Food security: the challenge of increasing wheat yield and the importance of not compromising food safety

Detecting major introgressions in wheat and their putative origins using coverage analysis

Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.

Genome-wide survey of the dehydrin genes in bread wheat (Triticum aestivum L.) and its relatives: identification, evolution and expression profiling under various abiotic stresses

BACKGROUND

Bread wheat (Triticum aestivum) is an important staple cereal grain worldwide. The ever-increasing environmental stress makes it very important to mine stress-resistant genes for wheat breeding programs. Therefore, dehydrin (DHN) genes can be considered primary candidates for such programs, since they respond to multiple stressors.

RESULTS

In this study, we performed a genome-wide analysis of the DHN gene family in the genomes of wheat and its three relatives. We found 55 DHN genes in T. aestivum, 31 in T. dicoccoides, 15 in T. urartu, and 16 in Aegilops tauschii. The phylogenetic, synteny, and sequence analyses showed we can divide the DHN genes into five groups. Genes in the same group shared similar conserved motifs and potential function. The tandem TaDHN genes responded strongly to drought, cold, and high salinity stresses, while the non-tandem genes respond poorly to all stress conditions. According to the interaction network analysis, the cooperation of multiple DHN proteins was vital for plants in combating abiotic stress.

CONCLUSIONS

Conserved, duplicated DHN genes may be important for wheat being adaptable to a different stress conditions, thus contributing to its worldwide distribution as a staple food. This study not only highlights the role of DHN genes help the Triticeae species against abiotic stresses, but also provides vital information for the future functional studies in these crops.

Comparison of Winter Wheat Extraction Methods Based on Different Time Series of Vegetation Indices in the Northeastern Margin of the Qinghai–Tibet Plateau: A Case Study of Minhe, China

The northeastern margin of the Qinghai–Tibet Plateau (QTP) is an agricultural protection area in China’s new development plan, and the primary region of winter wheat growth within QTP. Winter wheat monitoring is critical for understanding grain self-sufficiency, climate change, and sustainable socioeconomic and ecological development in the region. However, due to the complex terrain and high altitude of the region, with discontinuous arable land and the relatively low level of agricultural development, there are no effective localization methodologies for extracting and monitoring the detailed planting distribution information of winter wheat. In this study, Sentinel-2A/B data from 2019 to 2020, obtained through the Google Earth Engine platform, were used to build time series reference curves of vegetation indices in Minhe. Planting distribution information of winter wheat was extracted based on the phenology time-weighted dynamic time warping (PT-DTW) method, and the effects of different vegetation indices’ time series and their corresponding threshold parameters were compared. The results showed that: (1) the three vegetation indices—normalized difference vegetation index (NDVI), normalized differential phenology index (NDPI), and normalized difference greenness index (NDGI)—maintained high mapping potential; (2) under the optimal threshold, >88% accuracy of index identification for winter wheat extraction was achieved; (3) due to improved extraction accuracy and resulting boundary range, NDPI and its corresponding optimal parameter (T = 0.05) performed the best. The process and results of this study have certain reference value for the study of winter wheat planting information change and the formulation of dynamic monitoring schemes in agricultural areas of QTP.

Major Genomic Regions for Wheat Grain Weight as Revealed by QTL Linkage Mapping and Meta-Analysis

Grain weight is a key determinant for grain yield potential in wheat, which is highly governed by a type of quantitative genetic basis. The identification of major quantitative trait locus (QTL) and functional genes are urgently required for molecular improvements in wheat grain yield. In this study, major genomic regions and putative candidate genes for thousand grain weight (TGW) were revealed by integrative approaches with QTL linkage mapping, meta-analysis and transcriptome evaluation. Forty-five TGW QTLs were detected using a set of recombinant inbred lines, explaining 1.76-12.87% of the phenotypic variation. Of these, ten stable QTLs were identified across more than four environments. Meta-QTL (MQTL) analysis were performed on 394 initial TGW QTLs available from previous studies and the present study, where 274 loci were finally refined into 67 MQTLs. The average confidence interval of these MQTLs was 3.73-fold less than that of initial QTLs. A total of 134 putative candidate genes were mined within MQTL regions by combined analysis of transcriptomic and omics data. Some key putative candidate genes similar to those reported early for grain development and grain weight formation were further discussed. This finding will provide a better understanding of the genetic determinants of TGW and will be useful for marker-assisted selection of high yield in wheat breeding.

Development and evaluation of an innovative grain cart with a pneumatic conveyor

In line with the requirements of the Egyptian government to find a solution for wheat transportation during the peak harvesting season, an innovative design for a grain cart with a capacity of 8 tons supplemented with a grain hopper, a lifting double-action pneumatic conveyor, and a built-in digital scale was tested and evaluated to facilitate the transport of wheat crops from farmers' fields to storage sites. The cart was manufactured in the workshop of a local industrial company. It was tested under varying operational conditions in different wheat production areas in terms of working performance, efficiency of the grain loading and unloading mechanism, precision of the grain weighing mechanism, and cost/ton. The cart will enable wheat farmers and traders to transport and deliver their crops easily to storage sites with minimal losses and maximum working efficiency. It will also increase farmers' profit because transportation cost by using this grain cart is less than that of the current conventional method. Moreover, the developed cart can secure wheat supply in government storage sites without any interruption during the peak wheat harvesting season.

Identification and Validation of Stable Quantitative Trait Loci for SDS-Sedimentation Volume in Common Wheat (Triticum aestivum L.)

Sodium dodecyl sulfate-sedimentation volume is an important index to evaluate the gluten strength of common wheat and is closely related to baking quality. In this study, a total of 15 quantitative trait locus (QTL) for sodium dodecyl sulfate (SDS)-sedimentation volume (SSV) were identified by using a high-density genetic map including 2,474 single-nucleotide polymorphism (SNP) markers, which was constructed with a doubled haploid (DH) population derived from the cross between Non-gda3753 (ND3753) and Liangxing99 (LX99). Importantly, four environmentally stable QTLs were detected on chromosomes 1A, 2D, and 5D, respectively. Among them, the one with the largest effect was identified on chromosome 1A (designated as QSsv.cau-1A.1) explaining up to 39.67% of the phenotypic variance. Subsequently, QSsv.cau-1A.1 was dissected into two QTLs named as QSsv.cau-1A.1.1 and QSsv.cau-1A.1.2 by saturating the genetic linkage map of the chromosome 1A. Interestedly, favorable alleles of these two loci were from different parents. Due to the favorable allele of QSsv.cau-1A.1.1 was from the high-value parents ND3753 and revealed higher genetic effect, which explained 25.07% of the phenotypic variation, mapping of this locus was conducted by using BC3F1 and BC3F2 populations. By comparing the CS reference sequence, the physical interval of QSsv.cau-1A.1.1 was delimited into 14.9 Mb, with 89 putative high-confidence annotated genes. SSVs of different recombinants between QSsv.cau-1A.1.1 and QSsv.cau-1A.1 detected from DH and BC3F2 populations showed that these two loci had an obvious additive effect, of which the combination of two favorable loci had the high SSV, whereas recombinants with unfavorable loci had the lowest. These results provide further insight into the genetic basis of SSV and QSsv.cau-1A.1.1 will be an ideal target for positional cloning and wheat breeding programs.

