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RationalUnderutilized species that are not widely cultivated (known as orphan crops) present opportunities to increase crop diversity and food security. Tef [Eragrostis tef (Zucc.) Trotter] is known for its high-quality grain and forage. Root-borne lodging is a major devastating problem in tef cultivation, leading to large economic losses and limiting its widespread adoption.ObjectiveThe aim of this study was to identify genomic regions that are associated with tef lodging.MethodsA tef diversity panel (TDP-300) comprised of 297 lines was assembled, genotyped, and phenotyped across 4 field environments. This unique panel, the first of its kind in tef, has the potential to facilitate tef research and breeding.ResultsGenome-wide association study identified 29 sites associated with lodging; in all cases with a minor allele conferring reduced lodging. The eleven sites of prime interest were located in or near genes, 5 of them with a putative role, of which 3 were found to be involved root development.ConclusionsThe identification of lodging-related sites in the current study may advance understanding of the mechanisms underlying tef lodging and crop improvement. The identification of genes related to root development support the importance of root traits in tef lodging, which should be targeted in future breeding.

Dissection of the genetic basis of wheat ionome is crucial for understanding the physiological and biochemical processes underlying mineral accumulation in seeds, as well as for efficient crop breeding. Most of the elements essential for plants are metals stored in seeds as chelate complexes with phytic acid or sulfur-containing compounds. We assume that the involvement of phosphorus and sulfur in metal chelation is the reason for strong phenotypic correlations within ionome. Adjustment of element concentrations for the effect of variation in phosphorus and sulfur seed content resulted in drastic change of phenotypic correlations between the elements. The genetic architecture of wheat grain ionome was characterized by quantitative trait loci (QTL) analysis using a cross between durum and wild emmer wheat. QTL analysis of the adjusted traits and two-trait analysis of the initial traits paired with either P or S considerably improved QTL detection power and accuracy, resulting in the identification of 105 QTLs and 617 QTL effects for 11 elements. Candidate gene search revealed some potential functional associations between QTLs and corresponding genes within their intervals. Thus, we have shown that accounting for variation in P and S is crucial for understanding of the physiological and genetic regulation of mineral composition of wheat grain ionome and can be implemented for other plants.

Tef (Eragrostis tef (Zucc.) Trotter) is an annual small grain, panicle bearing, C4 cereal crop native to Ethiopia, where it is a major staple food. The objectives of the present study were to characterize the responses of two tef genotypes to escalating phosphorus (P) and potassium (K) levels and to determine an optimum range for P and K at which tef performance is maximized. Two experiments were carried out in the Gilat Research Station, each testing two different genotypes of tef (405B and 406W), one experiment in pots in controlled conditions, and the other in the field. In both experiments, the highest grain yield increased until 6 mg L−1 P, and declined at 12 mg L−1 P. The decline was precipitous and significant in the pot experiment, and gradual and statistically insignificant in the field experiment. In the pots experiment, the grain yield increased until 40 mg L−1 K, with no significant decrease thereafter. The effect of K concentration was only seen in the grain yield and not in the size of the other plant organs. In the field experiment, grain yield was highest at 80 mg L−1 K, but it was not statistically different from 40 mg L−1. The effect of K on growth was only apparent at maturity and not at flowering.

Tef (Eragrostis tef (Zucc.) Trotter) is a C4 annual cereal, common in Ethiopia, where it was presumably domesticated. Worldwide interest in tef cultivation and consumption has considerably increased in the last few decades because it is a gluten-free grain with high nutritional value. Here we report on the genetic diversity and heritability in a tef germplasm collection characterized in Israel. A total of 408 accessions of tef held in the Israel Gene Bank were grown in 2015 under common garden (screen-house) conditions for propagation and initial phenotyping. A diversity panel, consisting of 273 accessions representing the entire collection's range of phenotypic diversity, was assembled and evaluated in small field plots in 2016. Further evaluation was conducted in 2017, in single-plant field plots (to eliminate admixtures). A representative plant (plot) was selected from each accession grown in 2017 and its single seed descent progenies where grown in 2018 in single-plant plots. The collection exhibited a wide diversity for each of the measured phenotypic traits, across all four environments. High grain yield was associated in most cases with early flowering time, whereas higher biomass was associated with late flowering. Heritability estimates, calculated based on the 2017, 2018 data, varied between 0.11 for plant biomass and 0.75 for 1000 grain weight. This study shows that tef can successfully grow and produce under irrigated Mediterranean conditions. The wide diversity available in our germplasm collection can provide the foundations for breeding new tef cultivars that are better adapted to these conditions.

