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In this study, we developed and optimized a multiplex polymerase chain reaction (PCR) for simultaneous detection of two important leaf rust resistance genes Lr24 and Lr68. Seedling resistance gene Lr24 and slow rusting gene Lr68 encoding resistance to leaf rust were identified in forty-one advanced salt-tolerant wheat genotypes using molecular markers viz. Sr24#50 and csGS, respectively. For re-validation of PCR reaction results, a seedling resistance test (SRT) was performed in controlled glasshouse conditions. Genotypes were evaluated under epiphytotic conditions for SRT by artificial inoculation with a spectrum of Puccinia triticina pathotypes. Results of SRT were supplemented by PCR results, indicated that the gene Lr24/Sr24 conferred leaf rust resistance in two wheat genotypes namely HD 2851 and KRL2029. In advanced line KRL2029, along with Lr24/Sr24 other rust resistance genes (Lr26/Sr31/ Yr9) were also present. Molecular marker csGS for a known slow rusting gene Lr68 was amplified in fifteen salt-tolerant wheat genotypes indicated the presence of Lr68 in these lines. These lines could also be utilized as donors for slow rusting characteristics. Combination of both the genes could provide resistance to leaf rust and stem rust. Presences of respective genes in salt-tolerant lines were confirmed by SRT as well as molecular markers separately and multiplex PCR assay was designed. Multiplex PCR method allowed to reduce the cost and time of analyses as well as reducing the workload.

Wheat is the second most cultivated cereal crop in the world and is an important crop in India. Leaf (brown) rust, caused by Puccinia triticina, was the most prevalent among the three rusts found in all the wheat-growing areas of India, Bhutan, and Nepal during 2016 to 2019. Leaf rust samples from wheat crops in these countries were pathotyped using the wheat differential genotypes and binomial Indian system of nomenclature. To facilitate international communication, each pathotype identified was also tested using the North American differentials. A total of 33 pathotypes were identified from 1,086 samples, including three new pathotypes: 61R47 (162-5 = KHTPM) and 93R49 (49 = NHKTN) from India and 93R57 (20-1 = NHKTN) from Nepal. Two pathotypes, 121R60-1 (77-9/52 = MHTKL) and 121R63-1 (77-5 = THTTM), accounted for 79.46% of the population. Virulence on Lr19 was identified in 0.27% of the samples from Nepal only. The proportion of pathotype 121R60-1 (77-9 = MHTKL) increased to 57.55% during these years. Virulence was not observed on Lr9, Lr24, Lr25, Lr28, Lr32, Lr39, Lr45, and Lr47 in the population of the Indian subcontinent. Eighteen polymorphic simple sequence repeat (SSR) primer pairs tested on the isolates amplified 48 alleles with an average of 2.66 alleles per primer pair. Based on SSR genotyping, these pathotypes could be grouped into two clades with another two subclades each. Many of the Lr genes present in Indian wheat germplasm (Lr1, Lr3a, Lr10, Lr11, Lr14a, Lr15, Lr16, Lr17, Lr20, Lr23, and Lr26) were ineffective for a majority of pathotypes. Most of these varieties possessed a high degree of leaf rust resistance. The field resistance of wheat varieties could be attributed to the interaction of genes, unknown resistance, or adult plant resistance.

In vitro haploid production followed by chromosome doubling greatly enhances the production of complete homozygous wheat lines in a single generation. This work aimed to develop wheat doubled haploid genetic stock resistant to yellow and brown rust via intergeneric hybridization with Imperata cylindrica and its further characterization. The wheat doubled haploid (DH) line was developed by crossing wheat F1 (HS 542/China 84-40,022) with I. cylindrica. This DH-1 was tested against eight races of yellow (110S119, 110S247, 238S119, 78S84, 110S84, 111S68, T and P) and eighteen races of brown rust (11,12-5, 12-7, 12A, 77, 77-1, 77-2, 77-5, 77-7, 77-8, 77-10, 77A-1, 104-2, 107-1, 108-1, 162-1, 77-9 and 104-1) at seedling stage and with mix race of yellow and brown rust in adult plant stage (at Dhaulakuan, Bajaura and Shimla). At the seedling stage, DH-1 showed resistance to all the yellow and brown rust pathotypes except for 77-5 race of brown rust. The adult plant response of this DH line also showed resistance to both yellow and brown rust. Based on host pathogen interaction, the DH-1 was postulated to carry leaf rust resistant genes Lr26 + Lr23 + 1 + and yellow rust resistant gene Yr9 + gene. Molecular characterization of the DH line with gene-specific primers showed that the developed DH-1 contains leaf rust resistance genes Lr34, Lr26 and Lr32. The DH-1 has semi-spreading growth habit, erect flag leaf attitude, plant height of 94 cm, have scurs and 1000 grain weight of 36 g. The results highlight I. cylindrica-mediated chromosome elimination technique of doubled haploid production as an effective tool for the development of wheat rust resistant lines in the shortest timeframe. This is the first report of genetic stock development for rust resistance in wheat via I. cylindrica-mediated DH technique.