Effect of ZnO Nanoparticles on Growth and Biochemical Responses of Wheat and Maize

Zinc is an essential element that is also renowned for widespread contamination and toxicity at high concentrations. The present study was carried out to analyze the responses induced by lower, as well as higher, doses of zinc (0-200 mg/L), in the form of zinc oxide nanoparticles (ZnO NPs) in wheat and maize, for a period of 21 days. Accumulation of zinc increases with increasing Zn doses in both wheat and maize, with higher doses being in wheat (121 mg/kg in root and 66 mg/kg in shoot) than in maize (95 mg/kg in root and 48 mg/kg in shoot). The activity of alpha-amylase showed increase, while that of dehydrogenase decline, in response to ZnO NPs. The length and biomass of plants and photosynthetic pigments increased slightly upon ZnO NPs supply. Malondialdehyde content showed a progressive increase in root and shoot of both plants. However, in response, antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, guaiacol peroxidase, and catalase) showed increase up to lower concentrations (100 mg/L) of ZnO NPs but decline variably at higher levels (150-200 mg/L) in wheat and maize. The results suggest that lower supply of ZnO NPs (100 mg/L) could be stimulatory to the growth of plants and can be recommended as a Zn fertilizer source for crop production.

A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.)

The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997-2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01-3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype-phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.

Increased Predictive Accuracy of Multi-Environment Genomic Prediction Model for Yield and Related Traits in Spring Wheat (Triticum aestivum L.)

Genomic selection (GS) has the potential to improve the selection gain for complex traits in crop breeding programs from resource-poor countries. The GS model performance in multi-environment (ME) trials was assessed for 141 advanced breeding lines under four field environments via cross-predictions. We compared prediction accuracy (PA) of two GS models with or without accounting for the environmental variation on four quantitative traits of significant importance, i.e., grain yield (GRYLD), thousand-grain weight, days to heading, and days to maturity, under North and Central Indian conditions. For each trait, we generated PA using the following two different ME cross-validation (CV) schemes representing actual breeding scenarios: (1) predicting untested lines in tested environments through the ME model (ME_CV1) and (2) predicting tested lines in untested environments through the ME model (ME_CV2). The ME predictions were compared with the baseline single-environment (SE) GS model (SE_CV1) representing a breeding scenario, where relationships and interactions are not leveraged across environments. Our results suggested that the ME models provide a clear advantage over SE models in terms of robust trait predictions. Both ME models provided 2-3 times higher prediction accuracies for all four traits across the four tested environments, highlighting the importance of accounting environmental variance in GS models. While the improvement in PA from SE to ME models was significant, the CV1 and CV2 schemes did not show any clear differences within ME, indicating the ME model was able to predict the untested environments and lines equally well. Overall, our results provide an important insight into the impact of environmental variation on GS in smaller breeding programs where these programs can potentially increase the rate of genetic gain by leveraging the ME wheat breeding trials.

Molecular Cytogenetic Identification of a Novel Wheat-Thinopyrum ponticum 1JS (1B) Substitution Line Resistant to Powdery Mildew and Leaf Rust

Thinopyrum ponticum (2n = 10x = 70) is a wild relative of wheat with high tolerance to both biotic and abiotic stresses; it has been wildly used in wheat genetic improvement. A disomic substitution line named SN19647 was derived from a cross between Triticum aestivum and the wheat-Th. ponticum partial amphiploid SNTE20 (2n = 8x = 56). It was evaluated for disease resistance and characterized via sequential fluorescence in situ hybridization (FISH)-genomic in situ hybridization (GISH) and molecular markers. The results showed that SN19647 carried resistance to both powdery mildew and leaf rust. It contained 42 chromosomes with a pair of wheat chromosome 1B replaced by a pair of J^S chromosomes from Th. ponticum. In addition to chromosomal substitution events, structural variation also occurred on wheat chromosomes 2A, 5A, 6B, and 7B. Based on marker analysis, 19 markers specific to the J^S chromosome were obtained, of which seventeen markers belonged to homoeologous group one. These results indicated that SN19647 was a 1J^S (1B) substitution line. Compared with the known 1J^S (1D) substitution line CH10A5, it was found that 17 markers generated different specific bands to Th. ponticum, confirming the novelty of the 1J^S chromosome in SN19647. Therefore, SN19647, resistant to powdery mildew and leaf rust, was a novel 1J^S (1B) substitution line that can be used in wheat genetic improvement.

Oligosaccharins as Elicitors of Defense Responses in Wheat

Wheat is a highly relevant crop worldwide, and like other massive crops, it is susceptible to foliar diseases, which can cause devastating losses. The current strategies to counteract wheat diseases include global monitoring of pathogens, developing resistant genetic varieties, and agrochemical applications upon diseases' appearance. However, the suitability of these strategies is far from permanent, so other alternatives based on the stimulation of the plants' systemic responses are being explored. Plants' defense mechanisms can be elicited in response to the perception of molecules mimicking the signals triggered upon the attack of phytopathogens, such as the release of plant and fungal cell wall-derived oligomers, including pectin and chitin derivatives, respectively. Among the most studied cell wall-derived bioelicitors, oligogalacturonides and oligochitosans have received considerable attention in recent years due to their ability to trigger defense responses and enhance the synthesis of antipathogenic compounds in plants. Particularly, in wheat, the application of bioelicitors induces lignification and accumulation of polyphenolic compounds and increases the gene expression of pathogenesis-related proteins, which together reduce the severity of fungal infections. Therefore, exploring the use of cell wall-derived elicitors, known as oligosaccharins, stands as an attractive option for the management of crop diseases by improving plant readiness for responding promptly to potential infections. This review explores the potential of plant- and fungal-derived oligosaccharins as a practical means to be implemented in wheat crops.

Response of Lignin Metabolism to Light Quality in Wheat Population

The low red/far-red (R/FR) light proportion at the base of the high-density wheat population leads to poor stem quality and increases lodging risk. We used Shannong 23 and Shannong 16 as the test materials. By setting three-light quality treatments: normal light (CK), red light (RL), and far-red light (FRL), we irradiated the base internodes of the stem with RL and FRL for 7h. Our results showed that RL irradiation enhanced stem quality, as revealed by increased breaking strength, stem diameter, wall thickness and, dry weight per unit length, and the total amount of lignin and related gene expression increased, at the same time. The composition of lignin subunits was related to the lodging resistance of wheat. The proportion of S+G subunits and H subunits played a key role in wheat lodging resistance. RL could increase the content of S subunits and G subunits and the proportion of S+G subunits, reduce the proportion of H subunits. We described here, to the best of our knowledge, the systematic study of the mechanism involved in the regulation of stem breaking strength by light quality, particularly the effect of light quality on lignin biosynthesis and its relationship with lodging resistance in wheat.

Risk assessment and ecotoxicological effects of leachates extracted from industrial district soils of Nanjing, China

With the intensification of industrial development and urbanization, soil pollution is increasingly prominent. Therefore, the potential adverse effects caused by industrial activities need to be investigated. In this study, nine soil samples were collected from the industrial district of Nanjing, China, and the heavy metal concentrations were analyzed. Ambient severity of health (ASI) and ambient severity of ecology (ASII) caused by heavy metals in soil extracts were also evaluated via the multi-media environmental goals (MEG). The environmental risk assessment model was used to assess the health risk of soil extracts. The toxicity of soil extracts was diagnosed for wheat and Vicia faba. The results indicate that the contents of heavy metals were significantly different among the nine soil samples and mass concentration of heavy metals were as followed: Pb > Mn > As > Zn > Cd. Except for CK and S9, the total health impact of all sampling sites were greater than 1. Also, the total ecological hazard degrees of the five heavy metals were all greater than 1, which showed that the soil extracts were harmful to human health and ecological environment. According to the risk characterization model, the carcinogen risk of soil extracts was 1 to 10 orders of magnitude higher than that of non-carcinogens. Drinking water intake was the most direct and primary exposure route. In addition, the ecotoxicological results indicated that with the increase of heavy metal concentration, the activity of amylase (AMS) decreased, while the activity of peroxide (POD) increased, indicating that the soil extracts were toxic to V. faba. The micronucleus rates of V. faba root tips in the sampling soils were significantly higher compared with the control group, reflecting the higher genotoxicity. Our study provides theoretical support for the evaluation of potential health and ecological risks in this industrial district.