Precision irrigation aims at improving productivity and sustainability by addressing spatial as well as temporal variability of soil and crop water status. This chapter presents three case studies from south-eastern USA, Israel and Spain which relate to different attributes of precision irrigation: (1) type of precision: whether it targets the spatial variability by using variable-rate irrigation (VRI) system or the temporal variability by using automatic triggering of the irrigation, (2) type of irrigation system, and (3) type of data the system uses for irrigation decisions. Each of the case studies addresses a unique combination of attributes and together they draw a more complement picture of precision irrigation. All case studies have shown that well-timed data provides decision support for VRI management, i.e. soil moisture sensor-data (south-eastern USA and Spain) and thermal aerial imagery (Israel). The three case studies showed that precision irrigation treatments performed better than uniform irrigation. Yield increased by 4.3–12% and water-use efficiency (WUE) was improved by 14–40%. The reliance on point-sensor data in the case studies from south-eastern USA and Spain dictated the use of pre-determined irrigation management zones (IMZ), yet, enabled adaptive in season irrigation management. In season remotely sensed images can be further used for adaptive IMZ, i.e. to modify their boundaries, yet it currently suits VRI in drip irrigation. From these case studies, it can be seen that full VRI implementation, which adapts for spatial and temporal changes, faces “site-specific” challenges, i.e. every irrigation system is unique, and thus requires tailored solutions.

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 inRhopalosiphum 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.

Background The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. Results We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. Conclusions In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.

Worldwide demand for tef (Eragrostis tef) as a functional food for human consumption is increasing, thanks to its nutritional benefits and gluten-free properties. As a result, tef in now grown outside its native environment in Ethiopia and thus information is required regarding plant nutrition demands in these areas, as well as resulting grain health-related composition. In the current work, two tef genotypes were grown in Israel under irrigation in two platforms, plots in the field and pots in a greenhouse, with four and five nitrogen treatments, respectively. Nutritional and health-related quality traits were analyzed, including mineral content, fatty acid composition, hydrophilic and lipophilic antioxidative capacity, total phenolic content and basic polyphenolic profile. Our results show that tef genotypes differ in their nutritional composition, e.g. higher phenolic contents in the brown compared to the white genotype. Additionally, nitrogen availability positively affected grain fatty acid composition and iron levels in both experiments, while negatively affecting total phenolics in the field trials. To conclude, nitrogen fertilization is crucial for crop growth and productivity, however it also implicates nutritional value of the grains as food. These effects should be considered when fertilizing tef with nitrogen, to optimize both crop productivity and nutritional effects.

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.

BAPGEAPSISUPDATINRA; Productivity of grain crops in semi-arid environments is often affected by drought, which is likely to increase due to predicted climate changes. Wild pea (Pisum fulvum, Pf) accessions sampled across its ecological amplitude in Israel (350-850 mm annual precipitation) were used to assess the genetic diversity for drought responses. We hypothesized that native species evolving under east Mediterranean climate carry adaptive traits to cope with drought stress. Accessions were classified according to SNP variation pattern and habitat ecogeographic parameters. Significant differences were found between the accession groups, but grouping in both systems did not match. Subsequently, 52 Pf accessions and three domesticated pea (Pisum sativum) genotypes were evaluated under well-watered (600mm) and water-limited (300mm) treatments. Total dry matter, grain yield, harvest index and average grain weight were higher in domesticated pea than wild Pf, however several Pf accessions exhibited lower drought susceptibility indices (i.e. greater stability across environments) than domesticated genotypes. Of special interest are a number of Pf genotypes in which low susceptibility to water stress was coupled with relatively high productivity. The sampling habitats of those low susceptibility - high productivity accessions are characterized by mild (400-530mm) annual precipitation. Further sampling and evaluation of Pf from such locations may improve our understanding of pea drought adaptation and yield physiology.