A total of 263 accessions representing a cross section of the recently developed common wheat genotypes in India showing flag leaf tip necrosis (LTN) were characterized for the LTN-associated pleiotropic adult plant resistance (PAPR) genes, Lr34/Yr18/Sr57 (Lr34 +), Lr46/Yr29/Sr58 (Lr46 +), and Lr67/Yr46/Sr55 (Lr67 +) using closely linked molecular markers. They were evaluated for seedling resistance to important rust pathotypes, and for multi-environmental field resistance to the three rusts. About 79% of the genotypes carried the PAPR genes singly or in different two genes’ combinations. The genes Lr67 + and Lr34 + occurred much more frequently than Lr46 + . While field resistance to leaf and stem rusts was usually associated with seedling resistance, that to stripe rust was based largely on the adult-plant resistance. Intermediate to low levels of resistance were provided by the three PAPR genes individually, and no clear-cut additive effects on rust resistance were apparent among the various gene combinations. Considerable diversity was observed for resistance to all the three wheat rusts. Additional genes for resistance were indicated in many genotypes which need to be characterized. The identified diverse sources of multiple rust resistance can be utilized in breeding for rust resistance along with desired agronomic traits.

In wheat, leaf rust caused by Puccinia triticina Eriks is a major disease that causes major losses in production. In the present study, microsatellite or SSR (simple sequence repeat) markers were developed for P. triticina using the transcriptome data obtained during wheat-P. triticina interactions. A total of 37,268 P. triticina differentially expressed transcripts were obtained in the comparative transcriptomics and of these, 6809 (1.8%) transcripts carried SSRs. Tri-nucleotide SSRs were the most abundant (52%) among the identified SSRs. Primer pairs were synthesized for 50 PtESSRs, of which 28 were found to be polymorphic in P. triticina pathotypes of the Indian subcontinent. The number of alleles per locus ranged from 2 to 12 with an average of 5.72. Polymorphic information content (PIC) ranged from 0.29 to 0.96 with an average of 0.69. The observed heterozygosity ranged from 0.10 to 0.48 with an average of 0.21. Interestingly, one SSR marker, namely PtESSR7, could distinguish between different virulence groups of pathotypes. BLAST analysis and in silico prediction of fungal effectors suggested that some of the PtESSR markers may have the potential to be functional markers in the leaf rust pathology. Dendrogram analyses detected two clusters in the 48 P. triticina pathotypes. Results of this study suggest that the newly developed PtESSR markers are useful for genetic studies in P. triticina pathogen. No relationship was found between the genetic diversity and geographic distributions of the P. triticina populations.

Breeding resistant varieties of wheat is a continuous process and empirical disease control depends on deployment of diverse sources of genetic resistance to the deadly rusts. A total of 166 exotic wheat germplasm accessions were evaluated for resistance to wheat rusts having some component of resistance to either any of the three rusts and spot blotch. The data for adult plant resistance (APR) on leaf and stem rusts, was recorded at Wellington while yellow rust epiphytotic was artificially created at Karnal for identification of resistant lines. Based on APR data 85, 96 and 16 accessions were found completely resistant to leaf, stem and stripe rusts respectively. Based on the seedling resistance data against different pathotypes (10 each for leaf and stripe and 5 for stem rust) of each rust, nine, fifteen and five accessions were found highly resistant respectively. Based on the multi-environment adult plant resistance data and race specific seedling data, we were able to identify 28, accessions highly resistant to either one or two rusts. For spot blotch the evaluation was done at hotspot locations Wadura and Coochbehar and 26 accessions were found to be highly resistant against this disease. The lines so identified in this study are being used in the hybridization programs to enhance the levels of resistance.