Wheat consumption and prevalence of celiac disease: Correlation from a multilevel analysis

Celiac disease (CD) is triggered by both genetic and environmental factors. More than 1% of the world's population is affected by CD. In recent years, studies have confirmed a worldwide rising trend in CD prevalence. "Westernized diet" is one of the main factors of this increasing prevalence. However, the relationship between wheat consumption, its dynamics, and CD has not been adequately investigated on a global scale. This study aimed to perform a multilevel analysis of the association between wheat consumption and CD. Wheat consumption data from countries and continents were obtained from the database. The relative increase/decrease in wheat consumption over a long period (since 1961) and a short period (since 2004) were calculated using various statistical tools. The relationship between wheat consumption and celiac frequency was determined using the R-commander R package version 2.6-2. Pearson's correlation coefficient (r = 0.88) confirmed a high positive correlation between wheat consumption and the prevalence of biopsy-proven CD by estimating continent-wide wheat consumption data, but an insignificant correlation was found when the data were compared country-wide.

Genetic basis of some physiological traits and yield in early and late sowing conditions in bread wheat (Triticum aestivum L.)

The rise in human population necessitates the use of all available tools to enhance wheat productivity. In this regard, pre-breeding has mobilized novel underutilized genetic variation into breeding programs. However, this germplasm needs to be characterized for its efficient utilization. This investigation was initiated to evaluate the early and late sown wheat pre-breeding germplasm for physiology- and yield-related traits and to associate the mapped SNPs using association mapping approach. Our results indicate that the germplasm performed better in early sowing in comparison to late planting where grain yield (Yd) was found positively correlated with water use efficiency (WUE), heading time, and chlorophyll contents (Chl). We discovered a total of 210 associations involving 155 SNPs. Taking into consideration either early or late sowing and the mean values, only 12 marker traits were associated with trait germination, plant height, stomatal conductance, transpiration rate, Chl, carotenoids, and Yd. Our correlations and mapping results indicate that higher WUE along with Chl can be targeted as indirect physiological markers to enhance wheat yield.

Development and Exploitation of KASP Assays for Genes Underpinning Drought Tolerance Among Wheat Cultivars From Pakistan

High-throughput genotyping for functional markers offers an excellent opportunity to effectively practice marker-assisted selection (MAS) while breeding cultivars. We developed kompetitive allele-specific PCR (KASP) assays for genes conferring drought tolerance in common wheat (Triticum aestivum L.). In total, 11 KASP assays developed in this study and five already reported assays were used for their application in wheat breeding. We investigated alleles at 16 loci associated with drought tolerance among 153 Pakistani hexaploid wheat cultivars released during 1953-2016; 28 diploid wheat accessions (16 for AA and 12 for BB) and 19 tetraploid wheat (AABB) were used to study the evolutionary history of the studied genes. Superior allelic variations of the studied genes were significantly associated with higher grain yield. Favored haplotypes of TaSnRK2.3-1A, TaSnRK2.3-1B, TaSnRK2.9-5A, TaSAP-7B, and TaLTPs-1A predominated in Pakistani wheat germplasm indicating unconscious pyramiding and selection pressure on favorable haplotypes during selection breeding. TaSnRK2.8-5A, TaDreb-B1, 1-feh w3, TaPPH-7A, TaMOC-7A, and TaPARG-2A had moderate to low frequencies of favorable haplotype among Pakistani wheat germplasm pointing toward introgression of favorable haplotypes by deploying functional markers in marker-assisted breeding. The KASP assays were compared with gel-based markers for reliability and phenotypically validated among 62 Pakistani wheat cultivars. Association analyses showed that the favorable allelic variations were significantly associated with grain yield-contributing traits. The developed molecular marker toolkit of the genes can be instrumental for the wheat breeding in Pakistan.

Profiling, isolation and characterisation of beneficial microbes from the seed microbiomes of drought tolerant wheat

Climate change is predicted to increase the incidence and severity of drought conditions, posing a significant challenge for agriculture globally. Plant microbiomes have been demonstrated to aid crop species in the mitigation of drought stress. The study investigated the differences between the seed microbiomes of drought tolerant and drought susceptible wheat lines. Furthermore, it highlighted and quantified the degree of drought tolerance conferred by specific microbes isolated from drought tolerant wheat seed microbiomes. Metagenomic and culture-based methods were used to profile and characterise the seed microbiome composition of drought tolerant and drought susceptible wheat lines under rainfed and drought conditions. Isolates from certain genera were enriched by drought tolerant wheat lines when placed under drought stress. Wheat inoculated with isolates from these targeted genera, such as Curtobacterium flaccumfaciens (Cf D3-25) and Arthrobacter sp. (Ar sp. D4-14) demonstrated the ability to promote growth under drought conditions. This study indicates seed microbiomes from genetically distinct wheat lines enrich for beneficial bacteria in ways that are both line-specific and responsive to environmental stress. As such, seed from stress-phenotyped lines represent an invaluable resource for the identification of beneficial microbes with plant growth promoting activity that could improve commercial crop production.

Source-Sink Manipulation Affects Accumulation of Zinc and Other Nutrient Elements in Wheat Grains

To better understand the source–sink flow and its relationships with zinc (Zn) and other nutrients in wheat (Triticum aestivum L.) plants for biofortification and improving grain nutritional quality, the effects of reducing the photoassimilate source (through the flag leaf removal and spike shading) or sink (through the removal of all spikelets from one side of the spike, i.e., 50% spikelets removal) in the field of the accumulation of Zn and other nutrients in grains of two wheat cultivars (Jimai 22 and Jimai 44) were investigated at two soil Zn application levels. The kernel number per spike (KNPS), single panicle weight (SPW), thousand kernel weight (TKW), total grain weight (TGW) sampled, concentrations and yields of various nutrient elements including Zn, iron (Fe), manganese (Mn), copper (Cu), nitrogen (N), phosphorus (P), potassium (K), calcium (Ca) and magnesium (Mg), phytate phosphorus (phytate-P), phytic acid (PA) and phytohormones (ABA: abscisic acid, and the ethylene precursor ACC: 1-aminocylopropane-1-carboxylic acid), and carbon/N ratios were determined. Soil Zn application significantly increased the concentrations of grain Zn, N and K. Cultivars showing higher grain yields had lower grain protein and micronutrient nutritional quality. SPW, KNPS, TKW (with the exception of TKW in the removal of half of the spikelets), TGW, and nutrient yields in wheat grains were most severely reduced by half spikelet removal, secondly by spike shading, and slightly by flag leaf removal. Grain concentrations of Zn, N and Mg consistently showed negative correlations with SPW, KNPS and TGW, but positive correlations with TKW. There were general positive correlations among grain concentrations of Zn, Fe, Mn, Cu, N and Mg, and the bioavailability of Zn and Fe (estimated by molar ratios of PA/Zn, PA/Fe, PA × Ca/Zn, or PA × Ca/Fe). Although Zn and Fe concentrations were increased and Ca was decreased in treatments of half spikelet removal and spike shading, the treatments simultaneously increased PA and limited the increase in bioavailability of Zn and Fe. In general, different nutrient elements interact with each other and are affected to different degrees by source–sink manipulation. Elevated endogenous ABA levels and ABA/ACC ratios were associated with increased TKW and grain-filling of Zn, Mn, Ca and Mg, and inhibited K in wheat grains. However, the effects of ACC were diametrically opposite. These results provide a basis for wheat grain biofortification to alleviate human malnutrition.

