Leaf Rust Pathotypes Research Articles

Identification of Rust Resistance Genes in Wheat (Triticum aestivum L.) Using Molecular Markers and Host–Pathogen Interaction Tests

ABSTRACTThe leaf rust (Puccinia triticina f. sp. tritici), stripe rust (Puccinia striiformis f. sp. tritici), and stem rust (Puccinia graminis f. sp. tritici) are major fungal constraints affecting wheat production worldwide. Identifying and deploying wheat varieties with diverse resistance are the best ways to manage all the rusts. Therefore, a continuous search goes on to identify diverse germplasm with effective rust resistance that expresses at different stages of plant growth (seedling and adult plant). A set of 22 rust resistant wheat genotypes and 4 checks (controls), viz., Avocet‐Yr10, Avocet ‐Yr15, Agra Local, and respective positive checks were studied for characterising rust resistance genes using host–pathogen interactions complemented by molecular markers. Among 22 elite genotypes, 05 genotypes amplified 191 bp fragment with marker PSY1E1, confirmed the presence of gene Lr19/Sr25. These genotypes also expressed resistance to most virulent leaf rust pathotypes, 77‐5 and 77‐9 in host–pathogen interaction test (HPI). Seven genotypes showed the presence of Lr34/Yr18/Sr57/Pm38/Ltn1 in homozygous state, whereas G4 showed its presence in heterozygous condition. Among 22 genotypes, 16 genotypes possessed Yr10. Five genotypes (22.7%) exhibited two gene combinations, Lr19/Sr25, and Yr10 as revealed through the detection of 191 bp fragment with marker PSY1E1 and 260 bp fragment with co‐dominantly inherited microsatellite marker Xpsp3000, respectively. All five genotypes (G2, G3, G8, G9, and G18) also expressed brown glumes controlled by the gene Rg1 tightly linked to Yr10 on the 1BS chromosome. Broad spectrum rust resistance present in these lines in good agronomic backgrounds could be used as potent genetic donors for diverse and durable rust resistance breeding programmes in wheat.

Dissecting the rust resistance in salt tolerant wheat germplasm.

Wheat is one of the most important food crop cultivated across the globe which ensures sustainability and food security to massive world's population, but its production is threatened by both biotic factors like rust (caused by Puccinia species) and abiotic stresses such as salinity. In this study, 41 salt-tolerant wheat lines were screened for rust resistance at both seedling and adult plant stages. Rust resistance genes were characterized through gene matching technique and molecular markers analysis. Yr2 was confirmed in 23 lines, while Yr9 along with Lr26/Sr31 were postulated in six lines with the help of SRT and molecular markers. Except for KRL2013, none showed complete resistance to all Puccinia striiformis f. sp. tritici (Pst). Lr24/Sr24 genes were confirmed in HD2851 and KRL2029, and Lr13 was detected in a maximum of 24 wheat lines, with varying reaction responses to different leaf rust pathotypes. Several lines carried additional resistance genes such as Sr11, Sr28, and Lr68. Lr68 an effective race non-specific APR gene identified in 15 wheat lines with the help of CsGs-STS marker. Although many salt-tolerant wheat lines were susceptible to yellow rust during the seedling stage, a few lines showed APR in the years during 2020 and 2021. Three lines (KRL213, KRL219 and KRL238) showed complete resistance at adult plant stage to leaf rust. These findings offer insights into the genetic basis of rust resistance in salt-tolerant wheat, aiding breeding strategies.

Genomic Regions Associated with Resistance to Three Rusts in CIMMYT Wheat Line "Mokue#1".

