Literature Results

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Identification and characterization of Sr13, a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group

The Puccinia graminis f. sp. tritici (Pgt) Ug99 race group is virulent to most stem rust resistance genes currently deployed in wheat and poses a threat to global wheat production. The durum wheat (Triticum turgidum ssp. durum) gene Sr13 confers resistance to Ug99 and other virulent races, and is more effective at high temperatures. Using map-based cloning, we delimited a candidate region including two linked genes encoding coiled-coil nucleotide-binding leucine-rich repeat proteins designated CNL3 and CNL13. Three independent truncation mutations identified in each of these genes demonstrated that only CNL13 was required for Ug99 resistance. Transformation of an 8-kb genomic sequence including CNL13 into the susceptible wheat variety Fielder was sufficient to confer resistance to Ug99, confirming that CNL13 is Sr13. CNL13 transcripts were slightly down-regulated 2–6 days after Pgt inoculation and were not affected by temperature. By contrast, six pathogenesis-related (PR) genes were up-regulated at high temperatures only when both Sr13 and Pgt were present, suggesting that they may contribute to the high temperature resistance mechanism. We identified three Sr13-resistant haplotypes, which were present in one-third of cultivated emmer and durum wheats but absent in most tested common wheats (Triticum aestivum). These results suggest that Sr13 can be used to improve Ug99 resistance in a large proportion of modern wheat cultivars. To accelerate its deployment, we developed a diagnostic marker for Sr13. The identification of Sr13 expands the number of Pgt-resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.

Wenjun Zhang, Shisheng Chen, Zewdie Abate, Jayaveeramuthu Nirmala, Matthew N. Rouse, Jorge Dubcovsky

Proceedings of the National Academy of Sciences (US) · 2017

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Large-Scale Atmospheric Dispersal Simulations Identify Likely Airborne Incursion Routes of Wheat Stem Rust Into Ethiopia

In recent years, severe wheat stem rust epidemics hit Ethiopia, sub-Saharan Africa’s largest wheat-producing country. These were caused by race TKTTF (Digalu race) of the pathogen Puccinia graminis f. sp. tritici, which, in Ethiopia, was first detected at the beginning of August 2012. We use the incursion of this new pathogen race as a case study to determine likely airborne origins of fungal spores on regional and continental scales by means of a Lagrangian particle dispersion model (LPDM). Two different techniques, LPDM simulations forward and backward in time, are compared. The effects of release altitudes in time-backward simulations and P. graminis f. sp. tritici urediniospore viability functions in time-forward simulations are analyzed. Results suggest Yemen as the most likely origin but, also, point to other possible sources in the Middle East and the East African Rift Valley. This is plausible in light of available field surveys and phylogenetic data on TKTTF isolates from Ethiopia and other countries. Independent of the case involving TKTTF, we assess long-term dispersal trends (>10 years) to obtain quantitative estimates of the risk of exotic P. graminis f. sp. tritici spore transport (of any race) into Ethiopia for different ‘what-if’ scenarios of disease outbreaks in potential source countries in different months of the wheat season.

M. Meyer, L. Burgin, M. C. Hort, D. P. Hodson, and C. A. Gilligan

Phytopathology · Volume 107 · Issue 10 · 2017

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Identification and characterization of Sr13, a tetraploid wheat gene that confers resistance to the Ug99 stem rust race group

The Puccinia graminis f. sp. tritici (Pgt) Ug99 race group is virulent to most stem rust resistance genes currently deployed in wheat and poses a threat to global wheat production. The durum wheat (Triticum turgidum ssp. durum) gene Sr13 confers resistance to Ug99 and other virulent races, and is more effective at high temperatures. Using map-based cloning, we delimited a candidate region including two linked genes encoding coiled-coil nucleotide-binding leucine-rich repeat proteins designated CNL3 and CNL13. Three independent truncation mutations identified in each of these genes demonstrated that only CNL13 was required for Ug99 resistance. Transformation of an 8-kb genomic sequence including CNL13 into the susceptible wheat variety Fielder was sufficient to confer resistance to Ug99, confirming that CNL13 is Sr13. CNL13 transcripts were slightly down-regulated 2–6 days after Pgt inoculation and were not affected by temperature. By contrast, six pathogenesis-related (PR) genes were up-regulated at high temperatures only when both Sr13 and Pgt were present, suggesting that they may contribute to the high temperature resistance mechanism. We identified three Sr13-resistant haplotypes, which were present in one-third of cultivated emmer and durum wheats but absent in most tested common wheats (Triticum aestivum). These results suggest that Sr13 can be used to improve Ug99 resistance in a large proportion of modern wheat cultivars. To accelerate its deployment, we developed a diagnostic marker for Sr13. The identification of Sr13 expands the number of Pgt-resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.

