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Leaf rust, caused by Puccinia triticina (Pt), poses a constant threat to global wheat production, and novel leaf rust resistance genes are needed to combat the disease. A previous genome-wide association study (GWAS) identified a single nucleotide polymorphism (SNP) marker associated with leaf rust resistance in the terminal region of chromosome arm 5BS in the Iranian landrace PI 622111. An F 2 population and 175 F 2:3 families from cross PI 622111 × Yuanyu 3 were evaluated for response to Pt isolate Pt52-2 (MMPSD). Genotyping-by-sequencing analysis and genotyping of a subset of the F 2 plants identified 32 SNPs closely associated with leaf rust resistance in the target region. Some of these SNPs were converted into kompetitive allele-specific polymorphic (KASP) markers and used to genotype the F 2 population together with a set of simple sequence repeat (SSR) markers also located in the target genomic region. Linkage analysis delimited the leaf rust resistance gene in PI 622111, designated Lr622111, to a 0.4 Mb interval flanked by Xstars700 (7.22 Mb) and Xstars678 (7.62 Mb) in IWGSC RefSeq v.2.1. An allelism test involving 811 F 2 plants indicated that Lr622111 was allelic to Lr52. Since PI 622111 reacted differently from the Lr52 donor to Pt races in the GWAS, Lr622111 is considered a new Lr52 allele conferring a wide spectrum of resistance to current US Pt races. KASP marker Xstars-KASP239, which is 0.9 cM distal to Lr622111, can be widely used to tag Lr622111 in breeding populations., (Published 2025. This article is a U.S. Government work and is in the public domain in the USA. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Rhizomania is the most destructive sugar beet disease in the world, and in recent years, it has widespread in most of the sugar beet growing areas in Iran. Since the control of this soil-borne disease is a difficult task, the use of resistant genotypes is known as the best measure against the disease. The ultimate goal of sugar beet breeders is to produce genotypes that can be used in both infected and non-infected fields without any reduction in terms of yield and quality. Twenty-one sugar beet genotypes along with four controls were evaluated in randomized complete block design with four replications in fields with natural infection to rhizomania in five research stations. Important sugar beet traits including root yield, sugar yield, sugar content, and white sugar yield were evaluated for two years (2021 and 2022). For all traits, location was the main source of variation that spanned 33 to 55% of the total sum of the square followed by the location×year×genotype accounted for 3-40% of the variation. Based on the results of analysis of variance, multivariate stability parameters were computed to evaluate the genotypes' stability. The first two principal components (IPCA1 and IPCA2) generated by GGE biplot contributed for 31.3 and 17.5% difference in genotype×environment interaction for root yield, respectively. According to the GGE biplot, genotypes RM-11 and RM-12 were identified as the winning genotypes across environments for both root yield and white sugar yield traits whereas AMMI model identified RM-14 and RM-9 (for root yield) and RM-1 (for white sugar yield) as best genotypes. Based on the ideal genotype ranking, RM-11 and RM-10 were the best performer with a high mean yield as well as stability in the studied environments. The biplot rendered using the weighted average of absolute scores (WAASB) and root yield and white sugar yield identified RM-11 and RM-9 as superior genotypes in terms of yield and stability. The selected genotypes can be used in breeding programs to transfer the disease resistance and cultivar development., (© 2024. The Author(s).)

Fusarium head blight (FHB) is a devastating fungal disease affecting different cereals, particularly wheat, and poses a serious threat to global wheat production. Chitinases and β-glucanases are two important proteins involved in lysing fungal cell walls by targeting essential macromolecular components, including chitin and β-glucan micro fibrils. In our experiment, a transgenic wheat (Triticum aestivum) was generated by introducing chitinase and glucanase genes using Biolistic technique and Recombinant pBI121 plasmid (pBI-ChiGlu (-)). This plasmid contained chitinase and glucanase genes as well as nptII gene as a selectable marker. The expression of chitinase and glucanase was individually controlled by CaMV35S promoter and Nos terminator. Immature embryo explants from five Iranian cultivars (Arta, Moghan, Sisun, Gascogen and A-Line) were excised from seeds and cultured on callus induction medium to generate embryonic calluses. Embryogenic calluses with light cream color and brittle texture were selected and bombarded using gold nanoparticles coated with the recombinant pBI-ChiGlu plasmid. Bombarded calluses initially were transferred to selective callus induction medium, and later, they were transfferd to selective regeneration medium. The selective agent was kanamycin at a concentration of 25 mg/l in both media. Among five studied cultivars, A-Line showed the highest transformation percentage (4.8%), followed by the Sisun, Gascogen and Arta in descending order. PCR and Southern blot analysis confirmed the integration of genes into the genome of wheat cultivars. Furthermore, in an in-vitro assay, the growth of Fusarium graminearum was significantly inhibited by using 200 μg of leaf protein extract from transgenic plants. According to our results, the transgenic plants (T 1 ) showed the resistance against Fusarium when were compared to the non-transgenic plants. All transgenic plants showed normal fertility and no abnormal response was observed in their growth and development., (© 2024. The Author(s).)

