stem rust

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Seedling resistance to stem rust races in Pakistani wheat landraces

Resistance has been an environmentally friendly and proven means of controlling stem rust for more than a century; the problem is that resistance has not been durable. A collection of 100 wheat landrace accessions from the Institute of Agri-Biotechnology and Genetic Resources, NARC-Islamabad, was tested at the seedling stage for response to 11 of Pgt races with multiple virulences, including TTKSK (from Kenya), TRTTF (Yemen), TTTTF (USA), and RRTTF (Pakistan). Six accessions were resistant (IT 0; to 2) to race TTKSK, 11 to race RRTTF, and 9 to races TRTTF and TTTTF. Further tests with US races QTHJC and TPMKC indicated that the majority of these landraces were susceptible. The resistant landraces could be used as donor parents in crossing programs to broaden the genetic base for stem rust resistance in Pakistani wheat varieties.

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International Maize and Wheat Improvement Center (CIMMYT) Pakistan Office
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Resistance to stem rust among synthetic hexaploid wheat genotypes in Iran

Resistance is an effective and economic method of controlling wheat stem rust provided the resistance gene(s) remains effective. We studied the stem rust responses of 372 synthetic hexaploid wheats (SHW) originally from CIMMYT under natural field infection conditions at Kelardasht, a stem rust hotspot. Stem rust severities were recorded using the modified Cobb scale prior to harvest ripeness. Seventy six and 17% of the genotypes (93% in total) were scored susceptible or moderately susceptible, whereas only 5 and 2% (7% in total) were moderately resistant or resistant, respectively. Based on our results, 26% of the genotypes were considered to have resistance, displaying field responses of 40MS to 20MSS. Those SHWs resistant to local Pgt races at Kelardasht could be used as sources of resistance in Iranian wheat breeding programs. Race analysis of Pgt isolates from the trials and seedling response tests on the entire SHW set are in progress.

Cereal Pathology Unit, Department of Cereal Research, Seed and Plant Improvement Institute (SPII), Iran
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Progress in simultaneous selection for stable, high yielding, rust resistant wheat genotypes for Kenya

In the past decade Pgt race Ug99 and its variants have been a challenge to wheat production in Kenya. Towards identifying suitable varieties, 37 lines selected from rust screening nurseries and 3 checks were tested for yield and adult plant reaction to natural stem rust epidemics across 11 diverse Kenyan environments in 2013 and 2014. Trial locations were chosen to mainly represent key wheat growing areas as well as three new sites. Evaluations based on the AMMI linear-bilinear model indicated significant (P≤0.01) genotype (G), environment (E), and GE interactions with the first three principal components (PC) explaining ~70% of the observed variation. With a contribution of over 90% to total sum of squares, environment was the predominant source of variation and the genotypic effect was approximately twofold higher than the GE effect. Based on biplot projections, clusters of lines were most closely associated with specific environments. Biplots also pointed to at least five environments, clearly those in traditional wheat growing areas that were highly correlated and associated with positive PC suggesting a similar ability to discriminate genotypes. Each non-traditional testing environment was associated with negative PC and was uncorrelated in its discriminatory ability. Combined yield and stability results achieved through classifying genotypes based on Shukla’s stability variance and Kang’s stability rating, revealed four genotypes (R1357, R1362, R1372, and R1374) as desirable candidates. The hitherto popular variety Robin, used as the ‘best check’ for yield, posted an at least 10% lower yield relative to the highest yielding genotype (R1357). Moreover, Robin which was released as a high yielding variety with adult plant resistance in 2009, was not stable in performance across environments, perhaps due its current susceptibility to a new Pgt race (TTKTT) within the race Ug99 group, that is virulent to the SrTmp-based resistance.

Kenya Agricultural and Livestock Research Organization, Kenya
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Genetic diversity among Puccinia graminis f. sp. secalis and winter rye populations

Rye stem rust (caused by Puccinia graminis f. sp. secalis, Pgs) causes considerable yield losses in rye crops grown in continental climates. In Germany, stem rust resistance in rye has attracted little attention until now. In order to implement resistance breeding, it is of utmost importance to (1) analyze Pgs populations in terms of diversity and pathotype distribution, and (2) identify resistance sources in winter rye populations. Within a three-year research project, we analyzed 389 single-pustule-isolates, collected mainly from German rye-growing areas, on 15 rye inbred differentials with different avirulence/virulence patterns; among them, 226 pathotypes were identified and only 56 occurred more than once. The majority of isolates infected 5-6 differentials. This high diversity was confirmed by a Simpson index of 0.99, a high Shannon index (5.27) and an evenness index of 0.97. In parallel, we investigated stem-rust resistance among and within 122 genetically heterogeneous rye populations originating from 19 countries across 3 to 15 environments (location-year combinations) in two replicates. While 7 German commercial rye populations were highly susceptible, 11 non-adapted populations, mainly from Russia, Austria and the USA, were highly resistant, harboring 32-70% resistant stems on plots averaged across 8 to 10 environments. Selections for low disease severity at the adult-plant stage in the field also displayed resistance in leaf-segment tests (r=0.86, P<0.01). In conclusion, rye stem rust pathogen populations are highly diverse and the majority of resistances in rye populations are race-specific. The new Pgs isolate set firstly developed within the project covers the current spectrum of virulences and can be used to assess the effectiveness of stem rust resistance genes or sources. New pathotypes can be detected using this differential set and farmers and industry can be alerted to circumvent economic damage. In the long term, resistances from non-adapted populations should be introgressed into commercial rye cultivars.