Aerial thermal remote sensing can provide a means for collecting spatial plant water status data. Many studies have shown their potential in irrigation management but the adaptation of this technology is not straight forward. In this paper, knowledge accumulated in recent years on thermal imagery analysis methodology for water status mapping is summarized aiming at indicating alternatives to calculate the Crop Water Stress Index (CWSI) for commercial scale water status mapping. Based on literature overview, four forms of wet-baselines to calculate CWSI were selected, namely: artificial wet reference surface, two theoretical calculations and a statistical bio-indicator. These baselines were used to calculate CWSI based on multi-temporal aerial thermal images of cotton fields. CWSI based on a statistical bio-indicator and one of the theoretical wet-baselines provided the best correlations. It is argued though that the statistical one is preferable since it includes the plant characteristics and it is farmer-friendly. Based on bio-indicators, leaf water potential maps of three commercial fields were produced on several dates through the season. Water status spatial patterns were not static and the effect of static factors like sandy soil patches also changed through the season. The maps show the importance of in-season variability mapping for rational irrigation management. To improve current variable-rate irrigation, the concept of in-season irrigation management zones (IMZ) based on thermal-images should be considered and integrated with the delineation of static irrigation IMZ.

Background Characterization and quantification of visual plant traits is often limited to the use of tools and software that were developed to address a specific context, making them unsuitable for other applications. CoverageTool is flexible multi-purpose software capable of area calculation in cm2, as well as coverage area in percentages, suitable for a wide range of applications. Results Here we present a novel, semi-automated and robust tool for detailed characterization of visual plant traits. We demonstrate and discuss the application of this tool to quantify a broad spectrum of plant phenotypes/traits such as: tissue culture parameters, ground surface covered by annual plant canopy, root and leaf projected surface area, and leaf senescence area ratio. The CoverageTool software provides easy to use functions to analyze images. While use of CoverageTool involves subjective operator color selections, applying them uniformly to full sets of samples makes it possible to provide quantitative comparison between test subjects. Conclusion The tool is simple and straightforward, yet suitable for the quantification of biological and environmental effects on a wide variety of visual plant traits. This tool has been very useful in quantifying different plant phenotypes in several recently published studies, and may be useful for many applications. Electronic supplementary material The online version of this article (10.1186/s13007-019-0472-2) contains supplementary material, which is available to authorized users.

SummaryDissection of the genetic basis of ionome is crucial for the understanding of the physiological and biochemical processes underlying mineral accumulation in seeds, as well as for efficient crop breeding. Most of the elements essential for plants are metals stored in seeds as chelate complexes with phytic acid or sulfur-containing compounds. We assume that the involvement of phosphorus and sulfur in metal chelation is the reason for strong phenotypic associations within ionome. Thus, we adjusted element concentrations for the effect of variation in phosphorus and sulfur seed content. The genetic architecture of wheat grain ionome was characterize by QTL analysis using a cross between durum and wild emmer wheat. Adjustment for variation in P and S drastically changed phenotypic associations within ionome and considerably improved QTL detection power and accuracy, resulting in identification of 105 QTLs and 437 QTL effects for 11 elements. A search for candidate genes revealed some strong functional associations of genes involved in transport and metabolism of ions and elements. Thus, we have shown that accounting for variation in P and S is crucial for understanding of the physiological and genetic regulation of mineral composition of wheat grain ionome and can be implemented for other plants.

Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses in order to achieve maximum possible reproduction. The current study is the first to apply the linear regression residuals as a drought plasticity scores, while taking into account the differences in flowering phenology and trait variation under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity using a mapping population derived from a cross between durum wheat (Triticum durum) and wild emmer wheat (T. dicoccoides). We identified 79 QTLs, of which 33 were plastic in response to water stress and exhibited epistatic interactions and/or pleiotropy between the initial and plasticity traits.Vrn-B3 (TaTF1)residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer, demonstrating the high potential of wild relatives for wheat improvement. Our study presents a new approach for quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.HighlightThe study presents a new approach for quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.

The primary stages of domestication and consequent polyploidization processes of bread wheat (Triticum aestivum, BBAADD) have diminished the genetic diversity within cultivated wheat germplasm. Wild emmer wheat (Triticum dicoccoides, BBAA), the progenitor of wheat, is a promising source for beneficial agronomical traits; however, introgression of such alleles into bread wheat was hampered by various factors, such as necrosis in F1 pentaploid hybrids, failed seedling establishment, and frequent sterility. Therefore, we suggest to utilize durum wheat (Triticum durum, BBAA) as a bridge for transferring favorable alleles into bread wheat. We propose to screen wild emmer germplasm for valuable traits, cross promising accessions with durum varieties, confirm the phenotype in segregating populations, map the target gene(s)/quantitative trait loci (QTLs), and use marker-assisted selection for introgression into bread wheat. Here, we discuss the proposed concept and provide examples of successful transfer of traits such as drought resistance, high grain protein, resistance to stripe rust, powdery mildew, and fusarium head blight.

Developing new crops adapted to arid conditions is a promising approach to meet the increasing demand for food production under expanding aridity. Tef [Eragrostis tef (Zucc.) Trotter] is a C4 cereal crop cultivated mainly in Ethiopia and the Horn of Africa, and known for its high resilience to stressful environments. Due to their tiny size, tef seeds are traditionally sown by broadcasting and lightly covering with soil. Under semiarid Mediterranean conditions, a deeper sowing may guarantee seedling establishment while saving on irrigation water. The objective of this study was, therefore, to determine the effects of sowing depth on tef emergence, development, lodging, and productivity. Tef seeds were sown at different depths in test tubes and pots, and in two field experiments. In tubes and pots, time from sowing to emergence increased about twofold and emergence rate decreased in the deepest sowing (3 cm) treatment compared to controls (0 cm). In the pot and field trials, deep sowing (3 cm) significantly reduced plant height, shoot and root biomass, and lodging. Sowing depths of 1&ndash, 2 cm allowed successful plant establishment while not exacting penalties on plant emergence or development, hence this range appears to be optimal for sowing irrigated tef.

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving drought resistance in domesticated wheat. Nevertheless, wild germplasm has not been widely used in wheat breeding for abiotic stress resilience. In the current study, a near isogenic line NIL-7A-B-2, introgressed with a drought-related QTL from wild emmer wheat on chromosome 7A, and its recurrent parent, bread wheat cv. BarNir, were investigated under four environments across 2 years-water-limited and well-watered conditions in a rain-protected screen-house (Year 1) and two commercial open field plots under ample precipitation (Year 2). NIL-7A-B-2 exhibited an advantage over BarNir in grain yield and biomass production under most environments. Further physiological analyses suggested that enhanced photosynthetic capacity and photochemistry combined with higher flag leaf area are among the factors underlying the improved productivity of NIL-7A-B-2. These were coupled with improved sink capacity in NIL-7A-B-2, manifested by greater yield components than its parental line. This study provides further support for our previous findings that introgression of wild emmer QTL alleles, using marker assisted selection, can enhance grain yield and biomass production across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of yield and drought resistance.