Hyperspectral Estimation Models of Winter Wheat Chlorophyll Content Under Elevated CO2

Chlorophyll content is an important indicator of winter wheat health status. It is valuable to investigate whether the relationship between spectral reflectance and the chlorophyll content differs under elevated CO₂ condition. In this open-top chamber experiment, the CO₂ treatments were categorized into ambient (aCO₂; about 400 μmol⋅mol^-1) or elevated (eCO₂; ambient + 200 μmol⋅mol^-1) levels. The correlation between the spectral reflectance and the chlorophyll content of the winter wheat were analyzed by constructing the estimation model based on red edge position, sensitive band and spectral index methods, respectively. The results showed that there was a close relationship between chlorophyll content and the canopy spectral curve characteristics of winter wheat. Chlorophyll content was better estimated based on sensitive spectral bands and difference vegetation index (DVI) under both aCO₂ and eCO₂ conditions, though the accuracy of the models varied under different CO₂ conditions. The results suggested that the hyperspectral measurement can be effectively used to estimate the chlorophyll content under both aCO₂ and eCO₂ conditionsand could provide a useful tool for monitoring plants physiology and growth.

Genome-wide association study reveals the genetic basis of yield- and quality-related traits in wheat

BACKGROUND

Identifying the loci and dissecting the genetic architecture underlying wheat yield- and quality-related traits are essential for wheat breeding. A genome-wide association study was conducted using a high-density 90 K SNP array to analyze the yield- and quality-related traits of 543 bread wheat varieties.

RESULTS

A total of 11,140 polymorphic SNPs were distributed on 21 chromosomes, including 270 significant SNPs associated with 25 yield- and quality-related traits. Additionally, 638 putative candidate genes were detected near the significant SNPs based on BLUP data, including three (TraesCS7A01G482000, TraesCS4B01G343700, and TraesCS6B01G295400) related to spikelet number per spike, diameter of the first internode, and grain volume. The three candidate genes were further analyzed using stage- and tissue- specific gene expression data derived from an RNA-seq analysis. These genes are promising candidates for enhancing yield- and quality-related traits in wheat.

CONCLUSIONS

The results of this study provide a new insight to understand the genetic basis of wheat yield and quality. Furthermore, the markers detected in this study may be applicable for marker-assisted selection in wheat breeding programs.

Succession of the fungal endophytic microbiome of wheat is dependent on tissue-specific interactions between host genotype and environment

Fungi living inside plants affect many aspects of plant health, but little is known about how plant genotype influences the fungal endophytic microbiome. However, a deeper understanding of interactions between plant genotype and biotic and abiotic environment in shaping the plant microbiome is of significance for modern agriculture, with implications for disease management, breeding and the development of biocontrol agents. For this purpose, we analysed the fungal wheat microbiome from seed to plant to seeds and studied how different potential sources of inoculum contributed to shaping of the microbiome. We conducted a large-scale pot experiment with related wheat cultivars over one growth-season in two environments (indoors and outdoors) to disentangle the effects of host genotype, abiotic environment (temperature, humidity, precipitation) and fungi present in the seed stock, air and soil on the succession of the endophytic fungal communities in roots, flag leaves and seeds at harvest. The communities were studied with ITS1 metabarcoding and environmental climate factors were monitored during the experimental period. Host genotype, tissue type and abiotic factors influenced fungal communities significantly. The effect of host genotype was mostly limited to leaves and roots, and was location-independent. While there was a clear effect of plant genotype, the relatedness between cultivars was not reflected in the microbiome. For the phyllosphere microbiome, location-dependent weather conditions factors largely explained differences in abundance, diversity, and presence of genera containing pathogens, whereas the root communities were less affected by abiotic factors. Our findings suggest that airborne fungi are the primary inoculum source for fungal communities in aerial plant parts whereas vertical transmission is likely to be insignificant. In summary, our study demonstrates that host genotype, environment and presence of fungi in the environment shape the endophytic fungal community in wheat over a growing season.

Elaboration and Characterization of Vitreous Fertilizers and Study of Their Impact on the Growth, Photosynthesis, and Yield of Wheat (Triticum durum L.)

Four different phosphate glass formulations (F₀, F₁, F₂, and F₃) were developed according o wheat nutrient requirements to be used as controlled-release fertilizers. These glasses contain macro-elements (P₂O₅-K₂O-CaO-MgO), with the addition of microelements (Fe-Mn-Zn-B-Cu-Mo) in each formulation. The effects of these elements' addition on thermal properties, glass structure, and dissolution behaviors were investigated. Results showed that these glasses are composed essentially of metaphosphate chains and that the addition of micronutrients could change the chemical durability of phosphate glasses. A greenhouse experiment was performed using wheat (Triticum durum L.) to evaluate the efficiency of the four glasses, with or without application of chemical nitrogen (N) (N + VF and VF, respectively). The different formulas were tested using two rates of 0.3 and 1 g per plant. In addition to the vitreous fertilizer formulations, two other treatments were applied: control treatment with no amendment and Nitrogen-Phosphorus-Potassium treatment with the application of the conventional fertilizers on the base of optimal rates. After four months of cultivation, vitreous fertilizers application significantly improved growth (7% to 88%), photosynthetic (8% to 49%) parameters, and yield (29% to 33%) compared to NPK treatment and to the control. It has been found that formulas F₁, F₂, and F₃ may constitute a potential alternative to conventional fertilization due to their positive impact on wheat production and can be used in practice as an environmentally controlled-release fertilizer.

QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan

Background

The success of wheat production is largely dependent on local breeding projects that focus on the development of high-yielding cultivars with the use of novel molecular tools. One strategy for improving wheat productivity involves the deployment of diverse germplasms with a high potential yield. An important factor for achieving success involves the dissection of quantitative trait loci (QTLs) for complex agronomic traits, such as grain yield components, in targeted environments for wheat growth.

Methods

In this study, we tested the United Kingdom (UK) spring set of the doubled haploid (DH) reference population derived from the cross between two British cultivars, Avalon (winter wheat) and Cadenza (spring wheat), in the Northern, Central, and Southern regions (Karabalyk, Karaganda, Kyzylorda) of Kazakhstan over three years (2013–2015). The DH population has previously been genotyped by UK scientists using 3647 polymorphic DNA markers. The list of tested traits includes the heading time, seed maturation time, plant height, spike length, productive tillering, number of kernels per spike, number of kernels per meter, thousand kernel weight, and yield per square meter. Windows QTL Cartographer was applied for QTL mapping using the composite interval mapping method.

Results

In total, 83 out of 232 QTLs were identified as stable QTLs from at least two environments. A literature survey suggests that 40 QTLs had previously been reported elsewhere, indicating that this study identified 43 QTLs that are presumably novel marker-trait associations (MTA) for these environments. Hence, the phenotyping of the DH population in new environments led to the discovery of novel MTAs. The identified SNP markers associated with agronomic traits in the DH population could be successfully used in local Kazakh breeding projects for the improvement of wheat productivity.

Genome-wide association study in hexaploid wheat identifies novel genomic regions associated with resistance to root lesion nematode (Pratylenchus thornei)

Root lesion nematode (RLN; Pratylenchus thornei) causes extensive yield losses in wheat worldwide and thus pose serious threat to global food security. Reliance on fumigants (such as methyl bromide) and nematicides for crop protection has been discouraged due to environmental concerns. Hence, alternative environment friendly control measures like finding and deployment of resistance genes against Pratylenchus thornei are of significant importance. In the present study, genome-wide association study (GWAS) was performed using single-locus and multi-locus methods. In total, 143 wheat genotypes collected from pan-Indian wheat cultivation states were used for nematode screening. Genotypic data consisted of  > 7K SNPs with known genetic positions on the high-density consensus map was used for association analysis. Principal component analysis indicated the existence of sub-populations with no major structuring of populations due to the origin. Altogether, 25 significant marker trait associations were detected with - log10 (p value) > 4.0. Three large linkage disequilibrium blocks and the corresponding haplotypes were found to be associated with significant SNPs. In total, 37 candidate genes with nine genes having a putative role in disease resistance (F-box-like domain superfamily, Leucine-rich repeat, cysteine-containing subtype, Cytochrome P450 superfamily, Zinc finger C2H2-type, RING/FYVE/PHD-type, etc.) were identified. Genomic selection was conducted to investigate how well one could predict the phenotype of the nematode count without performing the screening experiments. Prediction value of r = 0.40 to 0.44 was observed when 56 to 70% of the population was used as a training set. This is the first report where GWAS has been conducted to find resistance against root lesion nematode (P. thornei) in Indian wheat germplasm.