Expression of five wheat (Triticum aestivum L.) housekeeping genes (HKGs), coding for ubiquitin (TaUBI, AY297059.2), elongation factor-1α (TaEF1α, BT009129.1), 18S ribosomal RNA (Ta18SrRNA, HG670306.1), glucose-6-phosphate dehydrogenase (TaG6PDH, AB029454) and actin (TaACT, AB181991), was analyzed using BestKeeper and NormFinder algorithms and genes with superior expression uniformity were identified in wheat leaves during pre-haustorial (early) stages of T. aestivum-Puccinia triticina (Pt) interaction. Results of expression stability analyses of the HKGs confirmed highly stable expressions of TaUBI and TaEF1α. The expression of TaACT was moderately stable and those of TaG6PDH and Ta18SrRNA were the least stable. Therefore, the HKGs TaUBI and TaEF1α are superior reference genes for normalization of gene expression during T. aestivum-Pt interaction studies, whereas the use of Ta18SrRNA as reference genes should be avoided in such studies. Furthermore, validation of expression stability of the best reference gene identified (TaUBI) in a cultivar exhibiting an incompatible interaction showed results similar to those obtained in a compatible interaction when plants were mock-treated and inoculated with the fungus. In summary, this study identified two superior reference genes, TaUBI and TaEF1α, useful for analyses of gene expression during pre-haustorial stages of wheat leaf rust infection.

Wheat stripe rust caused by Puccinia striiformis Westend. f.sp. tritici (Pst) is a global threat to wheat production. Genetic modification of defense-responsive factors in wheat rust interactions could help devise strategies to control stripe rust on wheat. This experiment studied the interaction between Pst pathotype 78S84 in PBW343 and FLW-3 by evaluating the quantitative temporal transcription profiles of defense-related genes at different time points. This is the first attempt to exhibit inter-connections among different proteins and depict a hypothetical model for the mechanism of R gene-mediated resistance. Transcript levels of LTP, AQP1, PR1, PR2, PR4, and PR10 were relatively higher under compatible interaction, while under incompatible interaction, transcript levels of COMT1, PRA2, WCAB, and PR9 were significantly high. This study projected the role of defense-responsive genes, inter-networking of proteins, and R gene-mediated resistance between wheat and stripe rust.

During the periodic purity checks of pathotypes 107-1(45R35=JCGPL) and 20(5R27=SGQPL) of Puccinia triticina in national repository at Shimla, India, mixtures of infection types were observed on the differential Lr3 and Lr15 , respectively. Single pustule isolations and further pure cultures in both the cases yielded new pathotypes designated as 57(45R39= KGTPL) and 20-2(57R27= SHKPL). Pathotype 57 was one step gain in virulence on Lr3 in 107-1 whereas 20-2 on Lr15 in mother culture of pathotype 20. The difference of virulence on one gene to each mother culture and their non occurrence in the field samples is indicative of mutation for virulence in situ . To ascertain the novelty of new pathotypes, detailed study on differentials, avirulence/virulence structure, DNA polymorphism using SSR markers, and other related information is presented in this publication. The new cultures are being maintained as PrtI 57 and PrtI 20-2 in the repository.

The outcome of different host-pathogen interactions is influenced by both genetic and epigenetic systems, which determine the response of plants to pathogens and vice versa. This review highlights key molecular mechanisms and conceptual advances involved in epigenetic research and the progress made in epigenetics of wheat-rust interactions. Epigenetics implies the heritable changes in the way of gene expression as a consequence of the modification of DNA bases, histone proteins, and/or non-coding-RNA biogenesis without disturbing the underlying nucleotide sequence. The changes occurring between DNA and its surrounding chromatin without altering its DNA sequence and leading to significant changes in the genome of any organism are called epigenetic changes. Epigenetics has already been used successfully to explain the mechanism of human pathogens and in the identification of pathogen-induced modifications within various host plants. Wheat rusts are one of the most vital fungal diseases throughout the major wheat-growing areas of the world. The epigenome in plant pathogens causing diseases such as wheat rusts is mysterious. The investigations of host and pathogen epigenetics in the wheat rusts system can offer a piece of suitable evidence for elucidation of the molecular basis of host-pathogen interaction. Besides, the information on the epigenetic regulation of the genes involved in resistance or pathogenicity will provide better insights into the complex resistance signaling pathways and could provide answers to certain key questions, such as whether epigenetic regulation of certain genes is imparting resistance to host in response of certain pathogen elicitors or not. In the last few years, there has been an upsurge in research on the host as well as pathogen epigenetics and its outcome in plant-pathogen interactions. This review summarizes the progress made in the areas related to the epigenetic control of host-pathogen interaction with particular emphasis on wheat rusts.

Wheat and barley yellow rust pathogens, Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), respectively, can change quickly in virulence. The present study was conducted using host differentials and microsatellite marker assay to determine the relationship of two newly detected atypical Pst pathotypes (6S0 and 7S0) with known pathotypes from wheat (46S103, 47S103, 46S119, 111S68 and 79S68) and barley (0S0-1, 4S0, 0S0 and 1S0). A set of 21 SSR markers were used to determine inter-relationship among these pathotypes. In toto, 79 alleles were detected across the 21 loci. Six markers (RJ22, SUNIPst9-40, SUNIPst09-48, SUNIPst10-48, SUNIPst11-01 and SUNIPst16-10) were found highly informative. The polymorphism information content (PIC) values of these markers were > 0.69. These markers provided useful information on genetic divergence of newly emerged Pst pathotypes. Principle component analysis (PCoA) explained 62.91% variation among the analysed pathotypes. The molecular variation studies showed that new Pst pathotypes (6S0 and 7S0) are more close to known pathotypes from barley than from wheat. The major distinction in term of virulence was that pathotype 7S0 possessed extra virulence for Yr1 and lacked virulence for rpsTr1 and rpsTr2.

