Harnessing phyllosphere and rhizobium bacteria for salt stress alleviation in common bean (Phaseolus vulgaris) Safoura Ansari, Seyed Abdolreza Kazemeini, Mozhgan Alinia, Mozhgan Sepehri, Ali Dadkhodaie, Saeid Eshghi, Vahid Alah Jahandideh Mahjenabadi BMC Plant Biology, 2026 Salinity is a major constraint to common bean (Phaseolus vulgaris) productivity, yet sustainable mitigation strategies remain limited. Here, we evaluated the interactive effects of salinity stress (0–8 dS m− 1), and plant growth-promoting bacteria inoculations, including Phyllosphere strains (P1 and P2), and Rhizobium (RB), and their combinations (P1 + RB, P2 + RB) on two common bean cultivars (Almas and Pak). Salinity significantly reduced plant height, chlorophyll pigments (Chl a and Chl b), chlorophyll fluorescence (Fv/Fm) and biomass, while elevating oxidative stress markers [malondialdehyde (MDA), hydrogen peroxide (H2O2)] and antioxidant enzyme activity (SOD, CAT). Bacterial treatments, particularly P1 + RB treatment alleviated salinity-induced damage by reducing oxidative stress (up to 68.4%), enhancing ion homeostasis (lower Na⁺, higher K⁺ and Ca²⁺), and maintaining photosynthetic efficiency (Fv/Fm). Almas exhibited greater tolerance than Pak, with lower MDA levels (21.7–25% reduction) and higher phenolic accumulation under stress. Together, these findings highlight the synergistic role of bacterial inoculants and cultivar selection in enhancing salinity tolerance, offering a promising strategy for improving legume resilience and productivity in saline agroecosystems.
Multipathotype Testing and Molecular Markers Identify Leaf Rust Resistance Genes in a Collection of Iranian Wheat Cultivars Saeideh Dorostkar, Mona Karbalivand, Ali Dadkhodaie, Bahram Heidari Journal of Phytopathology, 2026 Leaf rust, caused by Puccinia triticina ( Pt ), is one of the most prevalent wheat diseases worldwide, leading to substantial yield losses and reduced grain quality. Understanding the genetic basis of resistance and the diversity of leaf rust resistance ( Lr ) genes is crucial for effective disease management. In the present study, 32 Iranian wheat cultivars and 36 near isogenic lines were evaluated against seven Pt races at the seedling stage under greenhouse conditions. Additionally, the presence of the genes Lr10 , Lr19 , Lr24 and Lr37 was investigated using specific molecular markers. Phenotypic evaluation of genotypes revealed a wide range of infection types, varying from resistant ‘0; = ’ to highly susceptible ‘4’. ‘Pishtaz’, ‘Golestan’ and ‘Rasool’ were the most resistant cultivars. Molecular marker analysis identified the presence of Lr10 , Lr24 and Lr37 , either singly or in combination in 23 cultivars, whereas Lr19 was not detected in any genotype. The gene Lr24 was the most frequently occurring gene (59.38%), followed by Lr10 (53.12%) and Lr37 (43.75%). Notably, cultivars with identical Lr gene combinations often exhibited contrasting infection types, indicating a complex genotype–phenotype relationship and suggesting the involvement of epistatic interactions, uncharacterized resistance loci and local pathogen adaptation. Overall, although Lr24 emerged as the major contributor to leaf rust resistance in the studied germplasm, the absence of Lr19 highlights the need for incorporating additional resistance sources in breeding programs. These findings emphasise the need to broaden the resistance gene pool and deploy diverse genes to enhance the durability of leaf rust resistance in Iranian wheat cultivars.
Evaluation of Salinity Tolerance Threshold of Two Wheat Cultivars Via Photosynthetic Efficiency and Ion Homeostasis Elahe Gheisary, Seyed Abdolreza Kazemeini, Mozhgan Alinia, Ali Dadkhodaie, Mahboubeh Fazaeli, Andrea Mastinu Journal of Crop Health, 2025 The possible growth and production of wheat have been negatively influenced by salinity stress, which is a critical environmental factor. Therefore, our study aimed to determine the salinity tolerance threshold of two wheat cultivars (Amin and Barzegar) via photochemical efficiency and ion homeostasis under eight salinity levels (0.5, 2, 4, 6, 8, 10, 12, and 14 dS m−1) using a completely randomized design with three replicates. Both wheat cultivars experienced a decrease in the investigated leaf area from the 2 dS m−1 salinity level, with the shoot and root dry weight trends remaining unchanged until the 6 dS m−1 level, followed by a change in the shoot and root dry weight trends. Some significant interactions between salinity stress and cultivars were found in photosynthetic pigments and chlorophyll fluorescence parameters. Increasing salinity stress reduced the Fv/Fm, Fv/F0 and YPII in both wheat cultivars. However, a significant increase in non-photochemical quenching (NPQ) was observed as salinity intensity increased. The increase in NPQ was approximately 30% lower in Barzegar than that in Amin under severe stress. The antioxidant enzyme activity, K+ concentration, and K+/Na+ ratio in the cultivar Barzegar were remarkably higher than those in Amin; meanwhile, Amin maintained a higher Na+ concentration under salinity stress. Accordingly, photosynthesis parameters, redox, and ionic homeostasis were observed to be linked with salinity tolerance, and Amin and Barzegar were recognized as the sensitive (salt’s tolerance threshold: 3.67 dS m−1) and tolerant (salt’s tolerance threshold: 7.13 dS m−1) cultivars, respectively. Therefore, some wheat cultivars, such as Barzegar, could manage environmental stress by improving antioxidant enzyme activities, K+ concentration, and the K+/Na+ ratio to maintain a higher tolerance threshold when salinity stress is raised.