Food Security and the Dynamics of Wheat and Maize Value Chains in Africa and Asia

There is an ongoing debate about how best to feed the growing world population in the long run and associated implications for research and development. Some call for a new Green Revolution to secure the supply of staple foods, whereas others emphasize the importance of diversifying and improving people's diets. We aim to contribute to this debate by reviewing the case of wheat and maize value chains and their contribution to food security in Africa and Asia. We first identify drivers transforming food systems. We then apply these to the cereal value chains and disentangle their effects on food security. We thereby add to the three strands in the literature around production, consumption, and food system transformation and point to different research needs and recommendations for the future. The review highlights: (1) Wheat and maize production will be increasingly impaired by ecological drivers such as land degradation, water scarcity and climate change. (2) There are promising innovations to increase and maintain productivity, but constraints in adopting these innovations have to be overcome (i.e., access to seeds, finance, and education/training). (3) The drivers affect all four dimensions of food security, but first and foremost they determine the availability and stability of maize and wheat. This indirectly also influences the economic and physical access of people to maize and wheat. (4) Research tends to focus on improving the productivity and sustainability of wheat and maize farming which is largely interlinked with the availability dimension of food security. (5) The stability and utilization dimension of food security merits continued yet increased support. First, to address climate change and implications for biotic and abiotic stresses. Second, to promote healthier diets and enable the equitable transformation of food systems.

Roles of Si and SiNPs in Improving Thermotolerance of Wheat Photosynthetic Machinery via Upregulation of PsbH, PsbB and PsbD Genes Encoding PSII Core Proteins

Photosystem II is extremely susceptible to environmental alterations, particularly high temperatures. The maintenance of an efficient photosynthetic system under stress conditions is one of the main issues for plants to attain their required energy. Nowadays, searching for stress alleviators is the main goal for maintaining photosynthetic system productivity and, thereby, crop yield under global climate change. Potassium silicate (K2SiO3, 1.5 mM) and silicon dioxide nanoparticles (SiO2NPs, 1.66 mM) were used to mitigate the negative impacts of heat stress (45 °C, 5 h) on wheat (Triticum aestivum L.) cv. (Shandawelly) seedlings. The results showed that K2SiO3 and SiO2NPs diminished leaf rolling symptoms and electrolyte leakage (EL) of heat-stressed wheat leaves. Furthermore, the maximum quantum yield of photosystem II (Fv/Fm) and the performance index (PIabs), as well as the photosynthetic pigments and organic solutes including soluble sugars, sucrose, and proline accumulation, were increased in K2SiO3 and SiO2NPs stressed leaves. At the molecular level, RT-PCR analysis showed that K2SiO3 and SiO2NPs treatments stimulated the overexpression of PsbH, PsbB, and PsbD genes. Notably, this investigation indicated that K2SiO3 was more effective in improving wheat thermotolerance compared to SiO2NPs. The application of K2SiO3 and SiO2NPs may be one of the proposed approaches to improve crop growth and productivity to tolerate climatic change.

Foliar exposure of zinc oxide nanoparticles improved the growth of wheat (Triticum aestivum L.) and decreased cadmium concentration in grains under simultaneous Cd and water deficient stress

A pot study was conducted to explore the effectiveness of zinc oxide nanoparticles (ZnO NPs) foliar exposure on growth and development of wheat, zinc (Zn) and cadmium (Cd) uptake in Cd-contaminated soil under various moisture conditions. Four different levels (0, 25, 50, 100 mg/L) of these NPs were foliar-applied at different time periods during the growth of wheat. Two soil moisture regimes (70% and 35% of water holding capacity) were maintained from 6 weeks of germination till plant harvesting. The results revealed that the growth of wheat increased with ZnO NPs treatments. The best results were found in 100 mg/L ZnO NPs under normal moisture level. The lowest Cd and highest Zn concentrations were also examined when 100 mg/L NPs were applied without water deficit stress. In grain, Cd concentrations decreased by 26%, 81% and 87% in normal moisture while in water deficit conditions, the Cd concentrations decreased by 35%, 66% and 81% compared to control treatment when ZnO NPs were used at 25, 50 and 100 mg/L. The foliar exposure of ZnO NPs boosted up the leaf chlorophyll contents and also decreased the oxidative stress and enhanced the leaf superoxide dismutase and peroxidase activities than the control. It can be suggested that foliar use of ZnO NPs might be an efficient way for increasing wheat growth and yield with maximum Zn and minimum Cd contents under drought stress while decreasing the chances of NPs movement to other environmental compartment which may be possible in soil applied NPs.

A GWAS to identify the cereal cyst nematode (Heterodera filipjevi) resistance loci in diverse wheat prebreeding lines

Yield losses because of cereal cyst nematodes could be as high as 92%, causing a bottleneck for wheat production. An integrated approach (application of pesticides, crop rotation, and use of host resistance) is needed to manage this devastating pathogen where resistant cultivars are considered most effective. This necessitates the identification of nematode-resistant sources in the available germplasm. Here, we report on the genetic mapping of nematode resistance in 255 diverse prebreeding lines (PBLs) employing an association mapping strategy. Altogether, seven additive quantitative trait loci (QTL) were identified on chromosomes 1A, 2A, 2B, 2D, 3A, 6B, and 6D explaining a maximum of 9.42% phenotypic variation where at least five QTL (on chromosomes 2A, 2B, 2D, 6B, and 6D) are located on the same chromosomes that harbor the already known nematode resistance genes. Resistant PBLs carried Aegilops squarrosa (436) in their pedigree which could be the possible source of positive alleles. To add to it, better yield performance of the identified nematode-resistant lines under stress conditions indicates that the germplasm can provide both nematode resistance and high-yielding cultivars.

QTL mapping and validation of bread wheat flag leaf morphology across multiple environments in different genetic backgrounds

Eight major and stably expressed QTL for flag leaf morphology across eleven environments were identified and validated using newly developed KASP markers in seven biparental populations with different genetic backgrounds. Flag leaf morphology is a determinant trait influencing plant architecture and yield potential in wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population with a 55 K SNP-based constructed genetic map was used to map quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), area (FLA), angle (FLANG), opening angle (FLOA), and bend angle (FLBA) in eleven environments. Eight major QTL were detected in 11 environments with 5.73-54.38% of explained phenotypic variation. These QTL were successfully verified using the newly developed Kompetitive Allele Specific PCR (KASP) markers in six biparental populations with different genetic backgrounds. Among these 8 major QTL, two co-located intervals were identified. Significant interactions for both FLL- and FLW-related QTL were detected. Comparison analysis showed that QFll.sau-SY-2B and QFla.sau-SY-2B are likely new loci. Significant relationships between flag leaf- and yield-related traits were observed and discussed. Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat 'Chinese spring', T. turgidum, and Aegilops tauschii. Taken together, these results broaden our understanding on genetic basis of flag leaf morphology and provide clues for fine mapping and marker-assisted breeding wheat with optimized plant architecture for promising loci.