Identification and functional characterization of plant pathogen effectors promise to ameliorate future research and develop effective and sustainable strategies for controlling or containing crop diseases. Wheat is the second most important food crop of the world after rice. Rust pathogens, one of the major biotic stresses in wheat production, are capable of threatening the world food security. Understanding the molecular basis of plant-pathogen interactions is essential for devising novel strategies for resistance breeding and disease management. Now, it has been established that effectors, the proteins secreted by pathogens, play a key role in plant-pathogen interactions. Therefore, effector biology has emerged as one of the most important research fields in plant biology. Recent advances in genomics and bioinformatics have allowed identification of a large repertoire of candidate effectors, while the evolving high-throughput tools have continued to assist in their functional characterization. The repertoires of effectors have become an important resource for better understanding of effector biology of pathosystems and resistance breeding of crop plants. In recent years, a significant progress has been made in the field of rust effector biology. This review describes the recent advances in effector biology of obligate fungal pathogens, identification and functional analysis of wheat rust pathogens effectors and the potential applications of effectors in molecular plant biology and rust resistance breeding in wheat.

Brown (leaf) rust of wheat (Puccinia triticina) was widely prevalent in all the wheat growing areas of India and neighbouring countries during 2013–16. To have an effective rust management strategy, monitoring of virulence patterns of P. triticina on wheat were undertaken. Brown rust samples were analyzed from the wheat growing areas in India, Bangladesh, Bhutan and Nepal using standard differential Indian System and named as per the binomial system of nomenclature. A new pathotype 77-12 was also identified during this period. Thirty seven pathotypes of P. triticina were identified in 1427 samples. Five predominant pathotypes 121R63-1(77-5 = THTTM), 121R60-1(77-9 = MHTKL), 21R55 (104-2 = PHTTL), 21R63 (104-3 = PHTTL) and 77-11(125R28 = MGTTL) accounted for 75.1% of the population. All of the prevalent pathotypes are virulent to Lr1, Lr3, Lr10, Lr11,Lr12 Lr13, Lr14a, Lr16, Lr17, Lr23, Lr26. Virulences for Lr9 and Lr19 though recorded from India long back, however, were not observed during present surveys whereas virulence on Lr28 was identified in 0.4% samples only. The proportion of pathotype 121R60-1 (77-9 = MHTKL) has increased during these years and was recorded in 23.7% samples against 12% in the previous report. Brown rust of wheat was not observed on Lr9, Lr24, Lr25, Lr32, Lr39 and Lr45 in the field population of Indian subcontinent during 2013–16. Diversity of pathotypes detected during this period could, to some extent, be related to cultivation of different varieties but was also appeared to be affected by different weather patterns in different agro-ecological areas.

Resistance expressed by plants against different rust pathogens is a unique and a very well-coordinated process. The defense responsive genes are the performers of such responses in plants. Understanding the regulation and mechanism of action of these genes is a key constituent of strategic resistance breeding programmes. The present study is aimed at evaluating and comparing the temporal expression pattern of defense responsive genes during early infection phase in compatible and incompatible interactions between wheat and leaf rust to elucidate the molecular basis of Lr24- mediated rust resistance. Lr24 confers resistance to almost all the pathotypes of Puccinia triticina (Pt) reported from Indian subcontinent and Australia. Expression profiles of 10 pathogen responsive genes representing different classes were studied in susceptible (HS240) and resistant (HW2020) wheat near-isogenic lines interacting with Pt. The expression profiles of these genes revealed that the transcript levels of aquaporin, endochitinase, β-1,3-glucanase, Type 1 non-specific lipid transfer protein precursor, phenylalanine ammonia-lyase and caffeic acid O-methyltransferase were significantly higher in incompatible interaction. Relatively higher expression of phenylalanine ammonia-lyase and aquaporin was observed at the pre-haustorial stage [6 h post inoculation (hpi) and 12 hpi], while expression of endo-chitinase and lipid transfer protein was higher during the post-haustorial stage (24 hpi and 48 hpi) in the incompatible interaction. Induced expression of class III peroxidase was maintained throughout pre- and post-haustorial stages in the compatible interaction. The results of the current study could distinguish the defense responsive genes playing a critical role in wheat resistance or susceptibility to leaf rust. We feel that this understanding will allow devising novel strategies to regulate wheat leaf rust pathogen interactions through genetic engineering.