Fusarium oxysporum f.sp. cepae (FOC), as basal rot fungus, is the most detrimental pathogen causing a serious threat to onion productivity in the world. In this study, we first determined FOC tolerance in seven Iranian onion cultivars, two known international onions (Texas Early Grano and Sweet Yellow Spanish), and an Allium species related to the onion (Allium asarence) based on the infection severity. Then, a transcriptional screen was performed by comparing the transcript levels of some pathogen-responsive genes (ERF1, COI1, and TIR1) and their predicted miRNAs in the sensitive (Ghermeze Azarshahr Cv.) and the resistant (A. asarence) onions to determine key genes and their miRNAs involved in the defense responses of onions to FOC. From our results, a difference was found in the COI1 and ERF1 expression 48 h after inoculation with FOC as compared to the respective 24 and 72 h. It can be explained by either special mechanisms involved in raising energy consumption efficiency or the interactive effects of other genes in the jasmonic acid (JA) and ethylene (ET) signaling pathways. Moreover, expression analysis of the pathogen-responsive genes and their targeting miRNAs identified the miR-5629, which targets the COI1 gene as a likely key factor in conferring resistance in the FOC-resistant onion, i.e., A. asarence. However, exploring the function of the miRNA/target pair is highly recommended to deeply understand the effect of the miRNA/target pair-associated pathway in the control of A. asarense-FOC interaction., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Key Message: A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies., (© 2024. The Author(s).)

Leaf rust caused by Puccinia triticina Erikss. (Pt) is the most widely distributed and important wheat disease worldwide. The objective of the present study was to determine the frequency of Iranian Pt races, their virulence to key resistance genes and map quantitative trait loci (QTL) for resistance to different Pt races from 185 globally diverse wheat genotypes using a genome-wide association study (GWAS) approach. The virulence pattern of the 33 Pt isolates from various wheat-growing areas of Iran on 55 wheat differentials showed that the FKTPS and FKTTS were relatively frequent pathotypes among the 18 identified races. The weighted average frequency of virulence on the resistance genes Lrb, Lr3bg, Lr14b, Lr16, Lr24, Lr3ka, Lr11 and Lr20 were high (> 90%). However, low virulence on the resistant genes Lr2a, Lr9, Lr19, Lr25, Lr28 and Lr29 indicates that these genes are still effective against the pathogen population in Iran at present. GWAS on a panel of 185 wheat genotypes against 10 Pt races resulted into 62 significant marker-trait associations (MTAs) belonged to 34 quantitative trait loci (QTL) across 16 chromosomes. Among them, 10 QTLs on chromosomes 1A, 1B, 3B, 3D, 4A, 6D, 7A and 7D were identified as potential novel QTLs, of which four QTLs (QLr.iau-3B-2, QLr.iau-7A-2, QLr.iau-7A-3 and QLr.iau-7D-2) are more interesting, as they are associated with resistance to two or more Pt races. The known and novel QTLs associated with different Pt races found here, can be used in future wheat breeding programs to recombine different loci for durable resistance against leaf rust races., (© 2023. The Author(s).)

