leaf rust

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Reactions of spring wheat genotypes in crossing block nursery to stem, leaf, and stripe rust

Rusts (Puccinia spp.) are the most significant disease affecting wheat yield and quality in Turkey. Knowing the resistance status of wheat genotypes in crossing program is an important issue for breeding programs. The aim of the study was to determine of the resistance of the 106 wheat genotypes consisting of Crossing Block Spring Wheat (CBSW) nursery developed by the International Winter Wheat Improved Project (IWWIP). For this purpose, adult plant and seedling test were conducted for yellow rust while only seedling test were conducted for leaf and stem rust. Evaluations were carried out at the research facilities of CRIFC at İkizce and Yenimahalle in Ankara in the 2014 season. For adult plant reactions; the genotypes were inoculated with local Pst populations (virulent on Yr2,6,7,8,9,25,27,Sd,Su,Avs). Stripe rust development on each entry were scored using the modified Cobb scale when the susceptible check Little Club had reached 80S infection severity in June, 2014. Coefficients of infections were calculated and values below 20 were considered to be resistant. For seedling test; the seedling was inoculated with local Pgt (avirulent on Sr24, Sr26, Sr27, and Sr31), Pt (avirulent on Lr9, Lr19, Lr24, and Lr28) and Pst populations. Stripe, leaf and stem rust development on each entry were scored after 14 days with 0-4 and 0-9 scale for leaf-stem rust and yellow rust, respectively. In seedling stage, thirty nine (37%), 47 (44%), and 20 (19%) genotypes were resistant to local Pgt, Pt, and Pst populations, respectively. In adult plant test, 46 (43%) genotypes were resistant to Pst.  The resistance genotypes to stem, leaf, and stripe rust were determined with this research.


The Central Research Institute for Field Crops, Turkey
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Identification of markers closely linked with adult plant leaf rust resistance gene Lr48 in wheat

Leaf rust is endemic to all wheat-growing regions of the world. Resistance to leaf rust in wheat cultivars is controlled either by all stage resistance (ASR) or by adult plant resistance (APR) genes. Although deployment of single ASR genes can provide high levels of resistance, these are usually overcome by virulence in pathogen populations. In contrast, individual APR genes often provide low levels of resistance and combinations of three to four genes are necessary to achieve adequate resistance for crop protection. This kind of APR has proven to be durable. APR gene Lr48 in a single plant selection of Condor (CSP44) was mapped on chromosome 2BS and was flanked by markers gwm429b (6.1 cM, distal) and barc7 (7.3 cM, proximal) (Bansal et al. 2008, Theor. Appl. Genet. 117:307-312). The present study was planned to identify markers more closely linked to Lr48. Selective genotyping by 90K Infinium Assay identified 27 SNP markers linked with Lr48. The SNP sequences were used to design Kompetitive Allele-Specific Primers (KASP). Eleven KASP markers showing clear clustering were genotyped on a RIL population using the CFX96 Touch™ real-time PCR detection system (Biorad, USA). KASP marker IWB72894 co-segregated with Lr48.

Vallence Nsabiyera
The University of Sydney, Plant Breeding Institute, Australia
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Monitoring the South African leaf rust population through a combined phenotyping and SSR genotyping approach

Leaf rust is a common wheat disease in South Africa. Annual surveys conducted by the Agricultural Research Council - Small Grain Institute (ARC-SGI) during the last 35 years used infection type (IT) data on a defined differential set to identify individual field isolates. Results from these surveys confirmed that the South African Pt population is affected by both local evolution and foreign introductions. A good correlation was found between avirulence/virulence phenotypes and simple sequence repeat (SSR) genotypes in the South African Pt population. We therefore evaluated whether identification of field isolates by SSR analysis would complement the traditional IT analysis using 47 field isolates collected during the 2013 growing season. Of the 39 phenotyped isolates, 35 were correctly genotyped while three were incorrectly genotyped only because the corresponding race was not included as a control. Five isolates that could not be phenotyped due to non-viable spores were successfully genotyped. The dominant race 3SA145 (North American race annotation CCPS) was represented by nine different genotypes sharing 82% genetic similarity. The SSR data further showed that the field isolates formed part of two distinct lineages with little admixture between them. This study confirmed the supporting value of SSR genotyping to traditional race analysis in monitoring the South African Pt population. 


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Department of Plant Sciences, University of the Free State, South Africa
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Determining the breeding value of CIMMYT’s International Bread Wheat Nursery (IBWSN) entries for leaf, stem and stripe rust resistance