Wheat is the second most cultivated cereal crop in the world and is an important crop in India. Leaf (brown) rust, caused by

Barley stripe rust, Puccinia striiformis f. sp. hordei, (PSH) occurs worldwide and is one of the major barley diseases of South Asia and North Africa. The aim of this study was to identify and map rust resistance loci at the seedling and the adult plant stages in 336 barley genotypes assembled at ICARDA as AM-2014. The seedling resistance to PSH was evaluated in the greenhouse individually for six virulent races originated from India. The adult stage resistance to PSH was evaluated in field located at Durgapura, Rajasthan, India. The AM-2014 panel was genotyped with infinium iSelect 9K barley SNP markers and genome-wide association studies were carried out using mixed linear model accounting for population structure (PCA) and kinship (K) as covariates. Eleven barley genotypes were identified resistant to all six PSH races at the seedling stage while these genotypes were also resistant at adult plant stage in the field. The most effective SNP markers (at least one for each QTL) associated with rust resistance was also identified using stepwise regression. A total of 17 and 25 resistance QTL to six races of PSH were identified in two- and six-rowed barley at the seedling stage, respectively. While, six and seven resistance QTL to PSH were detected at the adult stage in two- and six-rowed barley, respectively. The novel PSH resistant QTL detected at the seedling and adult stages are important for barley breeding programs globally.

The rhizosphere is a closely proximate area where plant roots and PGPR live together and produce various organic molecules, which boost plant growth and immunity. Metatranscriptomics is the best technique to study unexplored or unidentified microbes that help plants in terms of growth and also elicit induced systemic resistance against various plant pathogens. Metatranscriptomics provides direct access to the microbial community, which is not culturable on growth media. We have provided a holistic view in this chapter about rhizosphere, types of microbes which live in the rhizosphere, and how they affect plant health. We have discussed techniques that are used to study metatranscriptomic and bioinformatic tools to interpret the most valuable knowledge from sequencing data.

Resistance in modern wheat cultivars for stripe rust is not long lasting due to narrow genetic base and periodical evolution of new pathogenic races. Though, nearly 83 Yr genes conferring resistance to stripe rust have been cataloged so far, hardly few of them have been mapped and utilized in breeding programs. Characterization of wheat germplasm for novel sources of resistance and their incorporation into elite cultivars is required to achieve durable resistance and thus, to minimize the yield losses. Here, a genome-wide association study (GWAS) was performed on a set of 391 germplasm lines with the aim to identify quantitative trait loci (QTL) using 35K Axiom® array. Phenotypic evaluation disease severity against four stripe rust pathotypes i.e., 46S119, 110S119, 238S119 and 47S103 (T) at the seedling stage under glass house providing optimal conditions was carried out consecutively for two years (2018 and 2019 winter season). Association study revealed that a total of 40 QTLs were significantly associated with seedling-plant resistance to stripe rust. Out of these, 20 QTLs were found to be closely linked with previously reported yellow rust resistance genes/QTLs on chromosomes 1B, 2B, 5B and 6B while 20 novel QTLs were mapped on chromosomes 2D, 3A, 3D, 5A and 7D. These 20 novel QTLs identified in the present study might play a key role in marker-assisted breeding for developing stripe rust resistant wheat cultivars.

A new leaf rust resistance gene Lr80 was identified and closely linked markers were developed for its successful pyramiding with other marker-tagged genes to achieve durable control of leaf rust. Common wheat landrace Hango-2, collected in 2006 from the Himalayan area of Hango, District Kinnaur, in Himachal Pradesh, exhibited a very low infection type (IT;) at the seedling stage to all Indian Puccinia triticina (Pt) pathotypes, except the pathotype 5R9-7 which produced IT 3+. Genetic analysis based on Agra Local/Hango-2-derived F3 families indicated monogenic control of leaf rust resistance, and the underlying locus was temporarily named LrH2. Bulked segregant analysis using 303 simple sequence repeat (SSR) markers located LrH2 in the short arm of chromosome 2D. An additional set of 10 chromosome 2DS-specific markers showed polymorphism between the parents and these were mapped on the entire Agra Local/Hango-2 F3 population. LrH2 was flanked by markers cau96 (distally) and barc124 (proximally). The 90 K Infinium SNP array was used to identify SNP markers linked with LrH2. Markers KASP_17425 and KASP_17148 showed association with LrH2. Comparison of seedling leaf rust response data and marker locations across different maps demonstrated the uniqueness of LrH2 and it was formally named Lr80. The Lr80-linked markers KASP_17425, KASP_17148 and barc124 amplified alleles/products different to Hango-2 in 82 Australian cultivars indicating their robustness for marker-assisted selection of this gene in wheat breeding programs.

Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.

Wheat cultivation in India has been primarily dominated by the high productive environments of Indo-Gangetic plains. The North Western and North Eastern Plains are two mega environments for wheat production in the country in terms of area and production. For sustaining the high productivity levels in these areas, a constant demand of improved wheat varieties from the wheat breeding programs is desired. A high yielding bread wheat cultivar DBW187 (Karan Vandana) has been developed and released for cultivation in these areas after testing in trials under AICRP on Wheat and Barley. DBW187 is a high input responsive wheat genotype which has shown a significant yield superiority under early sown irrigated conditions of North Western Plains Zone over the checks HD2967 and HD3086 during 2018-19. Average yield of DBW187 during two years of testing was recorded to be 61.28q/ha. Earlier under evaluation in the North Eastern Plains Zone, this variety has shown an average yield of 48.8 q/ha with a potential yield of 64.7q/ha. The variety was released by Central Sub-committee on Crop Standards, Notification and Release of variety, Ministry of Agriculture, Government of India vide notification No. S.O. 1498(E) dated 01.04.2019 for cultivation in the NEPZ of India and subsequently it was extended to NWPZ vide notification S.O. 98(E) dated 06.01.2020. DBW187 is having a high yield potential along with disease resistance and superior grain quality. The ability to adopt across variable growing conditions in two different zones is a huge advantage for this genotype and will also go a long way in sustaining its cultivation in the region. DOI.10.25174/2582-2675/2020/99622

Surveys on wheat stem rust were conducted in major wheat-growing areas of the Indian subcontinent during 2009–2015 to determine the virulence phenotypes and simple sequence repeat (SSR) genotype diversity of Puccinia graminis Pers. f. sp. tritici Eriks. E. Henn (Pgt). Rust-infected stems or leaves of wheat were collected and inoculated on a susceptible wheat cultivar. Indian stem rust differential lines were used to designate Pgt pathotypes in these samples. About 80% of the samples analyzed during the study were from central and southern India. Twelve pathotypes of P. graminis f. sp. tritici were designated in 574 samples analyzed during the study. The severity and incidence of stem rust were maximum during 2013–2014 followed by 2012–2013. Pathotypes 40A and 11 designated in 36.8% and 32.6% of the samples, respectively, were the most predominant. The stem rust resistance genes Sr7a, Sr26, Sr27, Sr31, Sr32, Sr33, Sr39, Sr40, Sr43, SrTmp, and SrTt3 were found to confer resistance to all the pathotypes identified duing the study period. These genes in combination with other slow rusting genes could be used in stem rust resistance breeding programme for the Indian subcontinent. The analysis of SSR marker-based, genotypic and virulence-based phenotypic data revealed a high degree of variability in the Pgt population. The information generated here promises to be a useful guide for orienting rust resistance breeding programme and gene deployment for guarding South Asian wheat from the stem rust menace.

Population behaviour of two sets of pathotypes (77-5, 77-9, 104-2, 104-2; 77-5, 77-9, 104-2) of Puccinia triticina was studied in relation to wheat cultivars DBW71, DBW90, HD3086, HPW349, K1006, Local Wheat Hango (LWH), MP3336, PBW343, WH1124 and Agra Local at two temperature regimes under controlled greenhouse conditions. These wheat cvs belonged to different areas and were susceptible to all the pathotypes used in the studies. Predominance of a pathotype was the outcome of temperature, wheat variety and competition among the pathotypes. Both pathotype 77-9 and 104-2 were equally dominant in a population of 77-5, 77-9, 104-2 and 104-3. Pathotype 77-5 was less frequent. In a set of three pathotypes 77-5 was more frequent followed by 104-2 whereas 77-9 was nearly eliminated. Among the pathotypes used in the studies, 104-2 was the simplest and it emerged dominant on Agra Local and some other wheat cultivars. In fitness studies, pathotype 77-9 was found to possess less incubation period, latent period, produced more uredinio-pustules and urediniospores/cm2 as compared to other pathotypes. It is indicative of the fact that the pathotype 77-9 followed by 104-2 is more competitive and fit in population and can overtake other pathotypes in the years to come.

