crop" to a "genomic resource-rich crop." With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the "Omics" area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop.

Nitrogen fertility and abiotic stresses management in cotton crop: a review

This review outlines nitrogen (N) responses in crop production and potential management decisions to ameliorate abiotic stresses for better crop production. N is a primary constituent of the nucleotides and proteins that are essential for life. Production and application of N fertilizers consume huge amounts of energy, and excess is detrimental to the environment. Therefore, increasing plant N use efficiency (NUE) is important for the development of sustainable agriculture. NUE has a key role in crop yield and can be enhanced by controlling loss of fertilizers by application of humic acid and natural polymers (hydrogels), having high water-holding capacity which can improve plant performance under field conditions. Abiotic stresses such as waterlogging, drought, heat, and salinity are the major limitations for successful crop production. Therefore, integrated management approaches such as addition of aminoethoxyvinylglycine (AVG), the film antitranspirant (di-1-p-menthene and pinolene) nutrients, hydrogels, and phytohormones may provide novel approaches to improve plant tolerance against abiotic stress-induced damage. Moreover, for plant breeders and molecular biologists, it is a challenge to develop cotton cultivars that can tolerate plant abiotic stresses while having high potential NUE for the future.

Toward an Integrated Root Ideotype for Irrigated Systems

Breeding towards root-centric ideotypes can be a relatively quick trait-based strategy to improve crop resource use efficiency. Irrigated agriculture represents a crucial and expanding sector, but its unique parameters require traits distinct from previously proposed rainfed ideotypes. We propose a novel irrigated ideotype that integrates traits across multiple scales to enhance resource use efficiency in irrigated agroecosystems, where resources are concentrated in a relatively shallow 'critical zone'. Unique components of this ideotype include rapid transplant recovery and establishment, enhanced exploitation of localized resource hotspots, adaptive physiological regulation, maintenance of hydraulic conductivity, beneficial rhizosphere interactions, and salinity/waterlogging avoidance. If augmented by future research, this target could help to enhance agricultural sustainability in irrigated agroecosystems by guiding the creation of resource-efficient cultivars.

Genome-wide identification and analysis of biotic and abiotic stress regulation of small heat shock protein (HSP20) family genes in bread wheat

Small Heat Shock Proteins (sHSPs)/HSP20 are molecular chaperones that protect plants by preventing protein aggregation during abiotic stress conditions, especially heat stress. Due to global climate change, high temperature is emerging as a major threat to wheat productivity. Thus, the identification of HSP20 and analysis of HSP transcriptional regulation under different abiotic stresses in wheat would help in understanding the role of these proteins in abiotic stress tolerance. We used sequences of known rice and Arabidopsis HSP20 HMM profiles as queries against publicly available wheat genome and wheat full length cDNA databases (TriFLDB) to identify the respective orthologues from wheat. 163 TaHSP20 (including 109 sHSP and 54 ACD) genes were identified and classified according to the sub-cellular localization and phylogenetic relationship with sequenced grass genomes (Oryza sativa, Sorghum bicolor, Zea mays, Brachypodium distachyon and Setaria italica). Spatio-temporal, biotic and abiotic stress-specific expression patterns in normalized RNA seq and wheat array datasets revealed constitutive as well as inductive responses of HSP20 in different tissues and developmental stages of wheat. Promoter analysis of TaHSP20 genes showed the presence of tissue-specific, biotic, abiotic, light-responsive, circadian and cell cycle-responsive cis-regulatory elements. 14 TaHSP20 family genes were under the regulation of 8 TamiRNA genes. The expression levels of twelve HSP20 genes were studied under abiotic stress conditions in the drought- and heat-tolerant wheat genotype C306. Of the 13 TaHSP20 genes, TaHSP16.9H-CI showed high constitutive expression with upregulation only under salt stress. Both heat and salt stresses upregulated the expression of TaHSP17.4-CI, TaHSP17.7A-CI, TaHSP19.1-CIII, TaACD20.0B-CII and TaACD20.6C-CIV, while TaHSP23.7-MTI was specifically induced only under heat stress. Our results showed that the identified TaHSP20 genes play an important role under different abiotic stress conditions. Thus, the results illustrate the complexity of the TaHSP20 gene family and its stress regulation in wheat, and suggest that sHSPs as attractive breeding targets for improvement of the heat tolerance of wheat.