Wenjun Zhanga, Shisheng Chena, Zewdie Abate, Jayaveeramuthu Nirmala, Matthew N. Rouse, Jorge Dubcovsky

Proceedings of the National Academy of Sciences (US) · Volume 114 · Issue 45 · 2017

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Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

Three members of the Puccinia genus, P. triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; by comparison repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst (5.97 SNPs/kb) nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt. Of 1,358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host induced gene silencing of the HD and STE3 alleles reduced wheat host infection.

Christina A. Cuomo, Guus Bakkeren, Hala Badr Khalil, Vinay Panwar, David Joly, Rob Linning, Sharadha Sakthikumar, Xiao Song, Xian Adiconis, Lin Fan, Jonathan M. Goldberg, Joshua Z. Levin, Sarah Young, Qiandong Zeng, Yehoshua Anikster, Myron Bruce, Meinan Wang, Chuntao Yin, Brent McCallum, Les J. Szabo, Scot Hulbert, Xiaming Chen, John P. Fellers

G3 · Volume 7 · Issue 2 · 2017

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Identification and validation of single nucleotide polymorphic markers linked to Ug99 stem rust resistance in spring wheat

Wheat stem rust (Puccinia graminis f. sp. tritici Eriks. and E. Henn.) is one of the most destructive diseases world-wide. Races belonging to Ug99 (or TTKSK) continue to cause crop losses in East Africa and threaten global wheat production. Developing and deploying wheat varieties with multiple race-specific genes or complex adult plant resistance is necessary to achieve durability. In the present study, we applied genome-wide association studies (GWAS) for identifying loci associated with the Ug99 stem rust resistance (SR) in a panel of wheat lines developed at the International Maize and Wheat Improvement Center (CIMMYT). Genotyping was carried out using the wheat 9K iSelect single nucleotide polymorphism (SNP) chip. Phenotyping was done in the field in Kenya by infection of Puccinia graminis f. sp. tritici race TTKST, the Sr24-virulent variant of Ug99. Marker-trait association identified 12 SNP markers significantly associated with resistance. Among them, 7 were mapped on five chromosomes. Markers located on chromosomes 4A and 4B overlapped with the location of the Ug99 resistance genes SrND643 and Sr37, respectively. Markers identified on 7DL were collocated with Sr25. Additional significant markers were located in the regions where no Sr gene has been reported. The chromosome location for five of the SNP markers was unknown. A BLASTN search of the NCBI database using the flanking sequences of the SNPs associated with Ug99 resistance revealed that several markers were linked to plant disease resistance analogues, while others were linked to regulatory factors or metabolic enzymes. A KASP (Kompetitive Allele Specific PCR) assay was used for validating six marker loci linked to genes with resistance to Ug99. Of those, four co-segregated with the Sr25-pathotypes while the rest identified unknown resistance genes. With further investigation, these markers can be used for marker-assisted selection in breeding for Ug99 stem rust resistance in wheat.

Long-Xi Yu, Shiaoman Chao, Ravi P. Singh, Mark E. Sorrells

PLoS One · 2017

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Speed breeding for multiple disease resistance in barley

To respond faster to the changing climate, evolving pathogens and to feed a global population of 9–10 billion by 2050, plant breeders are exploring more efficient crop improvement strategies. In this study, we applied novel methodology for rapid trait introgression to the European two-rowed barley cultivar Scarlett. Scarlett is widely-grown in Argentina and is preferred for malting and brewing, yet lacks adequate disease resistance. We used four donor lines combining multiple disease resistance (i.e. leaf rust, net and spot forms of net blotch and spot blotch) in a modified backcross strategy, which incorporated both multi-trait phenotypic screens and the rapid generation advance technology ‘speed breeding’, to develop 87 BC1F3:4 Scarlett introgression lines (ILs) within two years. Phenotyping this set of lines in disease nurseries located in Australia and Uruguay revealed the ILs had high levels of multiple disease resistance. Preliminary yield testing of the 12 most promising ILs in Argentina identified three ILs that were significantly higher yielding than Scarlett at Balcarce, whereas all 12 ILs displayed yield equivalent to Scarlett at Tres Arroyos. We propose that this approach is useful to rapidly transfer genes for multiple target traits into adapted cereal cultivars or pyramiding desirable traits in elite breeding material.

Lee T. Hickey, Silvia E. Germán, Silvia A. Pereyra, Juan E. Diaz, Laura A. Ziems, Ryan A. Fowler, Greg J. Platz, Jerome D. Franckowiak, Mark J. Dieters

Euphytica · Volume 213 · Issue 64 · 2017

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Mining Vavilov’s Treasure Chest of Wheat Diversity for Adult Plant Resistance to Puccinia triticina