Understanding the genetic basis of rust resistance in elite CIMMYT wheat germplasm enhances breeding and deployment of durable resistance globally. "Mokue#1", released in 2023 in Pakistan as TARNAB Gandum-1, has exhibited high levels of resistance to stripe rust, leaf rust, and stem rust pathotypes present at multiple environments in Mexico and Kenya at different times. To determine the genetic basis of resistance, a F5 recombinant inbred line (RIL) mapping population consisting of 261 lines was developed and phenotyped for multiple years at field sites in Mexico and Kenya under the conditions of artificially created rust epidemics. DArTSeq genotyping was performed, and a linkage map was constructed using 7892 informative polymorphic markers. Composite interval mapping identified three significant and consistent loci contributed by Mokue: QLrYr.cim-1BL and QLrYr.cim-2AS on chromosome 1BL and 2AS, respectively associated with stripe rust and leaf rust resistance, and QLrSr.cim-2DS on chromosome 2DS for leaf rust and stem rust resistance. The QTL on 1BL was confirmed to be the Lr46/Yr29 locus, whereas the QTL on 2AS represented the Yr17/Lr37 region on the 2NS/2AS translocation. The QTL on 2DS was a unique locus conferring leaf rust resistance in Mexico and stem rust resistance in Kenya. In addition to these pleiotropic loci, four minor QTLs were also identified on chromosomes 2DL and 6BS associated with stripe rust, and 3AL and 6AS for stem rust, respectively, using the Kenya disease severity data. Significant decreases in disease severities were also demonstrated due to additive effects of QTLs when present in combinations.

Changes in aggressiveness in pathotypes of wheat leaf rust

A recommendation of: Cécilia FONTYN, Kevin JG MEYER, Anne-Lise BOIXEL, Ghislain DELESTRE, Emma PIAGET, Corentin PICARD, Frédéric SUFFERT, Thierry C MARCEL, Henriette GOYEAU Evolution within a given virulence phenotype (pathotype) is driven by changes in aggressiveness: a case study of French wheat leaf rust populations https://doi.org/10.1101/2022.08.29.505401

Stem and leaf rust-induced miRNAome in bread wheat near-isogenic lines and their comparative analysis.

Wheat rusts remain a major threat to global wheat production and food security. The R-gene-mediated resistance has been employed as an efficient approach to develop rust-resistant varieties. However, evolution of new fungal races and infection strategies put forward the urgency of unravelling novel molecular players, including non-coding RNAs for plant response. This study identified microRNAs associated with Sr36 and Lr45 disease resistance genes in response to stem and leaf rust, respectively. Here, small RNA sequencing was performed on susceptible and resistant wheat near-isogenic lines inoculated with stem and leaf rust pathotypes. microRNA mining in stem rust-inoculated cultivars revealed a total of distinct 26 known and 7 novel miRNAs, and leaf rust libraries culminated with 22 known and 4 novel miRNAs. The comparative analysis between two disease sets provides a better understanding of altered miRNA profiles associated with respective R-genes and infections. Temporal differential expression pattern of miRNAs pinpoints their role during the progress of infection. Differential expression pattern of miRNAs among various treatments as well as time-course expression of miRNAs revealed stem and leaf rust-responsive miRNAs and their possible role in balancing disease resistance/susceptibility. Disclosure of guide strand, passenger strand and a variant of novel-Tae-miR02 from different subgenome origins might serve as a potential link between stem and leaf rust defence mechanisms downstream to respective R-genes. The outcome from the analysis of microRNA dynamics among two rust diseases and further characterization of identified microRNAs can contribute to significant novel insights on wheat-rust interactions and rust management. KEY POINTS: • Identification and comparative analysis of stem and leaf rust-responsive miRNAs. • Chromosomal location and functional prediction of miRNAs. • Time-course expression analysis of pathogen-responsive miRNAs.