Endophytic fungal diversity of Fragaria vesca, a crop wild relative of strawberry, along environmental gradients within a small geographical area

BACKGROUND

Fungal endophytes are highly diverse ubiquitous asymptomatic microorganisms, some of which appear to be symbiotic. Depending on abiotic conditions and genotype of the plant, the diversity of endophytes may confer fitness benefits to plant communities.

METHODS

We studied a crop wild relative (CWR) of strawberry, along environmental gradients with a view to understand the cultivable root-derived endophytic fungi that can be evaluated for promoting growth and tolerating stress in selected plant groups. The main objectives were to understand whether: (a) suboptimal soil types are drivers for fungal distribution and diversity; (b) high pH and poor nutrient availability lead to fungal-plant associations that help deliver fitness benefits; and (c) novel fungi can be identified for their use in improving plant growth, and alleviate stress in diverse crops.

RESULTS

The study revealed that habitats with high pH and low nutrient availability have higher fungal diversity, with more rare fungi isolated from locations with chalky soil. Plants from location G were the healthiest even though soil from this location was the poorest in nutrients. Study of environmental gradients, especially extreme habitat types, may help understand the root zone fungal diversity of different functional classes. Two small in vitro pilot studies conducted with two isolates showed that endophytic fungi from suboptimal habitats can promote plant growth and fitness benefits in selected plant groups.

DISCUSSION

Targeting native plants and crop wild relatives for research offers opportunities to unearth diverse functional groups of root-derived endophytic fungi that are beneficial for crops.

Genetic Gains in Grain Yield of a Maize Population Improved through Marker Assisted Recurrent Selection under Stress and Non-stress Conditions in West Africa

Marker-assisted recurrent selection (MARS) is a breeding method used to accumulate favorable alleles that for example confer tolerance to drought in inbred lines from several genomic regions within a single population. A bi-parental cross formed from two parents that combine resistance to Striga hermonthica with drought tolerance, which was improved through MARS, was used to assess changes in the frequency of favorable alleles and its impact on inbred line improvement. A total of 200 testcrosses of randomly selected S₁ lines derived from the original (C₀) and advanced selection cycles of this bi-parental population, were evaluated under drought stress (DS) and well-watered (WW) conditions at Ikenne and under artificial Striga infestation at Abuja and Mokwa in Nigeria in 2014 and 2015. Also, 60 randomly selected S₁ lines each derived from the four cycles (C₀, C₁, C₂, C₃) were genotyped with 233 SNP markers using KASP assay. The results showed that the frequency of favorable alleles increased with MARS in the bi-parental population with none of the markers showing fixation. The gain in grain yield was not significant under DS condition due to the combined effect of DS and armyworm infestation in 2015. Because the parents used for developing the bi-parental cross combined tolerance to drought with resistance to Striga, improvement in grain yield under DS did not result in undesirable changes in resistance to the parasite in the bi-parental maize population improved through MARS. MARS increased the mean number of combinations of favorable alleles in S₁ lines from 114 in C₀ to 124 in C₃. The level of heterozygosity decreased by 15%, while homozygosity increased by 13% due to the loss of some genotypes in the population. This study demonstrated the effectiveness of MARS in increasing the frequency of favorable alleles for tolerance to drought without disrupting the level of resistance to Striga in a bi-parental population targeted as a source of improved maize inbred lines.

Major cereal crops benefit from biological nitrogen fixation when inoculated with the nitrogen-fixing bacterium Pseudomonas protegens Pf-5 X940

A main goal of biological nitrogen fixation research has been to expand the nitrogen-fixing ability to major cereal crops. In this work, we demonstrate the use of the efficient nitrogen-fixing rhizobacterium Pseudomonas protegens Pf-5 X940 as a chassis to engineer the transfer of nitrogen fixed by BNF to maize and wheat under non-gnotobiotic conditions. Inoculation of maize and wheat with Pf-5 X940 largely improved nitrogen content and biomass accumulation in both vegetative and reproductive tissues, and this beneficial effect was positively associated with high nitrogen fixation rates in roots. ¹⁵ N isotope dilution analysis showed that maize and wheat plants obtained substantial amounts of fixed nitrogen from the atmosphere. Pf-5 X940-GFP-tagged cells were always reisolated from the maize and wheat root surface but never from the inner root tissues. Confocal laser scanning microscopy confirmed root surface colonization of Pf-5 X940-GFP in wheat plants, and microcolonies were mostly visualized at the junctions between epidermal root cells. Genetic analysis using biofilm formation-related Pseudomonas mutants confirmed the relevance of bacterial root adhesion in the increase in nitrogen content, biomass accumulation and nitrogen fixation rates in wheat roots. To our knowledge, this is the first report of robust BNF in major cereal crops.