Background: Global wheat productivity is seriously challenged by a range of rust pathogens, especially leaf rust derived from Puccinia triticina. Since the most efficient approach to control leaf rust is genetic resistance, many efforts have been made to uncover resistance genes; however, it demands an ongoing exploration for effective resistance sources because of the advent of novel virulent races. Thus, the current study was focused on detecting leaf rust resistance-related genomic loci against the P. triticina prevalent races by GWAS in a set of Iranian cultivars and landraces., Results: Evaluation of 320 Iranian bread wheat cultivars and landraces against four prevalent rust pathotypes of P. triticina (LR-99-2, LR-98-12, LR-98-22, and LR-97-12) indicated the diversity in wheat accessions responses to P. triticina. From GWAS results, 80 leaf rust resistance QTLs were located in the surrounding known QTLs/genes on almost chromosomes, except for 1D, 3D, 4D, and 7D. Of these, six MTAs (rs20781/rs20782 associated with resistance to LR-97-12; rs49543/rs52026 for LR-98-22; rs44885/rs44886 for LR-98-22/LR-98-1/LR-99-2) were found on genomic regions where no resistance genes previously reported, suggesting new loci conferring resistance to leaf rust. The GBLUP genomic prediction model appeared better than RR-BLUP and BRR, reflecting that GBLUP is a potent model for genomic selection in wheat accessions., Conclusions: Overall, the newly identified MTAs as well as the highly resistant accessions in the recent work provide an opportunity towards improving leaf rust resistance., (© 2023. The Author(s).)

Parsley severe stunt-associated virus (PSSaV) is a recently identified nanovirus first reported in Germany. During a survey for identification of nanoviruses infecting apiaceous plants in south-eastern Iran, PSSaV was identified and characterized using a combination of rolling circle amplification (RCA) and high-throughput sequencing. Parsley plant samples were collected from vegetable production farms in Kerman province. From two symptomatic samples (39Ba and 40Ba), seven PSSaV components (DNA-C, -S, -M, -R, -N, -U1 and -U2) with two phylogenetically distinct variants of DNA-R (R1 and R2) were identified. In common with the German isolate of PSSaV, no DNA-U4 component was identified. In addition, associated alphasatellite molecules were identified in samples 39Ba [n = 6] and 40Ba [n = 5]. Sequence analyses showed that concatenated component sequences of the two Iranian PSSaVs share 97.2% nucleotide identity with each other and 82% to the German isolate. The coat proteins (CPs) of the PSSaV Iranian sequences share 97.2% amino acid identity and ~ 84% identity with that of the German isolate. Sequence and phylogenetic analyses of a total of 11 recovered alphasatellites from the two samples can be classified into the genera Fabenesatellite [n = 2], Milvetsatellite [n = 1], Mivedwarsatellite [n = 2], Subclovsatellite [n = 2], Sophoyesatellite [n = 4] in the family Alphasatellitidae. Identification of PSSaV and other nanoviruses in wild and cultivated plants in Iran reveals that nanoviruses could be causing yield reduction in crops plants in this country.

Background: Wheat stripe rust (caused by Puccinia striiformis f. sp. Tritici), is a major disease that causes huge yield damage. New pathogen races appeared in the last few years and caused a broke down in the resistant genotypes. In Egypt, some of the resistant genotypes began to be susceptible to stripe rust in recent years. This situation increases the need to produce new genotypes with durable resistance. Besides, looking for a new resistant source from the available wheat genotypes all over the world help in enhancing the breeding programs., Results: In the recent study, a set of 103-spring wheat genotypes from different fourteen countries were evaluated to their field resistant to stripe rust for two years. These genotypes included 17 Egyptian genotypes from the old and new cultivars. The 103-spring wheat genotypes were reported to be well adapted to the Egyptian environmental conditions. Out of the tested genotypes, eight genotypes from four different countries were found to be resistant in both years. Genotyping was carried out using genotyping-by-sequencing and a set of 26,703 SNPs were used in the genome-wide association study. Five SNP markers, located on chromosomes 2A and 4A, were found to be significantly associated with the resistance in both years. Three gene models associated with disease resistance and underlying these significant SNPs were identified. One immune Iranian genotype, with the highest number of different alleles from the most resistant Egyptian genotypes, was detected., Conclusion: the high variation among the tested genotypes in their resistance to the Egyptian stripe rust race confirming the possible improvement of stripe rust resistance in the Egyptian wheat genotypes. The identified five SNP markers are stable and could be used in marker-assisted selection after validation in different genetic backgrounds. Crossing between the immune Iranian genotype and the Egyptian genotypes will improve stripe rust resistance in Egypt.