Evaluation of Seedling Resistance and Marker Assisted Selection for Leaf Rust (Puccinia triticina) Resistance in Pakistani Wheat Landraces, Cultivars and Advanced Lines

Leaf rust is amongst major biotic constraints of wheat (Triticum aestivum L.) having ability to cause substantial yield reductions worldwide. A continuous exploration for novel sources of resistance is pre-requisite for its management. Objectives of study were to conduct resistance evaluation of 112 Pakistani landraces and 48 advanced lines/ cultivars at seedling stage with total 10 virulent pathotypes of leaf rust, 3 from Pakistan and 7 from U.S.A and to detect closely linked markers for Lr10, 16, 34 and 67 genes through marker-assisted selection (MAS). Findings revealed most of Pakistani landraces showed lack of resistance at seedling stage. Only 7 accessions of landraces and 11 advanced lines were found highly resistant against all pathotypes of Pakistan. Similarly, 10 advanced lines exhibited high resistance while variability in resistance was recorded for landraces against all pathotypes tested from USA. Marker-assisted selection revealed Lr genes i.e. Lr10, Lr16, Lr34 and Lr67 were present at various frequencies. Highest frequency was observed for Lr34 followed by Lr16 Lr67 while lowest was recorded for Lr10. These genetic resources and lines identified effective against Pakistan and USA pathotypes are potential sources for improvement of leaf rust (LR) resistance and can be utilized as valuable material for breeding resistant wheat cultivars.

Marker-assisted transfer of leaf and stripe rust resistance from Triticum turgidum var. durum cv. Trinakria to wheat variety HD2932.

A marker-assisted backcrossing program initiated to transfer leaf rust resistance gene LrTrk from Triticum turgidum cv. Trinakria to hexaploid wheat variety HD2932 cotransferred a stripe rust resistance gene, YrTrk, along with LrTrk. The cross of hexaploid recurrent parent HD2932 with tetraploid donor parent Trinakria produced pentaploid F1 plants. F1s were backcrossed with recurrent parent HD2932 to produce BC1F1 generation. Foreground and background selection was conducted in each backcross generation to identify plants for backcrossing or selfing. While foreground selection for LrTrk was carried out with linked and validated molecular marker Xgwm234, for background selection, 86 polymorphic SSR markers from the A and B genomes were used. Single selected plants from BC1F1 and BC2F1 generations backcrossed and selfed to produce BC2F1and BC2F2 generations, respectively. Background selection resulted in 83.72%, 91.86%, and 98.25% of RPG recovery in BC1F1, BC2F1, and BC2F2 generations, respectively. A total of 27 plants with LrTrk in homozygous state were identified in BC2F2 generation and selfed to produce 27 BC2F3 NILs. All the NILs were tested for leaf and stripe rust resistance at the seedling stage using seven Puccinia triticina and one Puccinia striiformis f.sp. tritici rust pathotypes. All the 27 NILs were found to be resistant to both leaf and stripe rust pathotypes. So, these NILs are designated to carry leaf and stripe rust resistance genes LrTrk/YrTrk.

Identification of Novel Broad-Spectrum Leaf Rust Resistance Sources from Khapli Wheat Landraces.

Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have evolved from wild emmer (Triticum turgidum var. dicoccoides), and harbors a good number of leaf rust resistance genes. In the present study, we are reporting on the screening of one hundred and twenty-three dicoccum wheat germplasm accessions against the leaf rust pathotype 77-5. Among these, an average of 45.50% of the germplasms were resistant, 46.74% were susceptible, and 8.53% had mesothetic reactions. Further, selected germplasm lines with accession numbers IC138898, IC47022, IC535116, IC535133, IC535139, IC551396, and IC534144 showed high level of resistance against the eighteen prevalent pathotypes. The infection type varied from “;”, “;N”, “;N1” to “;NC”. PCR-based analysis of the resistant dicoccum lines with SSR marker gwm508 linked to the Lr53 gene, a leaf rust resistance gene effective against all the prevalent pathotypes of leaf rust in India and identified from a T. turgidum var. dicoccoides germplasm, indicated that Lr53 is not present in the selected accessions. Moreover, we have also generated 35K SNP genotyping data of seven lines and the susceptible control, Mandsaur Local, to study their relationships. The GDIRT tool based on homozygous genotypic differences revealed that the seven genotypes are unique to each other and may carry different resistance genes for leaf rust.

