Prevalent races of wheat rust pathogens in Lebanon, Morocco, and Tunisia in 2022

During the 2022 rust surveys in Lebanon, Morocco, and Tunisia (WP1-OP2), rust samples were collected from survey sites. The collected rust samples were submitted to the Regional Cereal Rust Biocontainment Laboratory in Izmir, Turkey using the sampling kits and import permits granted by Turkish quarantine authorities. Viable samples were used in Races analysis. The race analysis confirmed the presence of stem rust races TKKTF and TKTTF in Lebanon and TKKTF, TKTTF, THTTF, and TTTTF in Morocco

Physiological races of Puccinia graminis f. sp. tritici in Iran and evaluation of seedling resistance to stem rust in Iranian wheat cultivars

Seedling assessment of 13 stem rust samples collected from southwest of Iran revealed that three collec- tions were virulent for Sr31 and Sr38. Physiological races of RTRTC, HRCTC, RRTTF, TTPTC, TTTQF, JTHTC and TTKSK were identified for nine collections tested against the north American differential lines. The virulence pattern of TTKSK previously identified in east Africa was identical to that of TTKSK in the present study, providing evidence for the migration of this race from East Africa to Iran. Low/ high infection type for the genes Sr22, Sr26, Sr27, Sr29, Sr32, Sr33, Sr35, SrNin/ Sr7a, Sr8b, Sr9f, Sr12, Sr15, Sr16, Sr17, Sr18, Sr20, Sr23, Sr34, SrPL, SrTt3+10, SrWld-1, and Sr42 was shown by nine collections. In evaluations of seedling resistance, high infection types of 3 to 4 were shown by all the 29 Iranian wheat cultivars tested with TTKSK. Presence of TTKSK, susceptibility of wheat cultivars and conducive conditions pose serious threats of stem rust to wheat production in Iran

Comparison of Genomic Prediction Methods for Yellow, Stem, and Leaf Rust Resistance in Wheat Landraces from Afghanistan

Wheat rust diseases, including yellow rust (Yr; also known as stripe rust) caused by Puccinia striiformis Westend. f. sp. tritici, leaf rust (Lr) caused by Puccinia triticina Eriks. and stem rust (Sr) caused by Puccinia graminis Pres f. sp. tritici are major threats to wheat production all around the globe. Durable resistance to wheat rust diseases can be achieved through genomic-assisted prediction of resistant accessions to increase genetic gain per unit time. Genomic prediction (GP) is a promising technology that uses genomic markers to estimate genomic-assisted breeding values (GBEVs) for selecting resistant plant genotypes and accumulating favorable alleles for adult plant resistance (APR) to wheat rust diseases. To evaluate GP we compared the predictive ability of nine different parametric, semi-parametric and Bayesian models including Genomic Unbiased Linear Prediction (GBLUP), Ridge Regression (RR), Least Absolute Shrinkage and Selection Operator (LASSO), Elastic Net (EN), Bayesian Ridge Regression (BRR), Bayesian A (BA), Bayesian B (BB), Bayesian C (BC) and Reproducing Kernel Hilbert Spacing model (RKHS) to estimate GEBV’s for APR to yellow, leaf and stem rust of wheat in a panel of 363 bread wheat landraces of Afghanistan origin. Based on five-fold cross validation the mean predictive abilities were 0.33, 0.30, 0.38, and 0.33 for Yr (2016), Yr (2017), Lr, and Sr, respectively. No single model outperformed the rest of the models for all traits. LASSO and EN showed the lowest predictive ability in four of the five traits. GBLUP and RR gave similar predictive abilities, whereas Bayesian models were not significantly different from each other as well. We also investigated the effect of the number of genotypes and the markers used in the analysis on the predictive ability of the GP model. The predictive ability was highest with 1000 markers and there was a linear trend in the predictive ability and the size of the training population. The results of the study are encouraging, confirming the feasibility of GP to be effectively applied in breeding programs for resistance to all three wheat rust diseases.info:eu-repo/semantics/publishedVersio

Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan

Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.info:eu-repo/semantics/publishedVersio

Surveillance and monitoring the cereal rust diseases in Lebanon, Morocco, and Tunisia in 2022

Tracking the movement of the wheat rust pathogens and monitoring their pathogenic variabilities are the main pillars in successful breeding for durable rust resistance and disease management programs. Despite the severe drought conditions in wheat growing areas in CWANA in 2022, the rust surveillance was coordinated by the Regional Cereal Rust Research Center-Turkey in Lebanon, Morocco, and Tunisia, following the BGRI rust surveillance protocols. The national rust surveillance teams at the Lebanese Agricultural Research Institute, Institut National de la Recherche Agronomique (Morocco), and INSTITUT NATIONAL DES GRANDES CULTURES-TUNISIA (Tunisia) conducted the rust surveys in target countries. The GPS coordinates of survey sites, the status of rust diseases, and crop phenology were collected and shared with the online Global Cereal Rust Surveillance and Monitoring System (https://rusttracker.cimmyt.org) following the BGRI standard rust surveillance protocol (https://rusttracker.cimmyt.org/wp-content/uploads/2011/11/2013-Updated-BGRI-protocols-v2-web.pdf)

Exploring the genetic diversity and population structure of wheat landrace population conserved at ICARDA genebank