Chickpea (Cicer arietinum L.) is the second largest pulse crop grown worldwide and ascochyta blight caused by Ascochyta rabiei (Pass.) Labr. is the most devastating disease of the crop in all chickpea growing areas across the continents. The pathogen A. rabiei is highly variable. The resistant sources available are not sufficient and new sources needs to be identified from time to time as resistance breakdown in existing chickpea varieties is very frequent due to fast evolution of new pathotypes of the pathogen. Therefore, this work was undertaken to evaluate the existing chickpea germplasm diversity conserved in Indian National Genebank against the disease under artificial epiphytotic conditions. An artificial standard inoculation procedure was followed for uniform spread of the pathogen. During the last five winter seasons from 2014-15 to 2018-19, a total of 1,970 accessions have been screened against the disease and promising accessions were identified and validated. Screening has resulted in identification of some promising chickpea accessions such as IC275447, IC117744, EC267301, IC248147 and EC220109 which have shown the disease resistance (disease severity score ≤3) in multiple seasons and locations. Promising accessions can serve as the potential donors in chickpea improvement programs. The frequency of resistant and moderately resistant type accessions was comparatively higher in accessions originated from Southwest Asian countries particularly Iran and Syria than the accessions originated from Indian sub-continent. Further large scale screening of chickpea germplasm originated from Southwest Asia may result in identifying new resistant sources for the disease., Competing Interests: The authors have declared that no competing interests exist.

Key Message: A new powdery mildew resistance gene conferring a wide spectrum of resistance to Bgt isolates in the USA, Pm63 , was identified in Iranian wheat landrace PI 628024 and mapped to the terminal region of the long arm of chromosome 2B. Powdery mildew is a globally important wheat disease causing severe yield losses, and host resistance is the preferred strategy for managing this disease. The objective of this study was to characterize a powdery mildew resistance gene in Iranian landrace PI 628024, which exhibited a wide spectrum of resistance to representative Blumeria graminis f. sp. tritici (Bgt) isolates collected from different regions of the USA. An F 2 population and F 2:3 lines derived from the cross PI 628024 × CItr 11349 were used in this study, and genetic analysis indicated that a single dominant gene, designated Pm63, conferred resistance to Bgt isolate OKS(14)-B-3-1. Linkage analysis located Pm63 to an interval of about 13.1 Mb on the long arm of chromosome 2B, spanning 710.3-723.4 Mb in the Chinese Spring reference sequence. Bin mapping assigned Pm63 to the terminal bin 2BL6-0.89-1.0, 1.1 cM proximal to STS marker Xbcd135-2 and 0.6 cM distal to SSR marker Xstars419. Allelism tests indicated that Pm63 is a new powdery mildew resistance gene, which differs from other genes in the terminal bin by origin, genomic location, and responses to a set of 16 representative US Bgt isolates. Pm63 can be widely used to enhance powdery mildew resistance in the Great Plains, western, and southeastern regions of the USA.

Oak decline is a complex syndrome in which several damaging agents interact and bring about a serious dieback in tree condition. Genetic diversity is a key factor for better adoption of natural populations to environmental stresses. The objective of this research was to identify the association of polymorphism patterns of different reproducible genomic Inter simple sequence repeats (ISSR markers) to level of dieback phenomena and also growth type in 18 different stands of Persian oak in central Zagros region. Totally, 180 trees were sampled and evaluated for growth type, tree diameter at breast height (DBH) and level of tree dieback. Genomic DNAs extracted of fresh leaves amplified using 15 multi-locus ISSR primers. The population structure determined using the Bayesian model-based clustering method implemented in STRUCTURE software by Monte Carlo Markov Chain (MCMC) method. Five distinct sub-populations (K=5) determined by the log likelihood of the data.  Genome wide association study (GWAS) performed using the generalized linear model (GLM) and the mixed linear model (MLM) with Kinship matrix. Informative alleles recognized for level of tolerance to dieback and tree growth type traits. It was observed a significant co-segregation for phenotypic data and some of amplified fragments. Identification of these informative DNA markers can be utilized for pre-screening of high quality oak seedlings in early growth stages and better management in restoration of damaged stands.