Leaf rust (LR) caused by Puccinia triticina, is among the most important diseases of wheat (Triticum aestivum L.) crops globally. Deployment of cultivars incorporating genetic resistance, such as adult plant resistance (APR) or all-stage resistance, is considered the most sustainable control method. APR is preferred for durability because it places lower selection pressure on the pathogen and is often polygenic. In the search for new sources of APR, here we explored a diversity panel sourced from the N. I. Vavilov Institute of Plant Genetic Resources. Based on DNA marker screening, 83 of the 300 lines were deemed to carry known APR genes; namely, Lr34, Lr46, and Lr67. Interestingly, lines carrying Lr67 were mostly landraces from India and Pakistan, reconfirming the likely origin of the gene. Rapid phenotypic screening using a method that integrates assessment at both seedling and adult growth stages under accelerated growth conditions (i.e., constant light and controlled temperature) identified 50 lines carrying APR. Levels of APR corresponded well with phenotypes obtained in a field nursery inoculated using the same pathotype (R2 = 0.82). The second year of field testing, using a mixture of pathotypes with additional virulence for race-specific APR genes (Lr13 and Lr37), identified a subset of 13 lines that consistently displayed high levels of APR across years and pathotypes. These lines provide useful sources of resistance for future research. A strategy combining rapid generation advance coupled with phenotyping under controlled conditions could accelerate introgression of these potentially novel alleles into adapted genetic backgrounds.

Riaz, A.; Athiyannan, N.; Periyannan, S.; Afanasenko, O.; Mitrofanova, O.; Aitken, E. A. B.; Lagudah, E.; Hickey, L. T.

Plant Disease · Volume 101 · Issue 2 · 2017

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Genetic mapping of stem rust resistance to Puccinia graminis f. sp. tritici race TRTTF in the Canadian wheat cultivar harvest

Stem rust, caused by Puccinia graminis f. sp. tritici, is a destructive disease of wheat that can be controlled by deploying effective stem rust resistance (Sr) genes. Highly virulent races of P. graminis f. sp. tritici in Africa have been detected and characterized. These include race TRTTF and the Ug99 group of races such as TTKSK. Several Canadian and U.S. spring wheat cultivars, including the widely grown Canadian cultivar ‘Harvest’, are resistant to TRTTF. However, the genetic basis of resistance to TRTTF in Canadian and U.S. spring wheat cultivars is unknown. The objectives of this study were to determine the number of Sr genes involved in TRTTF resistance in Harvest, genetically map the resistance with DNA markers, and use markers to assess the distribution of that resistance in a panel of Canadian cultivars. A doubled haploid (DH) population was produced from the cross LMPG-6S/Harvest. The DH population was tested with race TRTTF at the seedling stage. Of 92 DH progeny evaluated, 46 were resistant and 46 were susceptible which perfectly fit a 1:1 ratio indicating a single Sr gene was responsible for conferring resistance to TRTTF in Harvest. Mapping with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers placed the resistance gene distally on the chromosome 6AS genetic map, which corresponded to the location reported for Sr8. SSR marker gwm459 and 30 cosegregating SNP markers showed the closest linkage, mapping 2.2 cM proximal to the Sr gene. Gene Sr8a confers resistance to TRTTF and may account for the resistance in Harvest. Testing a panel of Canadian wheat cultivars with four SNP markers closely linked to resistance to TRTTF suggested that the resistance present in Harvest is present in many Canadian cultivars. Two of these SNP markers were also predictive of TRTTF resistance in a panel of 241 spring wheat lines from the United States, Canada, and Mexico.

Hiebert, C. W.; Rouse, M. N.; Jayaveeramuthu Nirmala; Fetch, T.

Phytopathology · Volume 107 · Issue 2 · 2017

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Highly predictive SNP markers for efficient selection of the wheat leaf rust resistance gene Lr16

Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Lr16 was previously mapped to the telomeric region of the short arm of wheat chromosome 2B. The goals of this study were to develop numerous single nucleotide polymorphism (SNP) markers for the Lr16 region and identify diagnostic gene-specific SNP marker assays for marker-assisted selection (MAS).

Kassa, M. T.; You, F. M.; Hiebert, C. W.; Pozniak, C. J.; Fobert, P. R.; Sharpe, A. G.; Menzies, J. G.; Humphreys, D. G.; Harrison, N. R.; Fellers, J. P.; McCallum, B. D.; McCartney, C. A.

BMC Plant Biology · Volume 17 · Issue 45 · 2017

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Farmers' perceptions on improved bread wheat varieties and formal seed supply in Ethiopia

The paper presents smallholder farmers' perceptions on attributes of bread wheat varieties based on primary data collected from 524 households in four major wheat growing areas of Ethiopia. The results indicated high value of attainment indices for improved varieties compared to landraces, which shows how the demanded attributes are embodied more in improved ones. Grain yield and yellow and stem rust resistance are attributes that are desired most compared to others. However, there is high variability in attainment indices among improved varieties for the different attributes, which suggests the need to target varieties for the different environments including disease and drought tolerance. The results also showed inconsistency between the value of attainment indices of varieties and the amount of seed supplied by the formal sector, which resulted in mismatch between demand and supply leading to considerable carryover seed. The formal sector needs to consider diversifying its bread wheat varietal portfolio and increase its capacity for seed supply to respond to emerging challenges and effectively address farmers' preferences.

Bishaw, Z.; Alemu, D.

International Journal of Plant Production · Volume 11 · Issue 1 · 2017

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