Leaf rust (Puccinia triticina Erikss.) is one of the most damaging pathogens of wheat (Triticum aestivum L.). With the rapid evolution of new races, worldwide distribution, and high genetic diversity, P. triticina has the ability to cause severe epidemics in wheat growing areas. In plants, salicylic acid (SA) and sugar-mediated defense pathways are expected to provide durable and broad-spectrum resistance. To understand the role of SA and sugar-mediated resistance mechanisms in wheat during early leaf rust infection, expression profiles of the key regulators of SA (TaEDS1, TaPAD4, TaNDR1, TaRAR1, TaSGT1, TaHSP90, TaEDS5, TaPAL, and TaNPR1) and sugar (TaHTP, TaSTP13A) pathways were analyzed in time-course experiments between two wheat near-isogenic lines (NILs) differing in the leaf rust resistance gene, Lr24. The quantification of candidate gene expression using reverse transcription quantitative real-time PCR at different time points post inoculation showed stage-specific transcriptional reprogramming between compatible and incompatible interactions. Interestingly, two distinct expression patterns were observed between two types of interactions. The genes acting upstream of SA in the SA pathway (TaEDS1, TaPAD4, TaNDR1, TaRAR1, TaSGT1, TaHSP90, TaEDS5) showed strong expressions at a later stage [48 h post inoculation (hpi)] of leaf rust infection in the compatible interaction compared to unchanged or slightly changed expressions in the incompatible interaction. Further, these genes showed similar expression patterns in either of the interactions, suggesting their cooperative or coordinated functions. On the other hand, the genes involved in SA biosynthesis (TaPAL), SA downstream signaling (TaNPR1), and sugar transportation (TaHTP, TaSTP13A) showed a strong expression at mid phase of infection between 6 and 24 hpi in the incompatible interaction compared to the compatible interaction. These expression patterns suggest that TaPAL and TaNPR1 play a positive regulatory role in the SA-mediated resistance pathway whereas TaHTP (Lr67) plays an important role in the sugar-mediated resistance pathway activated by the leaf rust resistance gene, Lr24.

A set of forty wheat cultivars comprising bread wheat, durum and triticale identified during 2010–2014 were tested for resistance to Indian pathotypes of leaf, stem and yellow rusts at seedling stage under controlled conditions. Eight Lr genes (Lr1, Lr3, Lr10, Lr13, Lr14a, Lr23, Lr24 and Lr26) were characterized based on differential interactions with specific rust races. Genes Lr23, Lr26 and Lr13 conferred leaf rust resistance in most of the accessions. Three Yr genes (YrA, Yr2 and Yr9) were inferred in 40 genotypes, where Yr2 followed by Yr9 were most frequent in conferring stripe rust resistance. Ten Sr genes, namely, Sr2, Sr5, Sr8a, Sr7b, Sr9b, Sr9e, Sr11, Sr13, Sr24 and Sr31, were postulated in these lines with predominance of Sr11, Sr31 and Sr2. These Lr, Sr and Yr genes were observed singly or in combination. Robust DNA markers were used to identify adult plant resistance genes Yr18/Lr34/Sr57, Lr68 and Sr2 and all stage resistance genes Lr24/Sr24, Sr28 and Yr9/Lr26/Sr31. STS marker iag95 showed pre...

Yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), is economically one of the most important diseases of wheat in India and worldwide. During four wheat-growing seasons (2015-19), a total of 951 yellow rust samples collected from farmers’ fields (n = 602) and trap plot nurseries (n = 349) were analyzed for virulence on 30 differentials. From this analysis, 11 distinct Pst pathotypes were identified. The virulence pattern of these pathotypes was also tested on 14 Avocet near-isogenic lines (NILs) and Avocet S. None of the pathotypes were virulent to Yr5, Yr10, Yr15, Yr16, Yr24, Yr32, and YrSP. Pathotype 46S119 (46E159) was most prevalent and widely distributed in all the areas and its overall frequency was maximum (56.2%) followed by 110S119 (110E159, 31.9%). However, the frequency of 46S119 has decreased gradually from 62.0% (2015-16) to 48.4% (2018-19). Pathotype 238S119 (238E159) being the most virulent among the identified pathotypes, was detected in 6.8% of samples. Each of the remaining pathotypes was identified in

The present study was conducted to transfer multiple rust resistance in a popular but rust susceptible wheat cultivar HS295. Selected derivatives WBM3632 and WBM3635 have been developed from a cross, HS295*2/FLW20//HS295*2/ FLW13 using bulk-pedigree method of breeding. Advance line WBM3697 selected from a breeding line WBM3532 was named as HS661. This line was evaluated for seedling resistance to a wide array of rust pathotypes and found to possess resistance to all the three rusts. HS661 was also tested under field conditions and showed adult plant resistance to leaf rust (AC1=0.6), stem rust (ACI=2.7) and strpe rust (AC1=3.8). Among 34 F3 lines, 28 were tested positive for SSR marker Xwmc221 indicating the presence of Lr19/Sr25. Out of 14 selected F4 lines from F3, nine were homozygous positive for Lr19/Sr25. The advanced breeding lines viz., WBM3632 (WBM3697) and WBM3635 were also positive for Lr19/Sr25 with SCAR marker SCS265512. SSR marker Xgwm1 producing 215 bp band in Avst-15, FLW13 and HS661 confirmed the presence of Yr15 . Agronomically, HS661 was comparable with recipient variety HS295 and superior to a standard check HS490 under late sown restricted irrigation production conditions of NHZ. HS661 may serve as a potential donor for creating new usable variability against all the three rusts.