Pisum fulvum is an annual legume native to Syria, Lebanon, Israel and Jordan. In certain locations, P. fulvum individuals were documented to display a reproductive dimorphism - amphicarpy, with both above and below ground flowers and pods. Herein we aimed to study the possible role of soil texture on amphicarpy in P. fulvum, to investigate the possible bio-climatic associations of P. fulvum amphicarpy and to identify genetic markers associated with this phenotype. A set of 127 germplasm accessions sampled across the Israeli distribution range of the species was phenotyped in two common garden nurseries. Land use and bioclimatic data were used to delineate the eco-geographic clustering of accession's sampling sites. Single nucleotide polymorphism (SNP) markers were employed in genome-wide association study to identify associated loci. Amphicarpy was subject to strong experimental site x genotype interaction with higher phenotypic expression in fine textured soil relative to sandy loam. Amphicarpy was more prevalent among accessions sampled in eastern Judea and Samaria and was weakly associated with early phenology and relatively modest above ground biomass production. Twelve SNP markers were significantly associated with amphicarpy, each explaining between 8 and 12 % of the phenotypic variation. In P. fulvum amphicarpy seems to be a polygenetic trait controlled by an array of genes that is likely to be affected by environmental stimuli. The probable selective advantage of the association between amphicarpy and early flowering is in line with its relative prevalence in drought prone territories subject to heavy grazing.

Irrigation of tomato (Solanum lycopersicum Mill) plants with brackish (including saline) water improves fruit taste and reduces yields. Salinity additionally leads to toughening of tomato fruit skin, the causative mechanism for which is unknown. The aim of this study is to characterize the effects of salinity on tomato fruit skin texture. Tomato (cherry and full size) plants were irrigated with fresh water (control, ED = 1.01 dS m−1) and saline water (up to 12.61 dS m−1). Organoleptic assessment was compared to the force needed to puncture the cherry tomato fruit skin and to specific skin dry weight. The skin structure of cherry and full-size tomatoes was characterized by light microscopy. Chemical characterization of cell walls building the skin of cherry tomatoes was conducted by Raman micro-spectroscopy. Skin penetration force was found to be linearly correlated with its specific weight and with consumers' perceived thickness. Fruit histology revealed a linear correlation between thickness of the sub-epidermis and salinity of the irrigation water. The tougher tomato skin obtained under conditions of salinity is attributed to increased number of hypodermal cell layers rather than to changes in cell wall composition.

Durum wheat, Triticum turgidum ssp. durum Desf., is an important crop particularly in the Mediterranean basin. Powdery mildew, caused by the pathogen Blumeria graminis f. sp. tritici (Bgt), is a major disease of wheat that results in significant yield losses worldwide. A recombinant inbred line (RIL) population, derived from a cross between durum wheat and wild emmer wheat, T. turgidum ssp. dicoccoides, was used for genomic dissection of quantitative and qualitative resistance loci against wheat powdery mildew based on a genomic map of >600 markers, evenly distributed across the A and B genomes of tetraploid wheat. The genetic analysis of the phenotypic reactions of the RIL population to two Bgt isolates revealed two different resistance mechanisms. The first is monogenic: a wild emmer wheat allele in a single locus conferring complete resistance to Bgt#15, previously designated as PmG16. The second one is polygenic: a set of durum wheat alleles, in five independent QTLs that control partial resistance to Bgt#66 in the RIL population, with a LOD score range of 3.4–19.8. One of them is a major quantitative resistance locus (QRL) that was mapped on chromosome 1A and explains 26.4 % of the variance. In most of the detected QRLs, the durum wheat alleles conferred resistance to powdery mildew. These findings are exceptional in the sense that, so far, only a few Pm alleles originated from a durum wheat background. Therefore, our results emphasize the high potential of exploiting the wide genetic diversity of tetraploid wheat germplasm for wheat breeding using modern wheat genomics tools.