On a quest for stress tolerance genes: membrane transporters in sensing and adapting to hostile soils

Abiotic stresses such as salinity, drought, and flooding severely limit food and fibre production and result in penalties of in excess of US$100 billion per annum to the agricultural sector. Improved abiotic stress tolerance to these environmental constraints via traditional or molecular breeding practices requires a good understanding of the physiological and molecular mechanisms behind roots sensing of hostile soils, as well as downstream signalling cascades to effectors mediating plant adaptive responses to the environment. In this review, we discuss some common mechanisms conferring plant tolerance to these three major abiotic stresses. Central to our discussion are: (i) the essentiality of membrane potential maintenance and ATP production/availability and its use for metabolic versus adaptive responses; (ii) reactive oxygen species and Ca(2+) 'signatures' mediating stress signalling; and (iii) cytosolic K(+) as the common denominator of plant adaptive responses. We discuss in detail how key plasma membrane and tonoplast transporters are regulated by various signalling molecules and processes observed in plants under stress conditions (e.g. changes in membrane potential; cytosolic pH and Ca(2+); reactive oxygen species; polyamines; abscisic acid) and how these stress-induced changes are related to expression and activity of specific ion transporters. The reported results are then discussed in the context of strategies for breeding crops with improved abiotic stress tolerance. We also discuss a classical trade-off between tolerance and yield, and possible avenues for resolving this dilemma.

Regulation of Chloroplast Protein Import by the Ubiquitin E3 Ligase SP1 Is Important for Stress Tolerance in Plants

Chloroplasts are the organelles responsible for photosynthesis in plants [1, 2]. The chloroplast proteome comprises ∼3,000 different proteins, including components of the photosynthetic apparatus, which are highly abundant. Most chloroplast proteins are nucleus-encoded and imported following synthesis in the cytosol. Such import is mediated by multiprotein complexes in the envelope membranes that surround each organelle [3, 4]. The translocon at the outer envelope membrane of chloroplasts (TOC) mediates client protein recognition and early stages of import. The TOC apparatus is regulated by the ubiquitin-proteasome system (UPS) in a process controlled by the envelope-localized ubiquitin E3 ligase SUPPRESSOR OF PPI1 LOCUS1 (SP1) [5, 6]. Previous work showed that SP1-mediated regulation of chloroplast protein import contributes to the organellar proteome changes that occur during plant development (e.g., during de-etiolation). Here, we reveal a critical role for SP1 in plant responses to abiotic stress, which is a major and increasing cause of agricultural yield losses globally [7]. Arabidopsis plants lacking SP1 are hypersensitive to salt, osmotic, and oxidative stresses, whereas plants overexpressing SP1 are considerably more stress tolerant than wild-type. We present evidence that SP1 acts to deplete the TOC apparatus under stress conditions to limit the import of photosynthetic apparatus components, which may attenuate photosynthetic activity and reduce the potential for reactive oxygen species production and photo-oxidative damage. Our results indicate that chloroplast protein import is responsive to environmental cues, enabling dynamic regulation of the organellar proteome, and suggest new approaches for improving stress tolerance in crops.

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Levels of the chloroplast E3 ligase SP1 influence plant abiotic stress tolerance

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Effects of SP1 on stress tolerance are linked to reactive oxygen species levels

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SP1 acts to deplete the chloroplast protein import (TOC) machinery under stress

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TOC depletion by SP1 is linked to reduced plastid import of photosynthesis proteins

Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses

Abiotic constraints are a source of concern in agriculture, because they can have a strong impact on plant growth and development, thereby affecting crop yield. The response of plants to abiotic constraints varies depending on the type of stress, on the species and on the organs. Although many studies have addressed different aspects of the plant response to abiotic stresses, only a handful has focused on the role of the cell wall. A targeted approach has been used here to study the expression of cell wall-related genes in different organs of alfalfa plants subjected for four days to three different abiotic stress treatments, namely salt, cold and heat stress. Genes involved in different steps of cell wall formation (cellulose biosynthesis, monolignol biosynthesis and polymerization) have been analyzed in different organs of Medicago sativa L. Prior to this analysis, an in silico classification of dirigent/dirigent-like proteins and class III peroxidases has been performed in Medicago truncatula and M. sativa. The final goal of this study is to infer and compare the expression patterns of cell wall-related genes in response to different abiotic stressors in the organs of an important legume crop.