Barley is an important coarse cereal, cultivated in Rabi season, particularly in the states of Uttar Pradesh, Rajasthan, Madhya Pradesh, Bihar, Punjab, Haryana, Himachal Pradesh and Jammu & Kashmir. Currently, it covers an area of about 0.66 million hectares under rainfed and irrigated crop. Seventy percent produce is used for cattle and poultry feed, 25% in industries for manufacturing malt and malt extracts and rest 5% for human consumption. The straw is also used for animal feed, bedding and to cover roofs of houses. Barley grains demand is increasing continuously because of its various uses and high nutritive value. Therefore, a substantial yield gain will be needed over the next several decades. A number of biotic and abiotic factors pose a challenge to increase production of barley. Barley diseases prominently rusts, net blotch, spot blotch, Septoria speckled leaf blotch, stripe disease, powdery mildew, barley yellow dwarf, and molya disease are the major biotic constraints in enhancing the barley grain production. Other diseases like black point and smuts, are important from the industrial point of view because these deteriorate the quality of malt and beer. This review seeks to provide an overview of different barley diseases and their management. Doi.org/10.25174/2249-4065/2018/83844

The rusts of wheat, caused by three species of Puccinia, are very devastating diseases and are major biotic constraints in efforts to sustain wheat production worldwide. Their capacity to spread aerially over long distances, rapid production of infectious uredospores, and abilities to evolve new pathotypes, makes the management of wheat pathogens a very challenging task. The development and deployment of resistant wheat varieties has proven to be the most economic, effective and efficient means of managing rust diseases. Rust resistance used in wheat improvement has included sources from the primary gene pool as well as from species distantly related to wheat. The 1BL/1RS translocation from cereal rye was used widely in wheat breeding, and for some time provided resistance to the wheat leaf rust, stripe rust, and stem rust pathogens conferred by genes Lr26, Yr9, and Sr31, respectively. However, the emergence of virulence for all three genes, and stripe rust resistance gene Yr27, has posed major threats to the cultivation of wheat globally. To overcome this threat, efforts are going on worldwide to monitor rust diseases, identify rust pathotypes, and to evaluate wheat germplasm for rust resistance. Anticipatory breeding and the responsible deployment of rust resistant cultivars have proven to be effective strategies to manage wheat rusts. Efforts are still however being made to decipher the recurrence of wheat rusts, their epidemiologies, and new genomic approaches are being used to break the yield barriers and manage biotic stresses such as the rusts. Efficient monitoring of pathotypes of Puccinia species on wheat, identification of resistance sources, pre-emptive breeding, and strategic deployment of rust resistant wheat cultivars have been the key factors to effective management of wheat rusts in India. The success in containing wheat rusts in India can be gauged by the fact that we had no wheat rust epiphytotic for nearly last five decades. This publication provides a comprehensive overview of the wheat rust research conducted in India.

Barley stripe rust is caused by Puccinia striiformis f.sp. hordei, (Psh), occurs worldwide, and is a major disease in South Asia. The aim of this work was to identify and estimate effects of loci underlying quantitative resistance to rust at seedling and adult plant stages. HI-AM panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program were screened at seedling and adult plant stages for resistance to Psh. Seedling resistance was evaluated with the five prevalent Psh races in India. Screening for the adult plant stage resistance was also performed in two different locations by inoculating with a mixture of the five races used for seedling screeing. The panel was genotyped using DaRT-Seq high-throughput genotyping platform. The genome-wide association mapping (GWAM) showed a total of 45 QTL located across the seven barley chromosomes for seedling resistance to the five races and 18 QTL for adult plant stage resistance. Common QTL for different races at seedling stage were found on all chromosomes except on chromosome 1H. Four common QTL associated with seedling and adult plant stage resistance were found on chromosomes 2, 5, and 6H. Moreover, one of the QTL located on the long arm of chromosome 5H showed stable effects across environments for adult plant stage resistance. Several QTL identified in this study were also reported before in bi-parental and association mapping populations studies validating current GWAM. However 15 new QTL were found at adult plant stage on all chromosomes except the 4H, explaining up to 36.79% of the variance. The promising QTL detected at both stages, once validated, can be used for MAS in Psh resistance breeding program globally.