The quest for durable rust resistance in wheat is burgeoning with the emergence of new virulent races. Breeders challenged with this unceasing plant-pathogen arms race have to devise strategies for effective evaluation and exploitation of the rust resistance genes. Considering the likely presence of useful variation for rust resistance in CIMMYT’s international bread wheat screening nurseries (IBWSN), we implemented genomic prediction in the 45th and 46th IBWSN entries to determine their genomic estimated breeding values (GEBV’s) for leaf, stem and stripe rust resistance. The 350 lines (45th IBWSN) and 329 lines (46th IBWSN) were phenotyped in replicated trials over two to three years in El Batan, Mexico (leaf rust); Njoro, Kenya (stem rust) and Toluca, Mexico (stripe rust). The filtered genotyping data for these two nurseries comprised of 6,786 and 11,218 genotyping by sequencing (GBS) markers. Our objective was to compare the GEBV’s estimated by four different models: multiple linear regression (MLR) with QTL-linked markers as fixed effects; Genomic-best linear unbiased prediction (G-BLUP); G-BLUP mixed model which includes QTL linked markers as fixed effects and Bayesian least absolute shrinkage and selection operator (LASSO). We observed that the prediction accuracies (calculated using 10-fold cross validation) were the highest for stripe rust (0.52 to 0.61), followed by stem rust (0.42 to 0.65) and leaf rust (0.15 to 0.45). Among the models, the MLR gave the lowest prediction accuracies (0.15,0.42 and 0.52), while G-BLUP (0.45,0.59 and 0.59), mixed G-BLUP (0.38,0.65 and 0.62) and the Bayesian LASSO (0.45,0.58 and 0.61) yielded relatively higher and almost similar accuracies. Overall, our results are promising and indicate that using genome-wide markers is advantageous than including only significant QTL-linked markers. We hope that implementing genomic prediction in breeding programs, would help to achieve rapid gains from selection and revolutionize our efforts in combating the rust pathogen.

Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, USA
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Utilizing biparental and association mapping techniques to identify leaf rust resistance in diverse wheat accessions

Leaf rust is common in wheat worldwide, consistently reducing yields by 5-15% or more.  Fungicides are applied to U.S. spring wheat to mitigate crop losses, but combinations of resistance genes can provide less expensive, effective control. We use biparental and association mapping approaches to identify resistance genes in two Minnesota varieties and 3,000 diverse global lines. Six populations developed from selected National Small Grains Collection lines were evaluated for seedling resistance, which has been mapped using bulk segregant analysis.  Two populations were developed to map adult plant resistance using recombinant inbred lines. Leveraging large association mapping panels can identify novel variants from the diverse NSGC lines.   The results will identify successful gene combinations underlying durable resistance and associated genetic markers. We will explore the utility of association mapping to identify leaf rust resistance genes and evaluate the global distribution of leaf rust resistance to inform worldwide wheat improvement.

Department of Agronomy and Plant Genetics, University of Minnesota, USA
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Current status of wheat rust and its management approaches in Nepal

Wheat is one of the three most important food crops of Nepal for which rusts (Puccinia triticina, P.striiformis and P.graminis) are major biotic stresses. Leaf rust is widespread and causes 14-20% yield losses and speculated that P.triticina over summer on self-sown wheat in hills of Nepal. Twenty two different pathotypes of P.triticina have been recorded while thirteen leaf rust resistant genes (Lr1, Lr3, Lr10, Lr13, Lr14a, Lr16, Lr17, Lr19, Lr23, Lr26, Lr27, Lr31 and Lr34) either singly or in combinations, impart resistance to wheat genotypes in Nepal. Yellow rust is also a major disease in mid and lower hills, river basin and valleys, causing 30-80 % grain yield losses. Twenty-nine pathotypes of P.striiformis have been recorded till now in Nepal while nine Yr genes (Yr2, Yr2 KSA, YrA, Yr6, Yr7, Yr9, Yr27, GA, and SU) have been postulated. Stem rust is a minor and sporadic disease in central, western, mid-western region late in the season. Nine Sr genes (Sr2, Sr5, Sr7b, Sr8, Sr8a, Sr9b, Sr11, Sr25 and Sr31) have been characterized. Vijay was the first Ug99 resistant wheat variety released for cultivation. Previous experiences show that Nepal served as a focal point of wheat rusts for further spread in the Gangetic plains of India due to presence of more than 25 species of Berberis in hills of Nepal. Efforts are underway to survey rusts infection on Berberis spp. Use of Tilt (Propiconazole), Triadimefon (Bayleton) and Indar (RH-124) was found effective to reduce leaf rust as well as foliar blight. Cultivation of resistant varieties in Nepal not only reduces rust severity in this country but also minimizes crop losses in other neighboring countries especially India. This demands the need for regional collaboration in South Asia to combat wheat rusts.

Plant Pathology Division, Nepal Agricultural Research Council (NARC), Nepal
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Wheat Gene Expression Differences Induced by Six Races of Puccinia triticina

Puccinia triticina, the causal agent of wheat leaf rust, is a devastating disease that can cause up to 40% yield loss. During fungal infection the host plant recognizes pathogen effectors, which trigger a host defense response. Changes in the pathogen effectors due to host selection pressure are responsible for the rapid development of new rust races and make durable resistance hard to obtain. The objectives of this study are to identify and characterize wheat genes that are utilized by races differently throughout infection and to understand functions of these genes using gene silencing. Six races of leaf rust were inoculated on a susceptible wheat variety and tissue was collected at six days post inoculation. RNA was sequenced and 63 wheat genes were identified that showed varying expression in response to the six races. 54 of these genes were evaluated in a time course study from zero days to six days post inoculation with the same six races. Real-time PCR was then used to analyze the timing of expression during early infection. The characterized genes have proposed functions involved in plant defense and stress, energy and metabolism, protein transport, replication, and RNA binding. Majority of the candidate genes showed three main expression patterns. However, race specific expression was found in three wheat genes that are affected by race shifts on Lr2A, Lr2C, and Lr17A. Sixteen potential susceptibility genes were also identified. Host susceptibility genes could be altered to provide durable resistance. RNAi was used to silence seven wheat genes to further understand their roles in leaf rust infection. T0 and T1 plants have been obtained and confirmed for the gene of interest. T2 plants were inoculated and observed for changes in susceptibility.