Analysis of NIA and GSNOR family genes and nitric oxide homeostasis in response to wheat-leaf rust interaction

Nitric oxide (NO) modulates plant response to biotic and abiotic stresses by S-nitrosylation-mediated protein post-translational modification. Nitrate reductase (NR) and S-nitrosoglutathione reductase (GSNOR) enzymes are essential for NO synthesis and the maintenance of Nitric oxide/S-nitroso glutathione (NO/GSNO) homeostasis, respectively. S-nitrosoglutathione, formed by the S-nitrosylation reaction of NO with glutathione, plays a significant physiological role as the mobile reservoir of NO. The genome-wide analysis identified nine NR(NIA) and three GSNOR genes in the wheat genome. Phylogenic analysis revealed that the nine NIA genes +were clustered into four groups and the 3 GSNORs into two groups. qRT-PCR expression profiling of NIAs and GSNORs was done in Chinese spring (CS), a leaf rust susceptible wheat line showing compatible interaction, and Transfer (TR), leaf rust-resistant wheat line showing incompatible interaction, post-inoculation with leaf rust pathotype 77–5 (121-R-63). All the NIA genes showed upregulation during incompatible interaction in comparison with the compatible reaction. The GSNOR genes showed a variable pattern of expression: the TaGSNOR1 showed little change, whereas TaGSNOR2 showed higher expression during the incompatible response. TaGSNOR3 showed a rise of expression both in compatible and incompatible reactions. Before inoculation and after 72 h of pathogen inoculation, NO localization was studied in both compatible and incompatible reactions. The S-nitrosothiol accumulation, NR, and glutathione reductase activity showed a consistent increase in the incompatible interactions. The results demonstrate that both NR and GSNOR plays significant role in defence against the leaf rust pathogen in wheat by modulating NO homeostasis or signalling.

Analysis of variation in agronomic characters and partial resistance to barley leaf rust (Puccinia hordei) pathotype ETPh7611 of barley landrace collections

Analysis of variation in agronomic characters and partial resistance to barley leaf rust (Puccinia hordei) pathotype ETPh7611 of barley landrace collections

Detection of Lr19/Sr25 in segregating populations of wheat (Triticum aestivum L.) using robust molecular markers

Marker assisted breeding (MAB) technology has been proved effective to transfer the genes of interest and also increased the accuracy of selection in wheat improvement programmes. The Agropyron elongatum derived 7D.7Ag translocation carrying Lr19/Sr25 is not only effective against leaf rust pathotypes but also effective against stem rust race Ug99 and its variants. Therefore, wheat breeding lines carrying Lr19/ Sr25 translocation segment have been developed worldwide. The present study was aimed for developing wheat genotypes with Lr19/ Sr25 using Xwmc221, PSY1-E1 and Gb DNA markers in segregating populations of wheat. We could infer that Xwmc221, PSY1-E1 and Gb are effective molecular markers to tag Lr19/Sr25 in segregating generations of wheat. The data also revealed consistency between host pathogen interaction (HPI) test and Xwmc221, PSY1-E1 and Gb molecular markers for selecting lines with Lr19/Sr25 in segregating generations. This work not only confirmed the robustness of the three Lr19/Sr25 markers but also demonstrated the application of both genotyping and phenotyping in making full-proof selection of superior progenies with gene of interest in wheat.

Mechanism of leaf rust resistance in wheat wild relatives, Triticum monococcum L. and T. boeoticum L.

AbstractTriticum monococcum L. and T. boeoticum L., diploid wild relatives of bread wheat (T. aestivum L.), possess resistance to leaf rust (also known as brown rust) caused by Puccinia triticina Eriks. Haustorium formation-based resistance mechanisms (i.e. pre-haustorial and post-haustorial resistance) to leaf rust have been studied and reported in various T. monococcum accessions. In the present study, the mechanism of leaf rust resistance in T. monococcum and T. boeoticum accessions was studied using confocal laser scanning microscopy. Components of resistance studied at a histological level against leaf rust pathotypes, a Mexican pathotype (TCB/TD) and a Swiss pathotype (97512-19), indicated different types of resistance mechanism operative in the two accessions. The resistance in T. monococcum ranged from pre-haustorial resistance against 97512-19 to post-haustorial resistance against TCB/TD. The response in T. boeoticum was post-haustorial with necrosis against the two pathotypes. Pre-haustorial resistance observed in T. monococcum could serve as a potential source of durable rust resistance in wheat breeding.