A near-isogenic line (NIL-7A-B-2), introgressed with a quantitative trait locus (QTL) on chromosome 7AS from wild emmer wheat (Triticum turgidum ssp. dicoccoides) into the background of bread wheat (Triticum aestivum L.) cv. BarNir, was recently developed and studied in our lab. NIL-7A-B-2 exhibited better productivity and photosynthetic capacity than its recurrent parent across a range of environments. Here we tested the hypothesis that root-system modifications play a major role in NIL-7A-B-2's agronomical superiority. Root-system architecture (dry matter and projected surface area) and shoot parameters of NIL-7A-B-2 and 'BarNir' were evaluated at 40, 62 and 82 days after planting (DAP) in a sand-tube experiment, and root tip number was assessed in a ‘cigar-roll’ seedling experiment, both under well-watered (WW) and water-limited (WL) treatments. At 82 DAP, under WL treatment, NIL-7A-B-2 presented greater investment in deep roots (depth 40-100 cm) than 'BarNir', with the most pronounced effect recorded in the 60–80 cm soil depth (60% and 40% increase for root dry matter and surface area, respectively). NIL-7A-B-2 had significantly higher root-tip numbers (~48%) per plant than 'BarNir' under both treatments. These results suggest that the introgression of 7AS QTL from wild emmer wheat induced a deeper root system under progressive water stress, which may enhance abiotic stress resistance and productivity of domesticated wheat.

Wheat domestication and subsequent evolution under domestication occurred since the dawn of agriculture and caused significant genetic changes that affected plant morphology, physiology and phenology. The majority of these traits are quantitative traits controlled by many genes. Correspondingly, the main goal of the current study is genetic dissection of the key domestication trait (brittle rachis) and traits evolved under domestication, based on quantitative phenotyping. Genetic mapping of quantitative trait loci (QTL) affecting brittle rachis, threshability, threshing efficiency, spike harvest index and kernel weight was conducted using a recombinant inbred lines population derived from a cross between Triticum durum and wild emmer wheat. Using a new quantitative phenotyping approach, we discovered novel QTLs underlying rachis fragility, spike threshability and other domestication-related traits and confirmed some of the known putative locations for QTLs affecting these traits. Overall, the number of domestication-related QTLs mapped to the A genome was twofold higher than those found on the B genome, in accordance with the concept of ‘genome asymmetry’, implying that the A genome is dedicated to the control of morphological traits, house-keeping metabolic reactions and yield components. Our results add a new dimension to this important concept and contribute to a better understanding of the initial steps of domestication evolution of cereals.

Thermal crop sensing technologies have potential as tools for monitoring and mapping crop water status. To create maps of water status from thermal images, a reliable relationship between direct water status measures like leaf water potential (LWP) and thermal water status measures like temperature and crop water stress index (CWSI) should be established for different crops and for different growth stages. The objective of this study was to define the relationships for cotton between LWP and CWSI derived from high-resolution ground-based thermal images and more specifically to examine whether robust relationships exist between the two measures for different varieties, through a cotton growing season, across seasons and under different geographical areas (different climate and soils). A dataset from three cotton growing seasons and from different geographical areas was built to explore the relationship between CWSI and LWP in cotton. CWSI was calculated based on ground-based thermal images and measured dry (T air + 5 °C) and wet references (Artificial wet reference surface—AWRS). A linear CWSI–LWP relationship was found with high coefficient of determination (R2 = 0.7). This relationship changed over the cotton growth stages and different CWSI–LWP relationships were established to the flowering, boll-filling and defoliation stages. The boll-filling relationship was found to be insensitive to a range of meteorological conditions. The flowering and the boll-filling models were initially validated using diagonal (oblique) thermal images from dates that were not used for calibration. For CWSI calculation, the average temperature of the lowest decile was used for the wet reference instead of the AWRS. The comparison between predicted and observed values of the validation sets yielded RMSE of 0.18 and 0.15 for the flowering and boll-filling stages, respectively. The successful use of the lowest decile as the wet reference enables a future application of the CWSI–LWP relationship to map LWP at a commercial field scale.

'Domestication syndrome' (DS) denotes differences between domesticated plants and their wild progenitors. Crop plants are dynamic entities; hence, not all parameters distinguishing wild progenitors from cultigens resulted from domestication. In this opinion article, we refine the DS concept using agronomic, genetic, and archaeobotanical considerations by distinguishing crucial domestication traits from traits that probably evolved post-domestication in Near Eastern grain crops. We propose that only traits showing a clear domesticated-wild dimorphism represent the pristine domestication episode, whereas traits showing a phenotypic continuum between wild and domesticated gene pools mostly reflect post-domestication diversification. We propose that our approach may apply to other crop types and examine its implications for discussing the timeframe of plant domestication and for modern plant science and breeding.

