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Despite the growing concerns about arsenic toxicity, information on tolerance and responsible genetic factors in wheat remains elusive. To address that, the present study aimed to screen the wheat varieties against arsenic based on growth parameters, yield, grain accumulation, and associated genes. A total of 110 wheat varieties were grown in arsenic-contaminated regions to record physio-morphological traits. The wheat 90K Infinium iSelect SNP array was used for the genome-wide association model to identify genomic regions. Wheat varieties such as Punjab-81, AARI-11, and Daman showed arsenic concentrations45 μg/kg in similar conditions as well as the impact on grain yield, chlorophyll, Thousand Kernel Weight, and plant height. Contrastingly, varieties like Kohistan-97, As-2002, Barani-70, and Pari-73 showed grain concentrations5 μg/kg grown under highly contaminated conditions. Three significant loci associated with arsenic accumulation in grain were identified on chromosomes 6A (qASG1-6A) and 6B (qASG3-6B and qASG4-6B). Annotation at these loci identified 39 wheat genes among which several were important for growth and tolerance against stress. The candidate gene (TraesCS6B02G429400) responsible for Glutathione-S-transferase was identified in the present study and must be investigated further using a transcriptomic approach. The present study provided background information for breeding prospects to improve wheat yield and tolerance against arsenic.

Stripe rust caused by Puccnina striiformis (Pst) is an economically important disease attacking wheat all over the world. Identifying and deploying new genes for Pst resistance is an economical and long-term strategy for controlling Pst. A genome-wide association study (GWAS) using single nucleotide polymorphisms (SNPs) and functional haplotypes were used to identify loci associated with stripe rust resistance in synthetic-derived (SYN-DER) wheats in four environments. In total, 92 quantitative trait nucleotides (QTNs) distributed over 65 different loci were associated with resistance to Pst at seedling and adult plant stages. Nine additional loci were discovered by the linkage disequilibrium-based haplotype-GWAS approach. The durable rust-resistant gene Lr34/Yr18 provided resistance in all four environments, and against all the five Pst races used in this study. The analysis identified several SYN-DER accessions that carried major genes: either Yr24/Yr26 or Yr32. New loci were also identified on chr2B, chr5B, and chr7D, and 14 QTNs and three haplotypes identified on the D-genome possibly carry new alleles of the known genes contributed by the Ae. tauschii founders. We also evaluated eleven different models for genomic prediction of Pst resistance, and a prediction accuracy up to 0.85 was achieved for an adult plant resistance, however, genomic prediction for seedling resistance remained very low. A meta-analysis based on a large number of existing GWAS would enhance the identification of new genes and loci for stripe rust resistance in wheat. The genetic framework elucidated here for stripe rust resistance in SYN-DER identified the novel loci for resistance to Pst assembled in adapted genetic backgrounds.

Green synthesis of nanomaterials is advancing due to its ease of synthesis, inexpensiveness, nontoxicity and renewability. In the present study, an eco-friendly biogenic method was developed for the green synthesis of nickel oxide nanoparticles (NiONPs) using phytochemically rich Berberis balochistanica stem (BBS) extract. The BBS extract was rich in phenolics, flavonoids and berberine. These phytochemicals successfully reduced and stabilised the NiNO3 (green) into NiONPs (greenish-gray). BBS-NiONPs were confirmed by using UV-visible spectroscopy (peak at 305 nm), X-ray diffraction (size of 31.44 nm), Fourier transform infrared spectroscopy (identified -OH group and Ni-O formation), energy dispersive spectroscopy (showed specified elemental nature) and scanning electron microscopy (showed rhombohedral agglomerated shape). BBS-NiONPs were exposed to multiple in vitro bioactivities to ascertain their beneficial biological applications. They exhibited strong antioxidant activities: total antioxidant capacity (64.77%) and 2, 2-diphenyl-1-picrylhydrazyl (71.48%), and cytotoxic potential: Brine shrimp cytotoxicity assay with IC50 (10.40 µg/mL). BBS-NiONPs restricted the bacterial and fungal pathogenic growths at 1000, 500 and 100 µg/mL. Additionally, BBS-NiONPs showed stimulatory efficacy by enhancing seed germination rate and seedling growth at 31.25 and 62.5 µg/mL. In aggregate, BBS extract has a potent antioxidant activity which makes the green biosynthesis of NiONPs easy, economical and safe. The biochemical potential of BBS-NiONPs can be useful in various biomedical and agricultural fields.