Variation Between Three Eragrostis tef Accessions in Defense Responses to Rhopalosiphum padi Aphid Infestation

Tef (Eragrostis tef), a staple crop that originated in the Horn of Africa, has been introduced to multiple countries over the last several decades. Crop cultivation in new geographic regions raises questions regarding the molecular basis for biotic stress responses. In this study, we aimed to classify the insect abundance on tef crop in Israel, and to elucidate its chemical and physical defense mechanisms in response to insect feeding. To discover the main pests of tef in the Mediterranean climate, we conducted an insect field survey on three selected accessions named RTC-144, RTC-405, and RTC-406, and discovered that the most abundant insect order is Hemiptera. We compared the differences in Rhopalosiphum padi (Hemiptera; Aphididae) aphid performance, preference, and feeding behavior between the three accessions. While the number of aphid progeny was lower on RTC-406 than on the other two, the aphid olfactory assay indicated that the aphids tended to be repelled from the RTC-144 accession. To highlight the variation in defense responses, we investigated the physical and chemical mechanisms. As a physical barrier, the density of non-granular trichomes was evaluated, in which a higher number of trichomes on the RTC-406 than on the other accessions was observed. This was negatively correlated with aphid performance. To determine chemical responses, the volatile and central metabolite profiles were measured upon aphid attack for 4 days. The volatile analysis exposed a rich and dynamic metabolic profile, and the central metabolism profile indicated that tef plants adjust their sugars and organic and amino acid levels. Overall, we found that the tef plants possess similar defense responses as other Poaceae family species, while the non-volatile deterrent compounds are yet to be characterized. A transcriptomic time-series analysis of a selected accession RTC-144 infested with aphids revealed a massive alteration of genes related to specialized metabolism that potentially synthesize non-volatile toxic compounds. This is the first report to reveal the variation in the defense mechanisms of tef plants. These findings can facilitate the discovery of insect-resistance genes leading to enhanced yield in tef and other cereal crops.

The Effect of Photoperiod Genes and Flowering Time on Yield and Yield Stability in Durum Wheat

This study analysed the effect of flowering time as influenced by photoperiod sensitivity genes on yield and yield stability in durum wheat. Twenty-three spring genotypes harbouring different allele combinations at Ppd-A1 and Ppd-B1 were grown in 15 field experiments at three sites at latitudes from 41° to 19° N (Spain, Mexico-North and Mexico-South). Low temperature and solar radiation before flowering and long day length during grain-filling characteristic for the Spanish site resulted in high grain number/m² (GN) and yield (GY), while a moderate GN combined with high solar radiation during grain-filling at Mexico-North led to heavier grains. Allele combination GS100-Ppd-A1a/Ppd-B1a reduced the flowering time up to nine days when compared with Ppd-A1b/Ppd-B1a. Differences in flowering time caused by Ppd-A1/Ppd-B1 allele combinations did not affect yield. Combinations GS105-Ppd-A1a/Ppd-B1b and Ppd-A1b/Ppd-B1b resulted in the highest GN, linked to spikelets/spike, which was higher in GS105-Ppd-A1a/Ppd-B1b due to more grains/spikelet. Flowering time caused by Eps had a minor effect on GN, spikes/m² and grains/spike, but late flowering resulted in reduced grain weight and GY. Allele combinations harbouring alleles conferring a similar photoperiod sensitivity response at Ppd-A1 and Ppd-B1 resulted in greater yield stability than combinations that carry alleles conferring a different response. Allele combination GS100-Ppd-A1a/Ppd-B1a was the most suitable in terms of yield and yield stability of durum wheat cultivated under irrigation within the studied latitudes.

Biogenic copper nanoparticles synthesized by using a copper-resistant strain Shigella flexneri SNT22 reduced the translocation of cadmium from soil to wheat plants

The mechanistic role of green copper nanoparticles (CuNPs) in cadmium (Cd) toxicity alleviation in plants is poorly understood. Here, the CuNPs, synthesized by using a bacterium Shigella flexneri SNT22, were confirmed through UV-vis spectroscopy with a characteristic peak at 334.50 nm. Moreover, FT-IR, XRD, SEM, and TEM techniques revealed that the spherical shaped crystals of CuNPs with a size range of 17.24 nm to 38.03 nm were stabilized by coating proteins. Diff ;erent levels of CuNPs (e.g., 25, 50, and 100 mg kg^-1 of soil) were examined in pots having Cd-mixed soil to evaluate their effect on wheat plants in a growth chamber under optimal environmental conditions. Treatment of soil with 100 mg kg^-1 of CuNPs increased plant length by 44.4 %, shoot dry weight by 28.26 %, nitrogen contents by 41.60 %, and phosphorus contents by 58.79 %, whereas decreased the acropetal Cd translocation by 49.62 %. An increase in the N, P, K⁺, Ca²⁺, K⁺/Na⁺, and Ca²⁺/Na⁺ contents and decrease in the Na⁺ concentration in wheat plants treated with CuNPs was also recorded. Overall, the results are valuable to establish a green CuNPs-based approach for sustainable wheat growth in metal-contaminated soils.

A comparative study of root cadmium radial transport in seedlings of two wheat (Triticum aestivum L.) genotypes differing in grain cadmium accumulation

The radial transport of cadmium (Cd) is essential for Cd influx in roots. The role of radial transport pathway on the Cd translocation from root to shoot among wheat genotypes are still poorly understood. This study explored the role of apoplastic and symplastic pathway on root Cd uptake and root-to-shoot translocation in Zhenmai 10 (ZM10, high Cd in grains) and Aikang 58 (AK58, low Cd in grains). Under Cd treatment, the deposition of Casparian strips (CSs) and suberin lamellae (SL) initiated closer to the root apex in ZM10 than that in AK58, which resulted in the lower Cd concentration in apoplastic fluid of ZM10. Simultaneously, Cd-induced expression levels of genes related to Cd uptake in roots were significantly higher in AK58 by contrast with ZM10, contributing to the symplastic Cd accumulation in AK58 root. Moreover, the addition of metabolic inhibitor CCCP noticeably decreased the Cd accumulation in root of both genotypes. Intriguingly, compared to ZM10, greater amounts of Cd were sequestrated in the cell walls and vacuoles in roots of AK58, limiting the translocation of Cd from root to shoot. Furthermore, the elevated TaHMA2 expression in ZM10 indicates that ZM10 had a higher capacity of xylem loading Cd than AK58. All of these results herein suggest that the radial transport is significant for Cd accumulation in roots, but it cannot explain the difference in root-to-shoot translocation of Cd in wheat genotypes with contrast Cd accumulation in grains.

A GBS-based GWAS analysis of adaptability and yield traits in bread wheat (Triticum aestivum L.)

Wheat is a foremost food grain of Pakistan and occupies a vital position in agricultural policies of the country. Wheat demand will be increased by 60% by 2050 which is a serious concern to meet this demand. Conventional breeding approaches are not enough to meet the demand of growing human population. It is paramount to integrate underutilized genetic diversity into wheat gene pool through efficient and accurate breeding tools and technology. In this study, we present the genetic analysis of a 312 diverse pre-breeding lines using DArT-seq SNPs seeking to elucidate the genetic components of emergence percentage, heading time, plant height, lodging, thousand kernel weight, and yield (Yd) which resulted in detection of 201 significant (p value < 10^-3) and 61 highly significant associations (p value < 1.45 × 10^-4). More importantly, chromosomes 1B and 2A carried loci linked to Yd in two different seasons, and an increase of up to 8.20% is possible in Yd by positive allele mining. We identified seven lines with > 4 positive alleles for Yd whose pedigree carried Aegilops squarrosa as one of the parents providing evidence that Aegilops species, apart from imparting resistance against biotic stresses, may also provide alleles for yield enhancement.

Cytokinin activity during early kernel development corresponds positively with yield potential and later stage ABA accumulation in field-grown wheat (Triticum aestivum L.)

