Leaf rust is one of the most important diseases of wheat and is caused by Puccinia triticina, a highly variable rust pathogen prevalent worldwide. Decoding the genome of this pathogen will help in unraveling the molecular basis of its evolution and in the identification of genes responsible for its various biological functions. We generated high quality draft genome sequences (approximately 100- 106 Mb) of two races of P. triticina; the variable and virulent Race77 and the old, avirulent Race106. The genomes of races 77 and 106 had 33X and 27X coverage, respectively. We predicted 27678 and 26384 genes, with average lengths of 1,129 and 1,086 bases in races 77 and 106, respectively and found that the genomes consisted of 37.49% and 39.99% repetitive sequences. Genome wide comparative analysis revealed that Race77 differs substantially from Race106 with regard to segmental duplication (SD), repeat element, and SNP/InDel characteristics. Comparative analyses showed that Race 77 is a recent, highly variable and adapted Race compared with Race106. Further sequence analyses of 13 additional pathotypes of Race77 clearly differentiated the recent, active and virulent, from the older pathotypes. Average densities of 2.4 SNPs and 0.32 InDels per kb were obtained for all P. triticina pathotypes. Secretome analysis demonstrated that Race77 has more virulence factors than Race 106, which may be responsible for the greater degree of adaptation of this pathogen. We also found that genes under greater selection pressure were conserved in the genomes of both races, and may affect functions crucial for the higher levels of virulence factors in Race77. This study provides insights into the genome structure, genome organization, molecular basis of variation, and pathogenicity of P. triticina. The genome sequence data generated in this study have been submitted to public domain databases and will be an important resource for comparative genomics studies of the more than 4000 existing Puccinia species.

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000–32,000 sequence contigs (N50;7.4–9.2 kb), which accounted for ~86X–105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2–70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence. SNP analysis revealed that ~47% of the gene sets are affected by nonsynonymous mutations. The extracellular secreted (ES) proteins presumably are well conserved among the three pathotypes, and perhaps purifying selection has an important role in differentiating pathotype 46S 119 from pathotypes K and 31. In the present study, we decoded the genomes of three pathotypes, with 81% of the total annotated genes being successfully assigned functional roles. Besides the identification of secretory genes, genes essential for pathogen-host interactions shall prove this study as a huge genomic resource for the management of this disease using host resistance.

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.

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A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat–Triticum aestivum, T. durum and T. dicoccum were screened sequentially at multiple disease hotspots, during the 2011–14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.

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Wheat is an important cereal food crop providing key nutrients to humankind. Rusts are the most destructive pathogens of cereal crops, with the exception of rice, across the world and resistant cultivars have been widely employed to reduce the yield losses caused by them. The modern intensive monoculture of cultivars and changing climatic conditions has created congenial conditions for the emergence of new virulent races such as Ug99, which is a great concern for world food security. Conventional breeding efforts have not been effective in quickly developing new varieties with durable and broad‐spectrum resistance against the rapidly evolving rust pathogen races. However, in the last two decades, biotechnological methods such as marker‐assisted selection (MAS) and transgenic technology have provided novel strategies for enhancing resistance levels and durability in crop plants in a short span of time. Nevertheless, broad application of transgenics in agriculture is hindered by biosafety apprehensions. In recent years, improved versions of biotechnological breeding methods such as genomic selection, genome editing technologies, cisgenesis and intragenesis, RNA‐dependent DNA methylation (RdDM), agroinfiltration and reverse breeding are gaining popularity. These technologies provide a tremendous capability to manipulate crop plants more precisely than before and accelerate crop improvement efforts for sustained food production as well as overcoming safety concerns associated with food crops.

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