In current report, nickel oxide nanoparticles (NiONPs) were synthesized using leaf extract of Berberis balochistanica (BB) an endemic medicinal plant. The BB leaves extract act as a strong reducing, stabilizing, and capping agent in the synthesis of BB@NiONPs. Further, BB@NiONPs were characterized using Uv-visible spectroscopy (UV-vis), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), Energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), and average size was calculated ~21.7 nm). Multiple in vitro biological activities were performed to determine their therapeutic potentials. The BB@NiONPs showed strong antioxidant activities in term of 2,2-diphenyl-1-picrylhydrazyl (DPPH) and total antioxidant capacity (TAC) with scavenging potential of 69.98 and 59.59% at 200 μg/ml, respectively. The antibacterial and antifungal testes were examined using different bacterial and fungal strains and dose-dependent inhibition response was reported. Laterally, cytotoxic and phytotoxic activities were studied using brine shrimp and radish seeds. The result determined potential cytotoxic activity with LD50 value (49.10 μg/ml) and outstanding stimulatory effect of BB@NiONPs on seed germination at lower concentrations as compared to control. Overall, result concluded that biosynthesis of NiONPs using leaf extracts of Berberis balochistanica is cheap, easy, and safe method and could be used in biomedical and agriculture field as nanomedicine and nano fertilizer.

Excess Ni intake has harmful implications on human health, which include chronic bronchitis, reduced lung function, and cancer of lung and nasal sinuses. Like other toxic metals, higher Ni accumulation in grains leads to excess intake by humans when the contaminated grains are consumed as food. There is little information about the genetic factors that regulate Ni uptake in plants. To investigate genetic architecture of Ni uptake in leaf and translocation to grain, we performed a genome-wide association study with genotyping from 90 K array in a historical bread wheat diversity panel from Pakistan. We observed that Ni toxicity caused more than 50 % reductions in biological yield and grain yield, other agronomic traits were also partly or severely affected. Genetic association study helped identify 23 SNP-trait associations involved in Ni uptake in leaf and translocation to grains. These 23 SNPs covered 15 genomic loci at chromosomes 1A, 2D, 3B, 4A and 4B of wheat. The favorable alleles of these SNPs were randomly distributed in subpopulations indicating no selection pressure for this trait during breeding improvement. These regions had 283 low-confidence and 248 high-confidence protein coding genes. Among these, 156 were annotated using databases of wheat and closely related grass species. Since there is no previous report on genetic information of Ni uptake and translocation, these results provide sufficient grounds for further research of candidate genes and varietal development.

Current study explored the effects of municipal sewage (MS) irrigation on heavy metal phyto-accretion, biochemical responses and human health risks of diverse wheat genotypes along with recycled municipal sewage (RMS). Mean concentrations of PO

Despite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat diversity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A. Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800, involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat.KEY MESSAGEWe report two new loci for P utilization efficiency on chromosomes 3A and 4A of wheat. The prioritized candidate genes at these loci can be investigated by molecular biology techniques to improve P efficiency in wheat and grass relatives.