Marker assisted pyramiding of stem rust, leaf rust and powdery mildew resistance genes for durable resistance in wheat (Triticum aestivum L.)

Wheat production is essential for food security. Stem and leaf rust diseases continually pose threat to wheat production. In recent years, climate change and intensive crop cultivation practices are making powdery mildew as a potential threat to wheat production. Deploying resistant cultivars are the most economic, reliable and sustainable way to manage the stem rust, leaf rust and powdery mildew of wheat. Using conventional selection system, it is difficult to select two or more genes in a single genotype. In such a situation, phenotype neutral selection based on marker-trait association along with seedling and adult plant reaction become inevitable. Stem rust, leaf rust and powdery mildew resistance genes, Sr24/Lr24 , Sr26 and Sr36/Pm6 were pyramided in the background of nine Indian wheat cultivars through marker assisted backcross approach. The presence of the rust and powdery mildew resistance genes were confirmed using microsatellite markers such as Sr24#12 ( Sr24/Lr24 ), Sr26#43 ( Sr26 ) and stm773 ( Sr36/Pm6 ) in the pyramided lines. Stable lines were selected at BC 3 F 4 generation. Seedling and adult plant reaction of pyramided lines showed resistance to most of the stem and leaf rust pathotypes prevailing in India. Using gene pyramids ( Sr24/Lr24 , Sr26 and Sr36/Pm6 ) that confer resistance to the predominant pathotypes of stem rust, leaf rust and powdery mildew could impart durability to the cultivars than single gene deployment.

Phenotypic and Molecular Assessment for Genetic Diversity of Egyptian Wheat Varieties

GENETIC diversity among plant species is important for improving plant traits. Its estimation is very essential to help selection of genetic resources in breeding programs. Moreover, it is the base for effective and successful crop enhancement and can be assessed by several methods i.e. using morphological trait (resistance to leaf rust) and molecular markers. In this study, genetic diversity was assessed among the 53 tested wheat varieties using 15 leaf rust pathotypes under greenhouse condition at seedling stage. In addition, the genetic diversity was assessed also using 10 molecular markers (microsatellite markers) linked to rust resistant genes. The cluster analysis indicated three sub-clusters based on phenotypic and molecular data. In general, low level (r= 0.15) of correlation was obtained between the phenotypic and the genotypic data, however, the molecular analysis is more efficient for estimating genetic diversity. Molecular analysis is an effi cient method because it’s not affected by environment, fast, more accurate and doesn’t need earlier pedigree information which can improve the effi cacy of molecular breeding practices.

Marker assisted stacking/pyramiding of stem rust, leaf rust and powdery mildew disease resistance genes (Sr2/Lr27/Yr30, Sr24/Lr24 and Sr36/Pm6) for durable resistance in wheat (Triticum aestivum L.)

Wheat being a staple food crop is essential for food security. Rust diseases like stem and leaf rust continues to be a serious threat to wheat production at national and international level. In recent years, powdery mildew disease is emerging as a threat to wheat production due to the climate change and intensive crop cultivation practices. Development of resistant cultivar is the most economical, reliable and sustainable way to control rusts and powdery mildew diseases. Stem rust, leaf rust and powdery mildew resistance genes viz., Sr2/Lr27/Yr30, Sr24/Lr24 and Sr36/ Pm6 were pyramided using marker assisted backcross breeding approach. Based on phenotypic observations, five populations were selected at BC4 F6 with respect to yield traits, leaf and stem rust and powdery mildew reactions. These populations were subjected to molecular marker analyses. Out of the five populations, Sr2+ were present in all the populations, while Sr24/Lr24 and Sr36/Pm6 was present in the fourth and fifth population. The identified population carrying Sr24/Lr24, Sr36/Pm6 and Sr2+ genes were stabilized at BC4 F7 generation. The use of gene stacks/pyramids of major (Sr24/Lr24 and Sr36/Pm6) and minor gene (Sr2+) that confer resistance to most of the pathotypes of stem rust, leaf rust and powdery mildew could impart durability and sustainability to the cultivars than single gene deployment.