Artemisia dracunculus L. (tarragon), a small shrubby perennial herb, is cultivated for the use of its aromatic leaves in seasoning, salads, etc., and in the preparation of tarragon vinegar. In the present work, genetic analysis of 29 cultivated individuals of this species was carried out employing 12 ISSR and 11 SRAP markers. A total of 59 (71.64%) and 79 (83.14%) polymorphic bands were detected by 12 ISSR primers and 11 SRAP primer pairs, respectively. High similarity for patterns of genetic diversity and clustering of individuals was observed using two ISSR and SRAP marker systems and combined data. Range of genetic similarity by ISSR markers was 0.14 to 0.95, by SRAP markers was 0.14 to 0.90, while this range varied from 0.18 to 0.91 by ISSR+SRAP. In the UPGMA cluster analysis (ISSR, SRAP and ISSR+SRAP), we always found two clusters, the first cluster included 22 individuals and the second contained seven individuals. The results demonstrated that both ISSR and SRAP methods were suitable for discriminating among the studied individuals and the SRAP markers were more efficient and preferable. The results of multiple regression analysis revealed statistically significant association between rust resistance and some molecular markers that they can provide clues for identification of the individuals with higher rust resistance. The molecular marker-based study of genetic diversity suggests that the germplasm studied representing the kind of variability would be a valuable genetic resource for future breeding. In addition, in situ conservation measures are recommended to preserve the valuable A. dracunculus genetic resources as the most effective and economical approach., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Fusarium Head Blight (FHB), caused mainly by Fusarium graminearum, is one of the most notorious diseases in North part of Iran. Due to lack of sufficient information regarding genetic diversity of FHB, the correlation between genetic diversity and geographic distribution of 52 isolates that collected from infected wheat kernels from four main grown region of North part of Iran were analyzed with 10 simple Sequence Repeat (SSR) primers and 15 Random Amplified Polymorphic DNA (RAPD) primers. The un-weighed pair group method using arithmetic means (UPGMA) was used and a dendrogram was constructed based on Jaccard's similarity coefficient. Principal Component Analysis (PCA) of SSR and RAPD markers revealed that the first two factors accounted for 51 and 41% of the total variance, respectively. SSR and RAPD data classified isolates into four and seven groups, respectively. SSR analysis showed that there was a correlation between genetic clusters of isolates and geographical origin in F. graminearum. However, results of cluster analysis using RAPD data didn't show any relation with geographical distribution but the results of this analysis confirmed a genetic variation among all isolates.

Two Iranian common wheat landraces AUS28183 and AUS28187 from the Watkins collection showed high levels of seedling resistance against Australian pathotypes of leaf rust and stripe rust pathogens. Chi-squared analyses of rust response segregation among F(3) populations derived from crosses of AUS28183 and AUS28187 with a susceptible genotype AUS27229 revealed monogenic inheritance of leaf rust and stripe rust resistance. As both genotypes produced similar leaf rust and stripe rust infection types, they were assumed to carry the same genes. The genes were temporarily named as LrW1 and YrW1. Molecular mapping placed LrW1 and YrW1 in the short arm of chromosome 5B, about 10 and 15 cM proximal to the SSR marker gwm234, respectively, and the marker cfb309 mapped 8-12 cM proximal to YrW1. LrW1 mapped 3-6 cM distal to YrW1 in two F(3) populations. AUS28183 corresponded to the accession V336 of the Watkins collection which was the original source of Lr52. Based on the genomic location and accession records, LrW1 was concluded to be Lr52. Because no other seedling stripe rust resistance gene has previously been mapped in chromosome 5BS, YrW1 was permanently named as Yr47. A combination of flanking markers gwm234 and cfb309 with phenotypic assays could be used to ascertain the presence of Lr52 and Yr47 in segregating populations. This investigation characterised a valuable source of dual leaf rust and stripe rust resistance for deployment in new wheat cultivars. Transfer of Lr52 and Yr47 into current Australian wheat backgrounds is in progress.

Ten wheat lines were studied to determine gene effects and combining ability in some bread wheat genotypes to yellow rust disease. Ten parental lines and F1 were evaluated in a randomized complete block design with three replications in Agricultural and Natural Resources Research Center, Mashhad, Iran. Two races (134E134A+ and 4E0A+) were used for this study. Latent Period (LP) and Infection Type (IT) were measured in the field and greenhouse. Results showed significant differences between races in their pathogenicity and between genotypes in their resistance to the pathogen. Diallel cross carried out between the parents and progenies and thereafter were analyzed by the method of Griffing and Haymans. The General Combining Ability (GCA) and Special Combining Ability (SCA) for all traits were significant and showed additive variance was more important. Test for validity of diallel hypothesis proved epistasis effect for all traits. P1, P2 and F1 showed significant difference between all traits in generations mean analysis. Average degree of dominance ranged from partial to over dominance for resistance or susceptibility. Dominance, additive and epistatic types of gene action were responsible for the genetic control of the traits. However, except for additive-additive component, non-additive effect of genes could not be fixed by self-fertilization.