Cadmium (Cd) toxicity is a serious threat to future food security and health safety. To identify genetic factors contributing to Cd uptake in wheat, we conducted a genome-wide association study with genotyping from 90K SNP array. A spring wheat diversity panel was planted under normal conditions and Cd stress (50 mg Cd/kg soil). the impact of Cd stress on agronomic traits ranged from a reduction of 16% in plant height to 93% in grain iron content. Individual genotypes showed a considerable variation for Cd uptake and translocation subdividing the panel into three groups: (1) hyper-accumulators (i.e. high Leaf(_Cd) and low Seed(_Cd)), (2) hyper-translocators (i.e. low Leaf(_Cd) and high Seed(_Cd)), and (3) moderate lines (i.e. low Leaf(_Cd) and low Seed(_Cd)). Two lines (SKD-1 and TD-1) maintained an optimum grain yield under Cd stress and were therefore considered as Cd resistant lines. Genome-wide association identified 179 SNP-trait associations for various traits including 16 for Cd uptake at a significance level of P < .001. However, only five SNPs were significant after applying multiple testing correction. These loci were associated with seed-cadmium, grain-iron, and grain-zinc: qSCd-1A, qSCd-1D, qZn-2B1, qZn-2B2, and qFe-6D. These five loci had not been identified in the previously reported studies for Cd uptake in wheat. These loci and the underlying genes should be further investigated using molecular biology techniques to identify Cd resistant genes in wheat., National Key Research and Development Program of China [2016YFD0101001]; Higher Education Commision, Pakistan [HECNRPU-3825], The National Key Research and Development Program of China, Grant/Award Number: 2016YFD0101001; Higher Education Commision, Pakistan, Grant/Award Number: HECNRPU-3825

This study was carried out to screen historical diversity panel of bread wheat against municipal wastewater (MW) and remediated wastewater (RW) irrigation to find tolerant and sensitive genotypes and their impact on yield attributes. The experiment was conducted in randomized complete block design (RCBD) with three water treatments, i.e., tap water (TW), RW, and MW. Yield attributes, health risk assessment, water and soil chemistry were recorded. Principal component analysis (PCA) was used to identify tolerant and sensitive genotypes of wheat on the basis of metal accumulation. Metal accumulation in grains increased in pattern KFeZn in all irrigation treatments. Tolerant genotypes in MW showed lowest hazard quotient (HQ) and hazard index (HI) values (adults 0.62; children 0.67) for Fe and Zn as compared to sensitive genotypes (adults 1.53; children 1.70). However, HI values in sensitive and tolerant genotypes of RW were recorded1. Mean values of yield attributes, i.e., plant height, spike length, spikelet per spike, grains per plant, biological yield, grain yield, and thousand kernel weight, were recorded in pattern, i.e., MWRWTW. In this study, yield attributes and human health are affected in both cases of higher and lower concentration of Fe and Zn metal. It is suggested that tolerant genotypes can prove useful for cultivation in areas receiving MW and also provide molecular breeding opportunities for seeking tolerance against metal stresses.

Design and implementation of wastewater treatment is inevitable due to toxic effects of wastewater irrigation on crops, soil and human health. Current investigation is the pioneer attempt on full-scale hybrid constructed wetland system (HCWS) built for municipal wastewater treatment from Pakistan. HCWS was comprised of vertical sub-surface flow constructed wetland (VSSF-CW) and five phyto-treatment ponds connected in series. Higher environmental risk was associated with untreated municipal wastewater usage in irrigation as estimated through discharge of metals to recipient soils. Treatment efficiency percentages recorded for HCWS reclaimed water quality parameters were, i.e., EC (56.68), TDS (56.86), alkalinity (39.67), chloride (39.68), sulfate (46.73), Na (28.80), Mn (65.24), Cr (78.07), Ni (81.02), BOD (68.74), total hardness (19.56), Fe (70.09), phosphate (55.40), Pb (80.48), COD (63.64), Mg (17.24), K (60.05), Co (100), Cu (67.73), Zn (59.97), Cd (100), and Ca (21.47) respectively. Wastewater treatment in HCWS was due to aquatic plants [Phragmites australis Cav. Trin. ex Steud., Canna indica L. Typha latifolia L., and Hydrocotyle umbellata L.], microbial activities and substrate based wetland processes. The HCWS treated water was well under irrigation standards and recommended for safer crop production in water scarce regions.