Virulence and Molecular Polymorphism of Puccinia Triticina Pathotypes in Egypt

Forty wheat leaf rust (Puccinia triticina) pathotypes were collected from eleven Egyptian governorates during the two growing seasons 2016/2017 and 2017/2018 were analyzed based on both virulence and molecular marker analysis. Virulence analysis was carried out on the basis of infection type of the tested pathotypes on 20 differential monogenic lines, each carrying single leaf rust resistance genes (Lr). Six simple sequence repeats (SSR) markers were used for molecular characterization of P. triticina to detect the genotypic variation among pathotypes. Almost all of the tested pathotypes were phenotypically and genetically varied that confirms a high diversity within Egyptian leaf rust populations. Cluster analysis based on both virulence analysis and molecular patterns classified the tested pathotypes to three main groups. A relatively weak correlation was found between virulence and molecular analysis (r = 0.03). High similarity was found between leaf rust populations in the three governorates; Sohag, Bani Sweif and Fayoum. Also, high similarity was found between leaf rust populations in the five; Egyptian governorates; Minufiya, Kafr-Elsheikh, Gharbiya, Alexandria and Qalyubia, while, wide variation was found between leaf rust populations of the three governorates; Beheira, Sharqiya and Dakahlia. The results of this study support using molecular markers analysis to estimate genetic diversity between P. triticina pathotypes.

Mapping of genes for leaf and stem rust resistance in bread wheat genotype Selection 212

Resistance genes for leaf and stem rusts in bread wheat line Selection212 are recessive in nature. Both leaf and stem rust resistance genes, named tentatively as LrSel212 and SrSel212, have been mapped to the short arm of chromosome 2B separated by genetic distance of 16.4 cM. Xwmc474 was the closest marker located between two genes, 5.6 cM proximal to LrSel212 and 10.8 cM distal to SrSel212. Leaf rust pathotype 77-5 is virulent to leaf rust resistance genes located on chromosome 2B viz., Lr13, Lr16, Lr23, Lr35 and Lr73, but avirulent to Selection212, suggesting that LrSel212 is distinct from these genes. Six stem rust resistance genes have been assigned to chromosome 2B viz., Sr19, Sr20, Sr23, Sr36, Sr39 and Sr40. Stem rust pathotype 40A used in genetic analysis was virulent to Sr19 and Sr20, but avirulent to Selection212; and the latter showed a significantly lower infection type in comparison to Sr39. Sr23 and Sr36 showed susceptibility to few other stem rust pathotypes to which Selection212 was resistant. While the response of Sr40 to Indian pathotypes of Pgt is not known, differences in the genetic distance and nature of inheritance between Selection212 and Sr40 indicate their distinct identity. However, test of allelism with Sr40 is required to confirm whether SrSel212 represents a different locus. Selection212 may be useful in broadening the genetic base of rust resistance in wheat.

Application of High Density Linkage Map Derived from Genotyping by Sequencing for Detection of QTL Conferring Resistance to Leaf Rust Races Spread in Egypt

Wheat is a major source of carbohydrates in Egypt, leaf rust disease is known to be the most common rust disease affected wheat genotypes. This study aimed to apply a constructed high density linkage map through Genotyping-by- sequencing (GBS) for detection of QTL resistant to important leaf rust races spread in Egypt. The applied map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. A mapping population of 204 RILs (F6:8) obtained from the cross between two parents of winter wheat ‘Harry’ x ‘Wesley’ through single seed decent method was used to identify QTL region associated with leaf rust resistance genes in wheat. Under the Green house condition in Egypt leaf rust pathotypes i.e NTTJT, PTTGS, PTTTT, TTTBT and TTTTT were used. High-density linkage map based on GBS derived SNPs were applied in this study for QTL mapping. The wheat genotype Harry was resistant to all tested pathotype while, the wheat genotype Wesley was susceptible to all tested pathotype. One major stable QTLs, for race NTTJT was identified on chromosome 6A flanked by markers XSNP3958 and XSNP3957 with a LOD 4.22. The identified SNP marker may be used to screen for resistance to specific races of leaf rust found in Egypt in further spring wheat breeding programs as marker assisted selection.