Early cytokinin activity and late abscisic acid dynamics during wheat kernel development correspond to cultivars with higher yield potential. Cytokinins represent prime targets for marker development for wheat breeding programs. Two major phytohormone groups, abscisic acid (ABA) and cytokinins (CKs), are of crucial importance for seed development. Wheat (Triticum aestivum L.) yield is, to a high degree, determined during the milk and dough stages of kernel development. Therefore, understanding the hormonal regulation of these early growth stages is fundamental for crop-improvement programs of this important cereal. Here, we profiled ABA and 25 CK metabolites (including active forms, precursors and inactive conjugates) during kernel development in five field-grown wheat cultivars. The levels of ABA and profiles of CK forms varied greatly among the tested cultivars and kernel stages suggesting that several types of CK metabolites are involved in spatiotemporal regulation of kernel development. The seed yield potential was associated with the elevated levels of active CK levels (tZ, cZ). Interestingly, the increased kernel cZ levels were followed by higher ABA production, suggesting there is an interaction between these two phytohormones. Furthermore, we analyzed the expression patterns of representatives of the four main CK metabolic gene families. The unique transcriptional patterns of the IPT (biosynthesis) and ZOG (reversible inactivation) gene family members (GFMs) in the high and low yield cultivars additionally indicate that there is a significant association between CK metabolism and yield potential in wheat. Based on these results, we suggest that both CK metabolites and their associated genes, can serve as important, early markers of yield performance in modern wheat breeding programs.

A proteomic analysis of grain yield-related traits in wheat

Grain yield, which is mainly contributed by tillering capacity as well as kernel number and weight, is the most important trait to plant breeders and agronomists. Label-free quantitative proteomics was used to analyse yield-contributing organs in wheat. These were leaf sample, tiller initiation, spike initiation, ovary and three successive kernel development stages at 5, 10 and 15 days after anthesis (DAA). We identified 3182 proteins across all samples. The largest number was obtained for spike initiation (1673), while the smallest was kernel sample at 15 DAA (709). Of the 3182 proteins, 296 of them were common to all seven organs. Organ-specific proteins ranged from 148 in ovary to 561 in spike initiation. When relative protein abundances were compared to that of leaf sample, 347 and 519 proteins were identified as differentially abundant in tiller initiation and spike initiation, respectively. When compared with ovary, 81, 35 and 96 proteins were identified as differentially abundant in kernels sampled at 5, 10 and 15 DAA, respectively. Our study indicated that two Argonaute proteins were solely expressed in spike initiation. Of the four expansin proteins detected, three of them were mainly expressed during the first 10 days of kernel development after anthesis. We also detected cell wall invertases and sucrose and starch synthases mainly during the kernel development period. The manipulation of these proteins could lead to increases in tillers, kernels per spike or final grain weight, and is worth exploring in future studies.

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

BACKGROUND

Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3'-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified.

RESULTS

Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat.

CONCLUSION

The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.

Dissection and validation of a QTL cluster linked to Rht-B1 locus controlling grain weight in common wheat (Triticum aestivum L.) using near-isogenic lines

This study dissected and validated a QTL cluster associated with thousand grain weight on chromosome 4B using multiple near-isogenic lines in common wheat. Grain size and weight are crucial components of wheat yield. Previously, we identified a QTL cluster for thousand grain weight (TGW) on chromosome 4B using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population. Here, near-isogenic lines (NILs) in the ND3338 background were developed to dissect and validate the QTL cluster. Based on six independent BC₃F_3:4 heterogeneous inbred families, the 4B QTL cluster was divided into two linked QTL intervals (designated 4B.1 and 4B.2 QTL). For the 4B.1 QTL, the Rht-B1 gene, of which Rht-B1b allele reduces plant height (PH) by 21.18-29.34 cm (34.34-53.71%), was demonstrated to be the most likely candidate gene with pleiotropic effects on grain size and TGW. For the 4B.2 QTL, the NIL^JD6 consistently showed an increase in TGW of 3.51-7.68 g (8.84-22.77%) compared with NIL^ND3338 across different field trials, along with a significant increase in PH of 2.26-6.71 cm (3.92-12.01%). Moreover, both QTL intervals had a larger effect on grain width than on grain length. Additionally, the first significant difference in 100-grain fresh weight and 100-grain dry weight between the NIL pairs of the 4B.1 QTL interval (Rht-B1) was observed at 6 days after pollination (DAP), while the differences were first visible at 30 DAP for the 4B.2 QTL interval. Collectively, our work provides a new example of QTL dissection for grain weight in wheat and lays a foundation for further map-based cloning of the major QTL that have potential applications in wheat molecular breeding for high yield.

Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields

Breeding for grain yield (GY) in bread wheat at the International Maize and Wheat Improvement Center (CIMMYT) involves three-stage testing at Obregon, Mexico in different selection environments (SEs). To understand the efficiency of selection in the SEs, we performed a large retrospective quantitative genetics study using CIMMYT's yield trials evaluated in the SEs (2013-2014 to 2017-2018), the South Asia Bread Wheat Genomic Prediction Yield Trials (SABWGPYTs) evaluated in India, Pakistan, and Bangladesh (2014-2015 to 2017-2018), and the Elite Spring Wheat Yield Trials (ESWYTs) evaluated in several sites globally (2003-2004 to 2016-2017). First, we compared the narrow-sense heritabilities in the Obregon SEs and target sites and observed that the mean heritability in the SEs was 44.2 and 92.3% higher than the mean heritabilities in the SABWGPYT and ESWYT sites, respectively. Second, we observed significant genetic correlations between a SE in Obregon and all the five SABWGPYT sites and 65.1% of the ESWYT sites. Third, we observed high ratios of response to indirect selection in the SEs of Obregon with a mean of 0.80 ± 0.21 and 2.6 ± 5.4 in the SABWGPYT and ESWYT sites, respectively. Furthermore, our results also indicated that for all the SABWGPYT sites and 82% of the ESWYT sites, a response greater than 0.5 can be achieved by indirect selection for GY in Obregon. We also performed genomic prediction for GY in the target sites using the performance of the same lines in the SEs of Obregon and observed moderate mean prediction accuracies of 0.24 ± 0.08 and 0.28 ± 0.08 in the SABWGPYT and ESWYT sites, respectively using the genotype x environment (GxE) model. However, we observed similar accuracies using the baseline model with environment and line effects and no advantage of modeling GxE interactions. Overall, this study provides important insights into the suitability of the Obregon SEs in breeding for GY, while the variable genomic predictabilities of GY and the high year-to-year GY fluctuations reported, highlight the importance of multi-environment testing across time and space to stave off GxE induced uncertainties in varietal yields.

Bacillus siamensis Reduces Cadmium Accumulation and Improves Growth and Antioxidant Defense System in Two Wheat (Triticum aestivum L.) Varieties

Bioavailability of cadmium (Cd) metal in the soils due to the scarcity of good quality water and industrial waste could be the major limiting factor for the growth and yield of crops. Therefore, there is a need for a prompt solution to the Cd toxicity, to fulfill increasing food demand resulting from growing world population. Today, a variable range of plant growth promoting rhizobacteria (PGPR) is being used at a large scale in agriculture, to reduce the risk of abiotic stresses on plants and increase crop productivity. The objective of this study was to evaluate the efficacy of Bacillus siamensis in relieving the Cd induced damage in two wheat varieties (i.e., NARC-2009 and NARC-2011) grown in Cd spiked soil at different concentrations (0, 20, 30, 50 mg/kg). The plants under Cd stress accumulated more Cd in the roots and shoots, resulting in severe oxidative stress, evident by an increase in malondialdehyde (MDA) content. Moreover, a decrease in cell osmotic status, and alteration in antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) were also observed in wheat plants under Cd stress. As a result, the Cd exposed plants showed a reduction in growth, tissue biomass, photosynthetic pigments, membrane stability, total soluble sugars, and amino acids, in comparison to control plants. The extent of damage was observed to be higher with an increase in Cd concentration. However, the inoculation of wheat with B. siamensis improved plant growth, reduced oxidative stress, and enhanced the activities of antioxidant enzymes in both wheat varieties. B. siamensis amendment brought a considerable improvement in every parameter determined with respect to Cd stress. The response of both wheat varieties on exposure to B. siamensis was positively enhanced, whereas NARC-2009 accumulated less Cd compared to NARC-2011, which indicated a higher tolerance to Cd stress mediated by B. siamensis inoculation. Overall, the B. siamensis reduced the Cd toxicity in wheat plants through the augmentation of the antioxidant defense system and sugars production.