Landraces are considered a valuable source of potential genetic diversity that could be used in the selection process in any plant breeding program. Here, we assembled a population of 600 bread wheat landraces collected from eight different countries, conserved at the ICARDA's genebank, and evaluated the genetic diversity and the population structure of the landraces using single nucleotide polymorphism (SNP) markers. A total of 11,830 high-quality SNPs distributed across the genomes A (40.5%), B (45.9%), and D (13.6%) were used for the final analysis. The population structure analysis was evaluated using the model-based method (STRUCTURE) and distance-based methods [discriminant analysis of principal components (DAPC) and principal component analysis (PCA)]. The STRUCTURE method grouped the landraces into two major clusters, with the landraces from Syria and Turkey forming two clusters with high proportions of admixture, whereas the DAPC and PCA analysis grouped the population into three subpopulations mostly according to the geographical information of the landraces, i.e., Syria, Iran, and Turkey with admixture. The analysis of molecular variance revealed that the majority of the variation was due to genetic differences within the populations as compared with between subpopulations, and it was the same for both the cluster-based and distance-based methods. Genetic distance analysis was also studied to estimate the differences between the landraces from different countries, and it was observed that the maximum genetic distance (0.389) was between the landraces from Spain and Palestine, whereas the minimum genetic distance (0.013) was observed between the landraces from Syria and Turkey. It was concluded from the study that the model-based methods (DAPC and PCA) could dissect the population structure more precisely when compared with the STRUCTURE method. The population structure and genetic diversity analysis of the bread wheat landraces presented here highlight the complex genetic architecture of the landraces native to the Fertile Crescent region. The results of this study provide useful information for the genetic improvement of hexaploid wheat and facilitate the use of landraces in wheat breeding programs

Diversity of thermal aptitude of Middle Eastern and Mediterranean Puccinia striiformis f. sp. tritici isolates from different altitude zones

The worldwide spread of wheat yellow rust lineage PstS1/S2 adapted to higher temperatures prompted us to investigate how diverse temperature responses of this lineage are in the Middle East, where diversity was previously observed within this lineage for pathotypes and genotypes. Here we highlight the diversity of response to temperature within a PstS1/S2 population. Twenty-six isolates from eight countries and different altitudes, which were tested under four combinations of cold and warm incubation and postincubation temperature conditions, showed diversity for infection efficiency (IE) and latency period (LP). IE of the various isolates ranged from 5.8% to 13.7% under cold (5°C) and 0.04% to 1% under warm (20°C) incubation temperatures. LP varied from 10.2 days under warm to 4.43 days under cold incubation. LP of isolates from the same country could differ by 2 days. Significant differences in thermal aptitudes of the isolates were observed between and within countries. IE and LP diversity was not related to altitude origin of the isolates on the whole; however, a trade-off between IE and LP was observed for isolates from low altitude (<400 m) under a warm regime. We showed diversity for thermal aptitude for IE and LP of isolates belonging to the same PstS1/S2 lineage. Understanding Pst temperature aptitude among geographically distant isolates of the same clonal lineage may help to identify the geographic range of pathogens and also to improve forecast models or breeding programmes

Molecular markers for tracking the origin and worldwide distribution of invasive strains of <i>Puccinia striiformis</i>

Investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. In the case of Puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P. striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East and Central Asia. In 2000, PstS2 was detected in Europe, where it never became prevalent. Additional SSR genotyping and virulence phenotyping revealed 10 and six variants, respectively, within PstS1 and PstS2, demonstrating the evolutionary potential of the pathogen. Overall, the results suggested East Africa as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2

Diversity of genes for resistance to stripe rust in wheat elite lines, commercial varieties and landraces from Lebanon and Syria

Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major threat to wheat production in Central and West Asia and North Africa (CWANA). Effective fungicides are available, but host resistance remains the most economical, effective and ecologically sustainable method for stripe rust control. Understanding the genetic diversity of resistance to Pst is a key element in breeding for durable rust resistance. Multipathotype tests were performed on 87 elite lines of bread wheat from the spring wheat breeding programme at the International Center for Agricultural Research in Dry Areas (ICARDA), 23 Lebanese bread and durum wheat varieties, and 28 Lebanese landraces, with 11 Pst pathotypes. Low and high infection types were identified for the resistance genes Yr1, Yr3, Yr4, Yr6, Yr7, Yr9, Yr17, Yr25, Yr27, and Yr32. All but one of these genes (Yr32 being the exception) were postulated. ICARDA elite lines displayed greater diversity for Yr genes than the Lebanese varieties and landraces. Yr27 was the most frequent Yr gene postulated singly in the Lebanese varieties. Yr7, together with other unidentified Yr genes, was the most frequent gene in the ICARDA elite lines. Combinations of two Yr genes were common in ICARDA elite lines. These results confirm that the landraces consist of several genotypes. Seventy-five percent of landraces were susceptible to all pathotypes, but they displayed resistance diversity, with different proportions of resistant seedlings. In two landraces, some plants were resistant to the Warrior pathotype, which has recently spread in CWANA regions, and to other pathotypes. This indicates the presence of new resistance genes in these landraces. Some landraces, elite ICARDA lines and Lebanese varieties were completely resistant to all pathotypes, and are therefore potential sources of new resistances