Background The metabolite content of a seed and its ability to germinate are determined by genetic makeup and environmental effects during development. The interaction between genetics, environment and seed metabolism and germination was studied in 72 tomato homozygous introgression lines (IL) derived from Solanum pennelli and S. esculentum M82 cultivar. Plants were grown in the field under saline and fresh water irrigation during two consecutive seasons, and collected seeds were subjected to morphological analysis, gas chromatograph-mass spectrometry (GC-MS) metabolic profiling and germination tests. Results Seed weight was under tight genetic regulation, but it was not related to germination vigor. Salinity significantly reduced seed number but had little influence on seed metabolites, affecting only 1% of the statistical comparisons. The metabolites negatively correlated to germination were simple sugars and most amino acids, while positive correlations were found for several organic acids and the N metabolites urea and dopamine. Germination tests identified putative loci for improved germination as compared to M82 and in response to salinity, which were also characterized by defined metabolic changes in the seed. Conclusions An integrative analysis of the metabolite and germination data revealed metabolite levels unambiguously associated with germination percentage and rate, mostly conserved in the different tested seed development environments. Such consistent relations suggest the potential for developing a method of germination vigor prediction by metabolic profiling, as well as add to our understanding of the importance of primary metabolic processes in germination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3376-9) contains supplementary material, which is available to authorized users.

Stevia rebaudiana (Bertoni) Bertoni is well known because of its accumulation of the sweet-tasting ent -kaurene diterpeneoid glycoside, which tastes about 300 times as sweet as sucrose. Although stevioside is one of the most abundant and best analyzed, more than 30 additional steviol glycosides so far have been identified and described. Stevioside concentration in the leaves is known to vary widely, depending on the growing conditions and agricultural practices. The present study aimed to examine the feasibility of growing Stevia as an open-field crop in Israel. In order to determine the agricultural practices required for optimizing Stevia biomass production and stevioside yield, effects of planting and harvest times upon plant development, biomass yield components, and stevioside content were examined. The optimal planting season, manifested in intensive plant development and maximal plant biomass yield, was at the beginning of spring, i.e., mid-March to early April. A minimal stand of 10 plants/m 2 was found more favorable than lower stands of 6, 8, or 10 plants/m 2′‘ . The optimal harvesting time, with the highest stevioside yield of about 30 g/m 2 was at the beginning of September, prior to flowering initiation. Moreover, harvesting at this time yielded increased leaf biomass, highly suitable for commercial stevioside extraction. Thus, Stevia rebaudiana offers substantial potential for introduction as a commercial agricultural crop for stevioside production in Israel.

†BackgroundandAims The harvesting method of wild and cultivated cereals has long been recognized as an important factor in the emergence of domesticated non-shattering ear genotypes. This study aimed to quantify the effects of spike brittleness and threshability on threshing time and efficiency in emmer wheat, and to evaluate the implications of post-harvest processes on domestication of cereals in the Near East. †Methods A diverse collection of tetraploid wheat genotypes, consisting ofTriticumturgidum ssp.dicoccoides ‐ the wild progenitor of domesticated wheat ‐ traditional landraces, modern cultivars (T. turgidum ssp. durum) and 150 recombinant (wild × modern) inbred lines, was used in replicated controlled threshing experiments to quantify the effects of spike brittleness and threshability on threshing time and efficiency. †Key Results The transition from a brittle hulled wild phenotype to non-brittle hulled phenotype (landraces) was associated with an approx. 30 % reduction in threshing time, whereas the transition from the latter to non-brittle free-threshing cultivars was associated with an approx. 85 % reduction in threshing time. Similar trends were obtained with groups of recombinant inbred lines showing extreme phenotypes of brittleness and threshability. †Conclusions In tetraploid wheat, both non-brittle spike and free-threshing are labour-saving traits that increase the efficiency of post-harvest processing, which could have been an incentive for rapid domestication of the Near Eastern cereals, thus refuting the recently proposed hypothesis regarding extra labour associated with the domesticated phenotype (non-brittle spike) and its presumed role in extending the domestication episode time frame.