Identification and characterization of the Quinoa AP2/ERF gene family and their expression patterns in response to salt stress Bahlanes Bakhtari, Hooman Razi, Abbas Alemzadeh, Ali Dadkhodaie, Ali Moghadam Scientific Reports, 2024 The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play crucial roles in plant growth, development, and responses to biotic and abiotic stresses. This study was performed to comprehensively identify and characterize the AP2/ERF gene family in quinoa (Chenopodium quinoa Willd.), a highly resilient pseudocereal crop known for its salinity tolerance. A total of 150 CqAP2/ERF genes were identified in the quinoa genome; these genes were unevenly distributed across the chromosomes. Phylogenetic analysis divided the CqAP2/ERFs into five subfamilies: 71 ERF, 49 DREB, 23 AP2, 3 RAV, and 4 Soloist. Additionally, the DREB and ERF subfamilies were subdivided into four and seven subgroups, respectively. The exon-intron structure of the putative CqAP2/ERF genes and the conserved motifs of their encoded proteins were also identified, showing general conservation within the phylogenetic subgroups. Promoter analysis revealed many cis-regulatory elements associated with light, hormones, and response mechanisms within the promoter regions of CqAP2/ERF genes. Synteny analysis revealed that segmental duplication under purifying selection pressure was the major evolutionary driver behind the expansion of the CqAP2/ERF gene family. The protein-protein interaction network predicted the pivotal CqAP2/ERF proteins and their interactions involved in the regulation of various biological processes including stress response mechanisms. The expression profiles obtained from RNA-seq and qRT-PCR data detected several salt-responsive CqAP2/ERF genes, particularly from the ERF, DREB, and RAV subfamilies, with varying up- and downregulation patterns, indicating their potential roles in salt stress responses in quinoa. Overall, this study provides insights into the structural and evolutionary features of the AP2/ERF gene family in quinoa, offering candidate genes for further analysis of their roles in salt tolerance and molecular breeding.
Phenotypic response of a core collection of Aegilops triuncialis accessions to wheat leaf rust and expression pattern of genes involved in resistance Marzieh Sadat Hosseini, Behnam Davoudnia, Ali Dadkhodaie, Bahram Heidari Journal of Phytopathology, 2024 Leaf rust caused by Puccinia triticina Eriks. is a serious threat to wheat production worldwide. Exploiting wild relatives can effectively help to improve the genetic resistance of wheat against rust. This study aimed to evaluate the responses of 34 Aegilops triuncialis accessions to seven Pt pathotypes and to analyse expression of genes associated with resistance at the seedling stage. Following multipathotype testing, two accessions with contrasting resistance were analysed at 0, 6, 12 and 24 h post‐inoculation for the expression profile of genes related to PR1, PR2, PR4, PR9, phenylalanine ammonia‐lyase and ATP‐binding cassette transporter. Of the accessions tested, eight showed high infection types of “3” to at least one Pt pathotype, while the remaining accessions had low ITs (“0;=” to “2+”) against all pathotypes. The relative expressions of all candidate genes increased at all‐time points, but the expression level in the incompatible interaction was significantly higher than that of the compatible. The close relationship between PR proteins, PAL, salicylic acid‐ and jasmonic acid‐responsive proteins, as well as the proteins involved in the production of reactive oxygen species and lignin, could point to the specific recognition of the pathogen followed by the timely and intense induction of the expression of PR genes as the main reasons for resistance in incompatible interaction. In conclusion, the present study identified potentially new sources of resistance in this Ae. triuncialis population, which can be exploited in wheat breeding programs.
Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis Maryam Salami, Bahram Heidari, Bahram Alizadeh, Jacqueline Batley, Jin Wang, Xiao-Li Tan, Ali Dadkhodaie, Christopher Richards Frontiers in Plant Science, 2024 IntroductionAn important strategy to combat yield loss challenge is the development of varieties with increased tolerance to drought to maintain production. Improvement of crop yield under drought stress is critical to global food security.MethodsIn this study, we performed multiomics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in two watering regimes [well-watered (WW) and drought stress (DS)] for 3 years. In the DS treatment, irrigation continued till the 50% pod development stage, whereas in the WW condition, it was performed throughout the whole growing season.ResultsThe results of the genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288-kbps LD decay distance analysis revealed 2,232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 were involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight, and grain yield in drought conditions. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation.DiscussionThe results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought-tolerant varieties.
Genetic Variation of Puccinia triticina Populations in Iran from 2010 to 2017 as Revealed by SSR and ISSR Markers Zahra Nemati, Ali Dadkhodaie, Reza Mostowfizadeh-Ghalamfarsa, Rahim Mehrabi, Santa Olga Cacciola Journal of Fungi, 2023 Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study.
Changes in biochemical characteristics of thirty-six Iranian wheat landraces in response to drought stress and their classification using multivariate analysis Journal of Animal and Plant Sciences, 2016