Exploiting the genome of Thinopyrum elongatum to expand the gene pool of hexaploid wheat

One hundred and thirty four introgressions from Thinopyrum elongatum have been transferred into a wheat background and were characterised using 263 SNP markers. Species within the genus Thinopyrum have been shown to carry genetic variation for a very wide range of traits including biotic and abiotic stresses and quality. Research has shown that one of the species within this genus, Th. elongatum, has a close relationship with the genomes of wheat making it a highly suitable candidate to expand the gene pool of wheat. Homoeologous recombination, in the absence of the Ph1 gene, has been exploited to transfer an estimated 134 introgressions from Th. elongatum into a hexaploid wheat background. The introgressions were detected and characterised using 263 single nucleotide polymorphism markers from a 35 K Axiom^® Wheat-Relative Genotyping Array, spread across seven linkage groups and validated using genomic in situ hybridisation. The genetic map had a total length of 187.8 cM and the average chromosome length was 26.8 cM. Comparative analyses of the genetic map of Th. elongatum and the physical map of hexaploid wheat confirmed previous work that indicated good synteny at the macro-level, although Th. elongatum does not contain the 4A/5A/7B translocation found in wheat.

Effect of Trade Openness on Food Security in the EU: A Dynamic Panel Analysis

The problem of food insecurity is growing across the world, including economically developed countries. In Europe, the question is not just about the total supply of foods, but it includes even the accessibility of prices and their nutritional and qualitative adequacy. In this context many countries recognize the importance of trade policies to ensure adequate levels of food security. The aim of this work was to analyze the impact of trade openness on the level of food security in European countries, using a dynamic panel analysis with the generalized method of moments (GMM) approach. We selected two different indicators of food security (average protein supply, average dietary energy supply adequacy) capable of offering information both on the quantity and on the nutritional quality of the food supply. In order to improve the robustness of the empirical results, we developed three different regressions, with three trade openness indicators (trade openness, tariff, globalization) for each food security indicator. The results showed that commercial opening has, on average, a statistically significant net positive impact on the food security of European countries. Additional results indicate that also economic development, together with the importance of the agricultural sector, can improve food security levels.

Phytotoxicity of Cu2+ and Cd2+ to the roots of four different wheat cultivars as related to charge properties and chemical forms of the metals on whole plant roots

The relationship between the chemical forms of Cu²⁺ and Cd²⁺ adsorbed on the roots of different wheat cultivars and their phytotoxic effects on the plants were investigated. The wheat varieties Dunmaiwang (DMW), Tekang 6 (TK6), Zhongmai895 (ZM895), and Chaojixiaomai (AK68) were used. The zeta potentials of wheat roots, measured by the streaming potential method, were used to characterize root charge properties. Results indicated that the changes in zeta potential at pH 4.01-6.61 were 14.7, 15.53, 13.01, and 12.06 mV for ZM895, AK68, DMW, and TK6, respectively. The negative charge and functional groups on ZM895 and AK68 roots were greater than on DMW and TK6 roots, which led to more exchangeable and complexed Cu²⁺ and Cd²⁺ on ZM895 and AK68 roots and increased Cu²⁺ and Cd²⁺ toxicity compared to DMW and TK6. Coexisting cations, such as Ca²⁺, Mg²⁺, K⁺, and NH₄⁺, alleviated Cu²⁺ and Cd²⁺ toxicity to wheat roots through competition for adsorption sites on the roots, which decreased exchangeable and complexed Cu²⁺ and Cd²⁺ on wheat roots. The Ca²⁺ and Mg²⁺ were most effective in alleviating heavy metal toxicity and they decreased exchangeable Cu²⁺ on AK68 roots by 39.14% and 47.82%, and exchangeable Cd²⁺ by 8.51% and 28.23%, respectively.

A Physio-Morphological Trait-Based Approach for Breeding Drought Tolerant Wheat

In the past, there have been drought events in different parts of the world, which have negatively influenced the productivity and production of various crops including wheat (Triticum aestivum L.), one of the world's three important cereal crops. Breeding new high yielding drought-tolerant wheat varieties is a research priority specifically in regions where climate change is predicted to result in more drought conditions. Commonly in breeding for drought tolerance, grain yield is the basis for selection, but it is a complex, late-stage trait, affected by many factors aside from drought. A strategy that evaluates genotypes for physiological responses to drought at earlier growth stages may be more targeted to drought and time efficient. Such an approach may be enabled by recent advances in high-throughput phenotyping platforms (HTPPs). In addition, the success of new genomic and molecular approaches rely on the quality of phenotypic data which is utilized to dissect the genetics of complex traits such as drought tolerance. Therefore, the first objective of this review is to describe the growth-stage based physio-morphological traits that could be targeted by breeders to develop drought-tolerant wheat genotypes. The second objective is to describe recent advances in high throughput phenotyping of drought tolerance related physio-morphological traits primarily under field conditions. We discuss how these strategies can be integrated into a comprehensive breeding program to mitigate the impacts of climate change. The review concludes that there is a need for comprehensive high throughput phenotyping of physio-morphological traits that is growth stage-based to improve the efficiency of breeding drought-tolerant wheat.

Strengths and Weaknesses of National Variety Trial Data for Multi-Environment Analysis: A Case Study on Grain Yield and Protein Content

Multi-environment trial studies provide an opportunity for the detailed analysis of complex traits. However, conducting trials across a large number of regions can be costly and labor intensive. The Australian National Variety Trials (NVT) provide grain yield and protein content (GPC) data of over 200 wheat varieties in many and varied environments across the Australian wheat-belt and is representative of similar trials conducted in other countries. Through our analysis of the NVT dataset, we highlight the advantages and limitations in using these data to explore the relationship between grain yield and GPC in the low yielding environments of Australia. Eight environment types (ETs), categorized in a previous study based on the time and intensity of drought stress, were used to analyze the impact of drought on the relationship between grain yield and protein content. The study illustrates the value of comprehensive multi-environment analysis to explore the complex relationship between yield and GPC, and to identify the most appropriate environments to select for a favorable relationship. However, the NVT trial design does not follow the rigor associated with a normal genotype × environment study and this limits the accuracy of the interpretation.

Genome-wide association study of agronomic and quality traits in a world collection of the wild wheat relative Triticum urartu

Triticum urartu (2n = 2x = 14, subgenome A^u A^u ), a wild diploid wheat progenitor, features broad allelic diversity for a number of traits of agronomic relevance. A thorough characterization of the diversity of T. urartu natural accessions may provide wheat breeders with new alleles potentially contributing to wheat improvement. In this study, we performed an extensive genotypic and phenotypic characterization of a world collection of 299 T. urartu ex situ accessions, developing 441 327 single nucleotide polymorphisms and recording trait values for agronomic and quality traits. The collection was highly diverse, with broad variation in phenology and plant architecture traits. Seed features were also varied, and analyses of flour quality reported 18 distinct patterns of glutenins, and carotenoid concentrations and sedimentation volumes in some cases surpassing those of cultivated materials. The genome-wide molecular markers developed on the collection were used to conduct a genome-wide association study reporting 25 highly significant quantitative trait nucleotides for the traits under examination, only partially overlapping loci already reported in wheat. Our data show that T. urartu may be considered a valuable allele pool to support the improvement of wheat agronomy and quality.