Drought stress ‘particularly at seedling stage’ causes morpho-physiological differences in wheat which are crucial for its survival and adaptability. In the present study, 209 recombinant inbred lines (RILs) from synthetic wheat (W7984)× ‘Opata’ (also known as SynOpRIL) population were investigated under well-watered and water-limited conditions to identify quantitative trait loci (QTL) for morphological traits at seedling stage. Analysis of variance revealed significant differences (P< 0.01) among RILs, and water treatments for all traits with moderate to high broad sense heritability. Pearson's coefficient of correlation revealed positive correlation among all traits except dry root weight that showed poor correlation with fresh shoot weight (FSW) under water-limited conditions. A high-density linkage map was constructed with 2639 genotyping-by-sequencing markers and covering 5047 cM with an average marker density of 2 markers/cM. Composite interval mapping identified 16 QTL distributed over nine chromosomes, of which six were identified under well-watered and 10 in water-limited conditions. These QTL explained from 4 to 59% of the phenotypic variance. Six QTL were identified on chromosome 7B; three for shoot length under water-limited conditions (QSL.nust-7B) at 64, 104 and 221 cM, two for fresh root weight (QFRW.nust-7B) at 124 and 128 cM, and one for root length (QRL.nust-7B) at 122 cM positions.QFSW.nust-7Bappeared to be the most significant QTL explaining 59% of the phenotypic variance and also associated with FSW at well-watered conditions. These QTL could serve as target regions for candidate gene discovery and marker-assisted selection in wheat breeding.

Chromium (Cr) toxicity is a rapidly increasing environmental concern and poses a major threat to plant growth as well as food chain. This study was carried out to screen spring wheat diversity panel against Cr toxicity to assess yield reduction, grain contamination extents and genomic regions associated with tolerance to Cr toxicity. The diversity panel was planted in control and Cr stress (26 mg Cr/kg soil) in paved plots, and several morphological and physiological traits were recorded. Wheat 90 K Infinium iSelect SNP array was used to identify genomic regions underpinning tolerance to Cr toxicity. Some wheat cultivars (Khosar-95, Miraj-08, Millet-11, Sarsabaz and NARC-11) had Cr concentration within international edible threshold limit (1 ppm), but showed greater reduction to grain yield (63–95%) due to higher leaf Cr concentrations (2.35–8.95 ppm). Contrastingly, wheat cultivars Auqab-00 and Pakistan-13 had lower yield reduction up to 9% and 39%, respectively but had higher concentration of Cr in seeds (2.1 and 3.5 ppm, respectively). Genome-wide association studies identified 71 loci linked with yield related traits under Cr stress and 48 loci for differences between control and Cr stress treatments. Further, gene ontology of trait-associated SNPs revealed proteins with significant importance in plant development and tolerance against heavy metal stress. To our knowledge, this is the first study for identification of genomic regions linked to Cr stress, suggesting that this could be useful to identify complex architecture of genetic factors as well as molecular breeding opportunities for tolerance to Cr stress.

Despite the economic importance of P utilization efficiency, information on genetic factors underlying this trait remains elusive. To address that, we performed a genome-wide association study in a spring wheat diversity panel ranging from landraces to elite varieties. We evaluated the phenotype variation for P utilization efficiency in controlled conditions and genotype variation using wheat 90 K SNP array. Phenotype variables were transformed into a smaller set of uncorrelated principal components that captured the most important variation data. We identified two significant loci associated with both P utilization efficiency and the 1st principal component on chromosomes 3A and 4A: qPE1-3A and qPE2-4A. Annotation of genes at these loci revealed 53 wheat genes, among which 6 were identified in significantly enriched pathways. The expression pattern of these 6 genes indicated that TraesCS4A02G481800, involved in pyruvate metabolism and TCA cycle, had a significantly higher expression in the P efficient variety under limited P conditions. Further characterization of these loci and candidate genes can help stimulate P utilization efficiency in wheat.

The present study aimed to reveal the impact of the stay-green trait in bread wheat under terminal heat stress. Field experiments (early and late sowing, for two consecutive years) were conducted to investigate the influence of terminal heat stress on the morpho-physiological traits in different stay-green types i.e., non-stay-green, moderately non-stay-green, moderately stay-green, and stay-green. In addition, the greenhouse experiment was performed to dissect the stay-green trait in functional stay-green, non-functional stay-green, and non-stay-green genotypes. The results of the field experiments confirmed that genotypes exhibiting the stay-green trait have a significantly high chlorophyll content, normalized difference vegetative index, grain yield, biological yield, kernel weight, and low canopy temperature under control and heat stress conditions. In the greenhouse experiment, functional stay-green and non-functional stay-green genotypes showed a high chlorophyll content and photochemical efficiency, whereas biological yield and grain yield showed a significant relation with the functional stay-green genotype under control and terminal heat stress treatments. The sequencing and expression analysis of chlorophyllide a oxygenase (CaO), light-harvesting complex (Cab), stay-green (SGR), and red chlorophyll catabolite reductase (RCCR) in functional stay-green, non-functional stay-green, and non-stay-green genotypes revealed variations in the exons of CaO and RCCR, and significant difference in the regulation of CaO and Cab at 7 days after anthesis under terminal heat stress. This study confirms that genotypes displaying the stay-green trait can aid wheat breeders to cope with increasing temperature in the impending decades.

Aspergillus tubingensis is an important pathogen of economically important crops. Different biotic stresses strongly influence the balance of metabolites in plants. The aim of this study was to understand the function and response of resistance associated metabolites which, in turn are involved in many secondary metabolomics pathways to influence defense mechanism of cotton plant. Analysis of non-targeted metabolomics using ultra high performance liquid chromatography–mass spectrometry (UPLC-MS) revealed abundant accumulation of key metabolites including flavonoids, phenylpropanoids, terpenoids, fatty acids and carbohydrates, in response to leaf spot of cotton. The principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA) and partial least squares discriminant analysis (PLS-DA) score plots illustrated the evidences of variation between two varieties of cotton under mock and pathogen inoculated treatments. Primary metabolism was affected by the up regulation of pyruvate and malate and by the accumulation of carbohydrates like cellobiose and inulobiose. Among 241 resistance related (RR) metabolites, 18 were identified as resistance related constitutive (RRC) and 223 as resistance related induced (RRI) metabolites. Several RRI metabolites, identified in the present study were the precursors for many secondary metabolic pathways. These included phenylpropanoids (stilbenes and furanocoumarin), flavonoids (phlorizin and kaempferol), alkaloids (indolizine and acetylcorynoline) and terpenoids (azelaic acid and oleanolic acid). Our results demonstrated that secondary metabolism, primary metabolism and energy metabolism were more active in resistant cultivar, as compared to sensitive cultivar. Differential protein and fatty acid metabolism was also depicted in both cultivars. Accumulation of these defense related metabolites in resistant cotton cultivar and their suppression in susceptible cotton cultivar revealed the reason of their respective tolerance and susceptibility against A. tubingensis.

Foods containing high amounts of either phytic acid or gliadin can pose a risk for development of iron deficiency and celiac disease, respectively. The present study was conducted to evaluate the effects of preselected gliadin degrading strains, Enterococcus mundtii QAUSD01 and Wickerhamomyces anomalus QAUWA03, on phytic acid and gliadin degradation in six wheat cultivars (Lasani 2008, Seher 2006, Chakwal 97, Shafaq 2006, Bars 2009, Barani 83). Tight junction proteins, trans-epithelial resistance (TER) and ruffle formation in Caco-2 cells were evaluated relative to Saccharomyces cerevisiae–mediated fermented and unfermented controls. Phytic acid degradation was demonstrated in all six cultivars fermented with E. mundtii QAUSD01 and W. anomalus QAUWA03 consortia. Among the six fermented cultivars, Shafaq 2006 showed relatively higher degradation of gliadin. In comparison to the other tested wheat varieties, fermentation of Lasani 2006 was associated with minimal toxic effects on Caco-2 cells in terms of ruffle formation, tight junction proteins and TER, which can be attributed to extensive degradation of toxic gliadin fragments.

édition online; Bread wheat derives from a grass ancestor structured in 7 protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing COS (Conserved Orthologous Set) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supradominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat. This article is protected by copyright. All rights reserved.

The current study provides one of the first attempts to identify tolerant, moderately sensitive, and highly sensitive wheat genotypes on the basis of heavy metal accumulation, biochemical attributes, and human health risk assessments on urban wastewater (UW) irrigation. Mean heavy metals (Fe, Co, Ni, Cu, Zn, Pb, Cd, Cr, Mn) and macro-nutrients (Na, K, Ca, Mg) levels increased in the roots, stem, and grains of studied genotypes. Except K (stem > root > grain), all metals were accumulated in highest concentrations in roots followed by stem and grains. Principal component analyses (PCA) identified three groups of UW-irrigated genotypes which were confirmed by hierarchical agglomerative cluster analyses (HACA). Wheat genotypes with the lowest metal accumulation were regarded as tolerant, whereas those with maximum accumulation were considered highly sensitive. Tolerant genotypes showed the lowest hazard quotient for heavy metals, i.e., Co, Mn, Cd, Cu, Fe, Pb, and Cr, and hazard index (HI) values (adults, 2.04; children, 2.27) than moderately and highly sensitive genotypes. Higher health risks (HI) associated with moderate (adults 2.26; children 2.53) and highly sensitive (adults 2.52; children 2.82) genotypes revealed maximum uptake of heavy metals. The heatmap showed higher mean biochemical levels of chlorophyll, carotenoids, membrane stability index (MSI%), sugars, proteins, proline, superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) in tolerant genotypes than remaining genotypes. With the lowest metal accumulation and advanced biochemical mechanisms to cope with the adverse effects of heavy metals in their plant bodies, tolerant genotypes present a better option for cultivation in areas receiving UW or similar type of wastewater.

Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.

In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.

Synthetic hexaploid wheat and their advanced derivatives (SYN-DERs) are promising sources for introducing novel genetic diversity to develop climate-resilient cultivars. In a series of field and laboratory experiments, we measured biochemical, physiological and agronomic traits in a diversity panel of SYN-DERs evaluated under well-watered (WW) and water-limited (WL) conditions. Analysis of variance revealed significant differences among genotypes, treatments and their interaction for all agronomic and physiological traits. Grain yield (GY) was reduced by 62.75% under WL, with a reduction of 38.10% in grains per spike (GS) and 19.42% in 1000-grain weight (TGW). In a Pearson’s coefficient correlation, GY was significantly correlated with GS, number of tillers per plant and TGW in both conditions. Path coefficient analysis showed that TGW and GS made the highest contribution to GY in WW and WL conditions, respectively. The traits examined in this experiment explained 59.6% and 63.01% of the variation in GY under WL and WW conditions, respectively; TGW, canopy temperature at spike and superoxide dismutase were major determinants of GY under WL conditions. The major flowering-time determinant gene Ppd-D1 was fixed in the diversity panel, with presence of the photoperiod-insensitive allele (Ppd-D1a) in 99% accessions. Wild-type alleles at Rht-B1 and Rht-D1, and presence of the rye translocation (1B.1R), favoured GY under WL conditions. Continuous variation for the important traits indicated the potential use of genome-wide association studies to identify favourable alleles for drought adaptation in the SYN-DERs. This study showed sufficient genetic variation in the SYN-DERs diversity panel to improve yields during droughts because of better adaptability than bread wheat.

