Stripe or yellow rust, caused by Puccinia striiformis Westend. f. sp. tritici is a major threat to bread wheat production worldwide. The breakdown in resistance of certain major genes and newly emerging aggressive races of stripe rusts pose serious concerns in all main wheat growing areas of the world. To identify new sources of resistance and associated QTL for effective utilization in future breeding programs an association mapping (AM) panel comprising of 600 bread wheat landraces collected from eight different countries conserved at ICARDA gene bank were evaluated for seedling and adult plant resistance against the PstS2 and Warrior races of stripe rust at the Regional Cereal Rust Research Center (RCRRC), Izmir, Turkey during 2016, 2018 and 2019. A set of 25,169 informative SNP markers covering the whole genome were used to examine the population structure, linkage disequilibrium and marker‐trait associations in the AM panel. The genome‐wide association study (GWAS) was carried out using a Mixed Linear Model (MLM). We identified 47 SNP markers across 19 chromosomes with significant SNP‐trait associations for both seedling stage and adult plant resistance. The threshold of significance for all SNP‐trait associations was determined by the false discovery rate (q) ≤ 0.05. Three genomic regions (QYr.1D_APR, QYr.3A_seedling and QYr.7D_seedling) identified in this study do not correspond to previously reported Yr genes or QTL, suggesting new genomic regions for stripe rust resistance.

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.

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.

A wheat rust survey was conducted in Iraq in 2019 and collected 27 stem rust (caused by Puccinia graminis Pers.:Pers. f. sp. tritici Erikks. & E. Henn.) samples. Seven samples were viable, and they were tested for races of P. graminis f. sp. tritici at the Regional Cereal Rust Research Center (RCRRC) in Izmir, Turkey under strict quarantine procedures. Two 0.5 cm segments of each infected stem sheath were incubated in a petri dish at 20°C for three hours for re-hydration of urediniospores, which were multiplied on 10-day old seedlings of susceptible cultivar Morocco grown in a spore free growth chamber at 18°C and 16 hours light. Inoculated seedlings underwent a dew period at 18°C for 16 hours dark and 8 hours fluorescent light and 95% relative humidity. Three days after moving the pots to a growth chamber with eight hours dark at 18°C and 16 hours light (300 µmol m-2s-1), each pot was covered using a cellophane bag. Bulk urediniospores of each collection were collected 14 days post-inoculation from a cellophane bag using a mini cyclone spore collector connected to a gelatin capsule. One ml of 3M Novec™ oil was added to each capsule, and spores were inoculated onto 20 North American stem rust differential lines using the standard procedures (Jin et al. 2008). Pre-inoculation, inoculation, incubation, and post-inoculation conditions were the same as above. Seedling infection types (ITs) were recorded 14 days post-inoculation using 0 to 4 scale (Stakman et al. 1962). Race designation followed the five- letter code nomenclature described by Jin et al. (2008). Out of the seven samples, four were typed as TKKTF, two as TKTTF, and one collected from an advanced breeding bread wheat line “Shahoo 2” (Inqalab 91*2/Tukuru) in a trial site at Halabja governorate showed mixed ITs of 11+ and 3+ for lines carrying Sr11, Sr24, Sr36, and Sr31. Three single pustule (SP) isolates were developed from the IT of 3+ pustules collected from the Sr31 tester line, and one SP isolate was developed from the IT 11+ pustule collected from the Sr11 source. After spore multiplication, the SP-derived isolates were inoculated on the 20 North American differential lines. To confirm virulence/avirulence on Sr24, Sr31, and Sr36, cultivars Siouxland (PI 483469, Sr24+Sr31) and Sisson (PI 617053, Sr36+Sr31) were also inoculated. All seedling assays were repeated three times. The three SP isolates virulent on Sr31 were designated as race TTKTT, and the SP isolate virulent on Sr11 was designated as TKTTF. Seedling ITs of 3+ and 0; were recorded for Siouxland and Sisson against TTKTT, respectively, and both cultivars showed IT of 1+ against TKTTF. Race TKTTF was similar to TKKTF except for additional virulence on Sr36, and TTKTT differed from the other two races being virulent on Sr24 and Sr31. DNA analysis of three TTKTT isolates from Kenya and the TTKTT isolate from Iraq using a diagnostic qPCR assay developed by the USDA-ARS Cereals Disease Laboratory (Ug99 RG stage 1, Szabo unpublished) confirmed that all tested isolates belonged to the Ug99 lineage. Race TTKTT was first reported from Kenya in 2014 (Patpour et al. 2016), and in 2018 from Ethiopia (Hei et al. 2020). We report the first detection of TTKTT in Iraq and the Middle East region. This represents only the third instance of a member of the Ug99 race group outside of Africa since first detection of race TTKSK in Yemen in 2006, and Iran in 2007 (Nazari et al. 2009). The continued spread of stem rust races with complex virulence and the increasing frequency and early onset of stem rust infections in the Middle East is a cause for concern. Continuous support for rust surveillance and race typing in this region remains crucial. References: Hei, N. B., et al. 2020. Plant Dis. 104:982. Jin, Y., et al. 2008. Plant Dis. 92:923-926. Nazari, K., et al. 2009. Plant Dis. 93:317. Patpour, M., et al. 2016. Plant Dis. 100:522. Stakman, E. C., et al. 1962. Identification of physiological races of Puccinia graminis var. tritici. U. S. Dep. Agric. ARS E-617.

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.