Diversity and Virulence Dynamics within Puccinia triticina Populations in Egypt

Leaf rust caused by Puccinia triticina Eriks., is one of the most common diseases of wheat (Triticum aestivum L.) in Egypt and worldwide. To investigate the population genetic structure of the causal pathogen, 468 single isolates were obtained from 193 samples collected from 12 Egyptian governorates and analyzed during 2016/17 and 2017/18 growing seasons. A total of 125 and 101 leaf rust pathotypes were designated during 2016/17 and 2017/18 growing seasons. The most frequent pathotype was STTTK (9.81% frequency), followed by race PTTNS (2.80% frequency) during 2016/17. While, pathotype PTTTT was occurred at a high frequency (12.16% frequency), followed by the four pathotypes; TTTBT, PTTGS, TTTTT and PTTCT (5.88, 5.10, 5.10 and 4.31%, respectively), during 2017/18. Pathotype STTTK is the most geographically distributed as it was detected in nine governorates in 2016/17, but in 2017/18, PTTTT is the most geographically distributed pathotype, where it was found in seven governorates. High similarity was found between leaf rust populations in the five locations, i.e. Domiatta, Sohag, Alexandria, Kafr El-Sheikh and Bani Sweif, during 2016/17 growing season. Also, high similarity was found between leaf rust pathogen populations of Kafr-Elsheikh, Sohag, Beheira, Dakahlia, Sharqiya, Domiatta, Gharbiya, Fayoum and Minufiy, during 2017/18 growing season. The phenotypic diversity within different populations under study was characterized using the three indexes; Shannon, Gleason and Simpson. Shannon index proved to be more suitable to accurately measure the phenotypic diversity between the tested populations of the causal pathogen, as it was sensitive to sample size, number of isolates, number of races and standard deviation of race frequency than the others.

H3K4/K9 acetylation and Lr28-mediated expression of six leaf rust responsive genes in wheat (Triticum aestivum).

Development of leaf rust-resistant cultivars is a priority during wheat breeding, since leaf rust causes major losses in yield. Resistance against leaf rust due to Lr genes is partly controlled by epigenetic modifications including histone acetylation that is known to respond to biotic/abiotic stresses. In the present study, enrichment of H3K4ac and H3K9ac in promoters of six defense responsive genes (N-acetyltransferase, WRKY 40, WRKY 70, ASR1, Peroxidase 12 and Sarcosine oxidase) was compared with their expression in a pair of near-isogenic lines (NILs) for the gene Lr28 following inoculation with leaf rust pathotype '77-5'; ChIP-qPCR was used for this purpose. The proximal and distal promoters of these genes contained a number of motifs that are known to respond to biotic stresses. The enrichment of two acetylation marks changed with passage of time; changes in expression of two of the six genes (N-acetyltransferase and peroxidase12), largely matched with changes in H3K4/H3K9 acetylation patterns of the two promoter regions. For example, enrichment of both the marks matched with higher expression of N-acetyltransferase gene in susceptible NIL and the deacetylation (H3K4ac) largely matched with reduced gene expression in resistant NIL. In peroxidase12, enrichment of H3K4ac and H3K9ac largely matched with higher expression in both the NILs. In the remaining four genes, changes in H3 acetylation did not always match with gene expression levels. This indicated complexity in the regulation of the expression of these remaining four genes, which may be controlled by other epigenetic/genetic regulatory mechanisms that need further analysis.