Department of Plant Pathology, Kansas State University, USA
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Durable rust resistance - Understanding “R” and “APR” in cereal hosts

Leaf rust is the most widely occurring disease of wheat worldwide. Resistance is the most practical and effective way to control the disease. Most leaf rust resistance genes are race-specific (“R”, qualitative resistance) and a relatively few are adult plant resistance genes, some of which have been described as slow rusting (“APR”, quantitative resistance). Due to limited knowledge, most resistance genes have been deployed in cultivars by an inefficient “blind” approach. This results in the well known “boom and bust cycle” (resistance followed by susceptibility) because the pathogen evolves rapidly and migrates over long distances. Therefore, a breeding-by-design approach is needed to achieve durable resistance. Pyramiding multiple R, APR or APR+R genes has been used successfully over many years to achieve durable resistance to leaf rust in Canada and some other countries. To further enhance this strategy we seek to understand the molecular mechanisms underlying key resistance genes. To identify the molecular mechanisms underlying rust resistance conferred by major R and APR genes, we performed an integrated systemic transcriptome analysis via RNA-seq on the Thatcher NILs with Lr16, Lr22a, Lr21, Lr34, Lr34+Lr16, and Lr67 challenged with Pt race BBBD. Sampling was conducted over a time series during the infection process of both seedlings and adult plants. Through RNA-seq we were able to capture the dynamic interactome of host-pathogen interactions conferred by these R and APR genes. Preliminary results revealed that resistance reactions conferred by R gene Lr21 and APR gene Lr67 were significantly different compared to other R and APR genes. Significantly, the Thatcher NIL line with Lr34+Lr16 showed the combines defense reactions of Lr16 and Lr34.     

National Research Council of Canada, Canada
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Association mapping for validation of genomic regions influencing adult plant resistance to leaf rust in Australian barley breeding germplasm

Elite barley breeding lines from the Australian Northern Region Barley Breeding Program were evaluated at the seedling and adult growth stages for resistance to leaf rust (LR) caused by Puccinia hordei. F3:5 lines derived from parental germplasm of different geographic origins were screened in the glasshouse and field spanning four years of trials. The 2009 and 2011 breeding populations (BP1 and BP2) comprised 360 lines and were genotyped with 3,244 polymorphic diversity arrays technology (DArT) markers. The 2012 and 2013 breeding populations (BP3 and BP4) comprised 320 lines genotyped with the DArT GBS array (DArTseq), providing 15,400 high quality polymorphic markers. Association mapping (AM) using the DArT/DArT-seq datasets and phenotypic data from 15 independent LR response assays identified a number of genomic regions associated with resistance. The BP1 and BP2 study detected a total of 15 QTL; 5 QTL co-located with catalogued LR resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, and Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. Markers in common between the DArT and DArTseq datasets enabled integration of mapping results for LR response across the four breeding populations and all QTL detected were visualised on a single map for validation. The adult plant resistance (APR) locus Rph20 was the only region detected in all field environments. Markers and their associated sequences identified in this study will be useful for building QTL combinations involving Rph20, thereby providing stable LR resistance in improved barley cultivars. We will also highlight the advantages of AM using breeding germplasm over traditional bi-parental mapping approaches that underutilise genetic diversity and divert valuable resources into populations of low breeding value.

The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Australia
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Genome-wide association mapping for wheat leaf rust resistance in Uruguay

Breeding for durable leaf rust resistance is a priority for our breeding programs; however, the availability of new resistance genes is a limiting factor. Two spring wheat populations totaling 186 lines derived from three resistant donors and two Uruguayan susceptible cultivars were used to detect genomic regions associated with seedling and field resistance to LR in Uruguay. AUDPC were recorded in three environments in the 2012 and 2013 cropping seasons, and seedling responses were determined using three Puccinia triticina races. The lines were also genotyped using GBS. A total of 5,222 SNP markers were used for genome-wide association analysis. Molecular markers were used to genotype APR genes Lr34 and Lr68. We identified 43 SNP markers significantly associated with seedling resistance and 19 for field resistance on chromosomes 1A, 1B, 1D, 2B, 2D, 3A, 4A, 5B, 6B, 7A, 7B and 7D. We confirmed the presence of Lr10 and Lr16 in seedling tests and Lr34 and Lr68 in field tests. Novel genomic regions were identified on chromosomes 4A associated with APR, and 5B associated with seedling resistance. These new resistance genes will be useful in breeding for durable LR resistance.

National Institute of Agricultural Research (INIA), La Estanzuela Experimental Station, Uruguay
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