Genetic dissection of tomato rootstock effects on scion traits under moderate salinity

Rootstock HKT1 genotype affected fruit [Na(+)] and non-commercial fruit yield; QTL analysis of rootstock-mediated scion nutrition is a powerful forward genetic approach to identify wild genes for rootstock breeding. The present study approaches the QTL dissection of rootstock effects on a commercial hybrid variety grafted on a population of RILs derived from Solanum pimpinellifolium, genotyped for 4370 segregating SNPs from the SolCAP tomato panel and grown under moderate salinity. Results are compared to those previously obtained under high salinity. The most likely functional candidate genes controlling the scion [Na(+)] were rootstock HKT1;1 and HKT1;2 as it was previously reported for non-grafted genotypes. The higher fruit [Na(+)] found when rootstock genotype was homozygote for SpHKT1 supports the thesis that scion HKT1 is loading Na(+) into the phloem sap in leaves and unloading it in sink organs. A significant increment of small, mostly seedless, fruits was found associated with SlHKT1 homozygous rootstocks. Just grafting increased the incidence of blossom end rot and delayed fruit maturation but there were rootstock RILs that increased commercial fruit yield under moderate salinity. The heritability and number of QTLs involved were lower and different than those found under high salinity. Four large contributing (>17%) rootstock QTLs, controlling the leaf concentrations of B, K, Mg and Mo were detected whose 2 Mbp physical intervals contained B, K, Mg and Mo transporter-coding genes, respectively. Since a minimum of 3 QTLs (two of them coincident with leaf K and Ca QTLs) were also found governing rootstock-mediated soluble-solids content of the fruit under moderate salinity, grafting desirable crop varieties on stress-tolerant rootstocks tenders an opportunity to increase both salt tolerance and quality.

Magnesium alleviates plant toxicity of aluminium and heavy metals

Magnesium (Mg) is an essential nutrient that can alleviate soilborne toxicity of many ions. This review paper critically assesses the literature on interactions and mechanisms influencing Mg alleviation of aluminium (Al) and heavy metal toxicity. Hydrated radii of Mg2+ and Al3+ are similar; therefore, these two ions compete for binding to ion transporters and other important biological molecules. In monocotyledonous species such as rice and wheat, millimolar concentrations of Mg alleviate Al toxicity, mainly by decreasing Al saturation and activity at cell wall and plasma membrane binding sites. In dicotyledonous legume species such as soybean (Glycine max), rice bean (Vigna umbellata) and broad bean (Vicia faba), micromolar concentrations of Mg may enhance biosynthesis of organic ligands and thus underpin alleviation of Al toxicity. Resistance to Al may be enhanced by increased expression of the genes coding for Mg transporters, as well as by upregulation of activity of Mg-transport proteins; intracellular Mg2+ activity may thus be increased under Al stress, which may increase the activity of H+-ATPases. In Vicia faba, Mg-related enhancement in the activity of plasma membrane H+-ATPase under Al stress was found to be due to post-translational modification (increased phosphorylation of the penultimate threonine as well as association with regulatory 14-3-3 proteins), resulting in increased resistance to Al stress. Magnesium can alleviate heavy metal stress by decreasing negative electrical potential and thus metal ion activities at the plasma membrane surface (physico-chemical competition), by enhancing activities of enzymes involved in biosynthesis of organic ligands, and by increasing vacuolar sequestration of heavy metals via increasing H+-pumping activity at the tonoplast. Future work should concentrate on characterising the role of intracellular Mg2+ homeostasis and Mg transporters in alleviating metal stress as well as in transcriptional, translational and post-translational regulation of H+-pumps and enzymes involved in biosynthesis and exudation of organic ligands.

The Shape of Ecosystem Management to Come: Anticipating Risks and Fostering Resilience

Global change is increasingly challenging the sustainable provisioning of ecosystem services to society. Addressing future uncertainty and risk has therefore become a central problem of ecosystem management. With risk management and resilience-based stewardship, two contrasting approaches have been proposed to address this issue. Whereas one is concentrated on anticipating and mitigating risks, the other is focused on fostering the ability to absorb perturbations and maintain desired properties. While they have hitherto been discussed largely separately in the literature, I here propose a unifying framework of anticipating risks and fostering resilience in ecosystem management. Anticipatory action is advocated when the predictability of risk is high and sufficient knowledge to address it is available. Conversely, in situations in which predictability and knowledge are limited, resilience-based measures are paramount. I conclude that, by adopting a purposeful combination of insights from risk and resilience research, we can make ecosystem services provisioning more robust to future uncertainty and change.