Modifying plant architecture is considered a promising breeding option to enhance crop productivity. Modern chickpea (Cicer arietinum L.) cultivars with either compound (wild-type) or simple leaf shapes are commercially grown but the relationships between leaf shape and yield are not well understood. In this study, a random sample of ‘Kabuli’ type progeny lines of both leaf types, derived from two crosses between modern American simple leaf cultivars and early-flowering wild-type breeding lines, were planted at different sowing densities. Leaf area development and final grain yield in genotypes of the two leaf types responded differently to changes in sowing densities. Compound leaf lines attained higher leaf area indices and higher grain yields at both low and high sowing densities. Yield responses of the simple leaf lines to increasing sowing density were significantly higher compared to compound leaf genotypes in two of three field experiments. The prospects for utilizing the simple leaf trait as a breeding target for short-season growing areas are discussed.

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm) and water-limited (290–320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass - specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.

Transcriptomic and metabolomic profiles were used to unravel drought adaptation mechanisms in wild emmer wheat (Triticum turgidum ssp. dicoccoides), the progenitor of cultivated wheat, by comparing the response to drought stress in roots of genotypes contrasting in drought tolerance. The differences between the drought resistant (R) and drought susceptible (S) genotypes were characterized mainly by shifts in expression of hormone-related genes (e.g., gibberellins, abscisic acid (ABA) and auxin), including biosynthesis, signalling and response; RNA binding; calcium (calmodulin, caleosin and annexin) and phosphatidylinositol signalling, in the R genotype. ABA content in the roots of the R genotype was higher in the well-watered treatment and increased in response to drought, while in the S genotype ABA was invariant. The metabolomic profiling revealed in the R genotype a higher accumulation of tricarboxylic acid cycle intermediates and drought-related metabolites, including glucose, trehalose, proline and glycine. The integration of transcriptomics and metabolomics results indicated that adaptation to drought included efficient regulation and signalling pathways leading to effective bio-energetic processes, carbon metabolism and cell homeostasis. In conclusion, mechanisms of drought tolerance were identified in roots of wild emmer wheat, supporting our previous studies on the potential of this genepool as a valuable source for novel candidate genes to improve drought tolerance in cultivated wheat.

The gene-pool of wild emmer wheat, Triticum turgidum ssp. dicoccoides, harbors a rich allelic repertoire for disease resistance. In the current study, we made use of tetraploid wheat mapping populations derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16) to identify and map a new powdery mildew resistance gene derived from wild emmer wheat. Initially, the two parental lines were screened with a collection of 42 isolates of Blumeria graminis f. sp. tritici (Bgt) from Israel and 5 isolates from Switzerland. While G18-16 was resistant to 34 isolates, Langdon was resistant only to 5 isolates and susceptible to 42 isolates. Isolate Bgt#15 was selected to differentiate between the disease reactions of the two genotypes. Segregation ratio of F(2-3) and recombinant inbreed line (F(7)) populations to inoculation with isolate Bgt#15 indicated the role of a single dominant gene in conferring resistance to Bgt#15. This gene, temporarily designated PmG16, was located on the distal region of chromosome arm 7AL. Genetic map of PmG16 region was assembled with 32 simple sequence repeat (SSR), sequence tag site (STS), Diversity array technology (DArT) and cleaved amplified polymorphic sequence (CAPS) markers and assigned to the 7AL physical bin map (7AL-16). Using four DNA markers we established colinearity between the genomic region spanning the PmG16 locus within the distal region of chromosome arm 7AL and the genomic regions on rice chromosome 6 and Brachypodium Bd1. A comparative analysis was carried out between PmG16 and other known Pm genes located on chromosome arm 7AL. The identified PmG16 may facilitate the use of wild alleles for improvement of powdery mildew resistance in elite wheat cultivars via marker-assisted selection.

Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge.