The increasing salinization of agricultural lands is a threat to global wheat production. Understanding of the mechanistic basis of salt tolerance (ST) is essential for developing breeding and selection strategies that would allow for increased wheat production under saline conditions to meet the increasing global demand. We used a set that consists of 150 internationally derived winter and facultative wheat cultivars genotyped with a 90K SNP chip and phenotyped for ST across three growth stages and for ionic (leaf K⁺ and Na⁺ contents) traits to dissect the genetic architecture regulating ST in wheat. Genome‐wide association mapping revealed 187 Single Nucleotide Polymorphism (SNPs) (R² = 3.00–30.67%), representing 37 quantitative trait loci (QTL), significantly associated with the ST traits. Of these, four QTL on 1BS, 2AL, 2BS and 3AL were associated with ST across the three growth stages and with the ionic traits. Novel QTL were also detected on 1BS and 1DL. Candidate genes linked to these polymorphisms were uncovered, and expression analyses were performed and validated on them under saline and non‐saline conditions using transcriptomics and qRT‐PCR data. Expressed sequence comparisons in contrasting ST wheat genotypes identified several non‐synonymous/missense mutation sites that are contributory to the ST trait variations, indicating the biological relevance of these polymorphisms that can be exploited in breeding for ST in wheat.

Roots perform vital roles for adaptation and productivity under water‐deficit stress, even though their specific functions are poorly understood. In this study, the genetic control of the nodal‐root architectural and anatomical response to water deficit were investigated among diverse spring barley accessions. Water deficit induced substantial variations in the nodal root traits. The cortical, stele, and total root cross‐sectional areas of the main‐shoot nodal roots decreased under water deficit, but increased in the tiller nodal roots. Root xylem density and arrested nodal roots increased under water deficit, with the formation of root suberization/lignification and large cortical aerenchyma. Genome‐wide association study implicated 11 QTL intervals in the architectural and anatomical nodal root response to water deficit. Among them, three and four QTL intervals had strong effects across seasons and on both root architectural and anatomical traits, respectively. Genome‐wide epistasis analysis revealed 44 epistatically interacting SNP loci. Further analyses showed that these QTL intervals contain important candidate genes, including ZIFL2, MATE, and PPIB, whose functions are shown to be related to the root adaptive response to water deprivation in plants. These results give novel insight into the genetic architectures of barley nodal root response to soil water deficit stress in the fields, and thus offer useful resources for root‐targeted marker‐assisted selection.

Key message SNP alleles on chromosomes 4BL and 6AL are associated with sensitivity to salt tolerance in wheat and upon validation can be exploited in the development of salt-tolerant wheat varieties. Abstract The dissection of the genetic and molecular components of salt stress response offers strong opportunities toward understanding and improving salt tolerance in crops. In this study, GWAS was employed to identify a total of 106 SNP loci (R² = 0.12–63.44%) linked to salt stress response in wheat using leaf chlorophyll fluorescence, grain quality and shoot ionic (Na⁺ and K⁺ ions) attributes. Among them, 14 SNP loci individually conferred pleiotropic effects on multiple independent salinity tolerance traits including loci at 99.04 cM (R² ≥ 14.7%) and 68.45 cM (R² ≥ 4.10%) on chromosomes 6AL and 4BL, respectively, that influenced shoot Na⁺-uptake, shoot K⁺/Na⁺ ratio, and specific energy fluxes for absorption (ABS/RC) and dissipation (DIo/RC). Analysis of the open reading frame (ORF) containing the SNP markers revealed that they are orthologous to genes involved in photosynthesis and plant stress (salt) response. Further transcript abundance and qRT-PCR analyses indicated that the genes are mostly up-regulated in salt-tolerant and down-regulated in salt-sensitive wheat genotypes including NRAMP-2 and OPAQUE1 genes on 4BL and 6AL, respectively. Both genes showed highest differential expression between contrasting genotypes when expressions of all the genes within their genetic intervals were analyzed. Possible cis-acting regulatory elements and coding sequence variation that may be involved in salt stress response were also identified in both genes. This study identified genetic and molecular components of salt stress response that are associated with Na⁺-uptake, shoot Na⁺/K⁺ ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat.

Nitrogen (N) is a vital component of crop production. Wheat yield varies significantly under different soil available N. Knowing how wheat responds to or interacts with N to produce grains is essential in the selection of N use efficient cultivars. We assessed in this study variations among wheat genotypes for productivity-related traits under three cropping systems (CS), high-nitrogen with fungicide (HN-WF), high-nitrogen without fungicide (HN-NF) and low-nitrogen without fungicide (LN-NF) in the 2015, 2016 and 2017 seasons. ANOVA results showed genotypes, CS, and their interactions significantly affected agronomic traits. Grain yield (GY) increased with higher leaf chlorophyll content, importantly under CS without N and fungicide supply. Yellow rust disease reduced the GY by 20% and 28% in 2015 and 2016, respectively. Moreover, averaged over growing seasons, GY was increased by 23.78% under CS with N supply, while it was greatly increased, by 52.84%, under CS with both N and fungicide application, indicating a synergistic effect of N and fungicide on GY. Fungicide supply greatly improved the crop ability to accumulate N during grain filling, and hence the grain protein content. Recently released cultivars outperformed the older ones in most agronomic traits including GY. Genotype performance and stability analysis for GY production showed differences in their stability levels under the three CS. The synergistic effect of nitrogen and fungicide on grain yield (GY) and the differences in yield stability levels of recently released wheat cultivars across three CS found in this study suggest that resource use efficiency can be improved via cultivar selection for targeted CS.

Salt stress is one the most destructive abiotic stressors, causing yield losses in wheat worldwide. A prerequisite for improving salt tolerance is the identification of traits for screening genotypes and uncovering causative genes. Two populations of F₃ lines developed from crosses between sensitive and tolerant parents were tested for salt tolerance at the seedling stage. Based on their response, the offspring were classified as salt sensitive and tolerant. Under saline conditions, tolerant genotypes showed lower Na⁺ and proline content but higher K⁺, higher chlorophyll content, higher K⁺/Na⁺ ratio, higher PSII activity levels, and higher photochemical efficiency, and were selected for further molecular analysis. Five stress responsive QTL identified in a previous study were validated in the populations. A QTL on the short arm of chromosome 1D showed large allelic effects in several salt tolerant related traits. An expression analysis of associated candidate genes showed that TraesCS1D02G052200 and TraesCS5B02G368800 had the highest expression in most tissues. Furthermore, qRT-PCR expression analysis revealed that ZIP-7 had higher differential expressions under saline conditions compared to KefC, AtABC8 and 6-SFT. This study provides information on the genetic and molecular basis of salt tolerance that could be useful in development of salt-tolerant wheat varieties.

Bread wheat is one of the most important crops for human diet but the increasing soil salinization is causing yield reductions worldwide. Physiological, genetic, transcriptomics and bioinformatics analyses were integrated to study the salt stress adaptation response in bread wheat. A comparative analysis to uncover the dynamic transcriptomic response of contrasting genotypes from two wheat populations was performed at both osmotic and ionic phases in time points defined by physiologic measurements. The differential stress effect on the expression of photosynthesis, calcium binding and oxidative stress response genes in the contrasting genotypes supported the greater photosynthesis inhibition observed in the susceptible genotype at the osmotic phase. At the ionic phase genes involved in metal ion binding and transporter activity were up-regulated and down-regulated in the tolerant and susceptible genotypes, respectively. The stress effect on mechanisms related with protein synthesis and breakdown was identified at both stress phases. Based on the linkage disequilibrium blocks it was possible to select salt-responsive genes as potential components operating in the salt stress response pathways leading to salt stress resilience specific traits. Therefore, the implementation of a systemic approach provided insights into the adaptation response mechanisms of contrasting bread wheat genotypes at both salt stress phases. Highlight: The implementation of a systemic approach provided insights into salt stress adaptation response mechanisms of contrasting bread wheat genotypes from two mapping populations at both osmotic and ionic phases.