The linked projections of the global population standing in 2050 of approximately 9.2 billion and the balanced annual increase in crop yields to ensure food security, with wheat considered as its major conduit have necessitated taking a careful multidisciplinary integrated look at what looms ahead. Keeping wheat as the major crop target, its outputs under irrigated and rain-fed conditions have become significant to address factors that pave the way for yield maximization both under plant improvement and plant management scenarios. Optimum experimental condition yields and realized national annual yields show tremendous gaps, and when farmers with smaller land holdings are involved, this gap is further broadened. In this chapter, we address yield discrepancies, focusing on drought due to three major factors present now and that may magnify in the future; this suggests the need to embrace all as working objectives in a tandem manner and in a holistic fashion. The genetic component has a pivotal slot that encompasses breeding for high yield per se and, where such genetic resource diversity is limiting, to explore the various wheat gene pools and harness the same. This option may permit researchers to capture the diversity of genetic resources that have so far been underutilized over an expanse that covers intraspecific, interspecific, and intergeneric hybridization. The working expanse addresses both biotic and abiotic stress production constraints and allows more precise handling of crop improvement around water-limiting conditions. Intervention using current molecular advances is a boon to swift progress. As with the exploitation of genomic diversity in prebreeding and breeding programs, the current setup may show the way forward to rely on genotypic platforms through accurate phenotypic information, thereby permitting stringent and reliable information for maximizing yields and other attributes essential for crop production to be gathered. This is where the various “omic” areas stand to efficiently support diverse research targets. Finally, it is paramount that water availability be seriously kept in focus. Timely natural supplies are risky, optimum availability for irrigating crops is showing less reliability, and water scarcity is acutely apparent; in addition, it is expected to become a major concern in the very near decades due to climate change and source supply shortages. Therefore alternatives for water provision are gaining importance coupled with the introduction of efficient management application systems. These interlinked facets form the contents of this chapter.

Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements.

Grain dietary fiber content in wheat not only affects its end use and technological properties including milling, baking and animal feed but is also of great importance for health benefits. In this study, integration of association genetics (seven detected loci on chromosomes 1B, 3A, 3D, 5B, 6B, 7A, 7B) and meta-QTL (three consensus QTL on chromosomes 1B, 3D and 6B) analyses allowed the identification of seven chromosomal regions underlying grain dietary fiber content in bread wheat. Based either on a diversity panel or on bi-parental populations, we clearly demonstrate that this trait is mainly driven by a major locus located on chromosome 1B associated with a log of p value >13 and a LOD score >8, respectively. In parallel, we identified 73 genes differentially expressed during the grain development and between genotypes with contrasting grain fiber contents. Integration of quantitative genetics and transcriptomic data allowed us to propose a short list of candidate genes that are conserved in the rice, sorghum and Brachypodium chromosome regions orthologous to the seven wheat grain fiber content QTL and that can be considered as major candidate genes for future improvement of the grain dietary fiber content in bread wheat breeding programs.

Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.

Recent updates in comparative genomics among cereals have provided the opportunity to identify conserved orthologous set (COS) DNA sequences for cross-genome map-based cloning of candidate genes underpinning quantitative traits. New tools are described that are applicable to any cereal genome of interest, namely, alignment criterion for orthologous couples identification, as well as the Intron Spanning Marker software to automatically select intron-spanning primer pairs. In order to test the software, it was applied to the bread wheat genome, and 695 COS markers were assigned to 1,535 wheat loci (on average one marker/2.6 cM) based on 827 robust rice-wheat orthologs. Furthermore, 31 of the 695 COS markers were selected to fine map a pentosan viscosity quantitative trait loci (QTL) on wheat chromosome 7A. Among the 31 COS markers, 14 (45%) were polymorphic between the parental lines and 12 were mapped within the QTL confidence interval with one marker every 0.6 cM defining candidate genes among the rice orthologous region.

The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.