Julius Kuehn-Institut, Institute of Plant Protection in Field Crops and Grassland, Germany
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Genetic analysis and molecular mapping of resistance in barley to the heterologous rust pathogens Puccinia graminis f. sp. avenae and P. triticina

Stem rust is considered one of the most important threats to world cereal production. The appearance and spread of the wheat stem rust pathogen [Puccinia graminis f. sp. tritici (Pgt)] race Ug99 has caused great concern for global wheat production. Barley is a host to different specialized pathogen species such as Pgt, but is characteristically a near nonhost to most non-adapted (heterologous) rust pathogens such as the wheat leaf rust pathogen [P. triticina] and oat stem rust pathogen [P. graminis f. sp. avenae (Pga)]. The barley research line SusPtrit, developed for susceptibility to heterologous rust pathogens, is a useful resource to study the genetics of nonhost resistance and to clone the genes involved, particularly due to the recent availability of the genome sequence. Studies in wheat suggest that resistance genes that are effective against multiple rust pathogens (pleiotropic) such as Lr34/Yr18/Sr55, confer durable disease control. We intercrossed the sequenced barley genotype Morex with SusPtrit to determine the inheritance of resistance to the wheat leaf rust and oat stem rust pathogens. The F2 population segregated for a single dominant resistance gene in response to both heterologous pathogens Pga and Pt. Subsequent progeny testing and genetic analysis of the segregating F3 population will be performed to map and determine the relationship between the resistance genes. Large F2 populations were developed to fine map and clone the genes, and ultimately to transfer them into related crop species as an alternative approach for crop protection.

The University of Sydney, Plant Breeding Institute, Australia
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Utilizing a natural population of inter-specific barberry hybrids in New England to characterize the genetics of Puccinia graminis resistance in Berberis thunbergii

In the northeastern United States, outside the boundaries of the 20th century federal barberry eradication zone, both common barberry (Berberis vulgaris) and Japanese barberry (B. thunbergii) are found in great abundance, to the extent that both are considered invasive species. Much less common and relatively less studied is their interspecific hybrid, B. ×ottawensis, which has been produced in the ornamental horticultural industry but which also occurs naturally.  Since B. vulgaris is a competent host of Puccinia graminis and B. thunbergii is not, B. ×ottawensis presents a unique system for characterizing the genetic mechanism(s) underlying what appears to be non-host resistance to P. graminis in B. thunbergii. In this study, a natural population of about 1,000 individuals (mixed B. vulgaris, B. thunbergii, and B. ×ottawensis) in Sheffield, MA, was investigated. While wide morphological variation was observed among and within the populations of all three species at the site, the most pronounced variation was observed among B. ×ottawensis individuals. A subset of the population was selected for genotyping by sequencing (GBS) and evaluated for reaction to P. graminis via controlled inoculations. The response was found to segregate clearly among B. ×ottawensis individuals; and GBS was shown to be a viable means of generating molecular markers in these species, despite the lack of a reference genome. These results suggest that P. graminis resistance in B. thunbergii can be genetically mapped, and mapping populations are currently under development to accomplish this goal. The genomic resources developed in this work may facilitate both barberry surveillance efforts and ornamental barberry testing programs. Furthermore, knowledge of the genetics of response to P. graminis in the alternate host has the potential to inform efforts in breeding for stem rust resistance in wheat.

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Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, USA
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Mapping and verification of two QTL conferring adult plant resistance to Pgt race TTKSK (Ug99) and domestic U.S. races in the Ecuadorian wheat cv. Morocho Blanco

The durability of stem rust resistance in wheat varieties is strengthened by the use of polygenic, and broad-spectrum sources of resistance. Adult plant resistance (APR) was observed in the mid-20th century Ecuadorian bread wheat cv. Morocho Blanco (PI 286545) in field tests at Njoro, Kenya, and at St. Paul. Morocho Blanco was susceptible to races TTKSK, RCRSC and TPMKC at the seedling stage. A doubled haploid (DH) mapping population was created from a cross between Morocho Blanco and the susceptible line LMPG-6 to identify loci associated with APR phenotypes. Eighty-eight DH lines were genotyped with approximately 90,000 SNPs using a custom Infinium assay from Illumina. Sixty-seven additional DH lines were used to verify SNPs associated with reduced stem rust levels. Severity and infection type were assessed on adult plants at the stem rust screening facility in Kenya in 2013 and 2014, and in two single race nurseries inoculated with races RCRSC and TPMKC at St. Paul in 2014. Two identified and verified QTL reducing stem rust severity were located on chromosome arms 2BS and 6AS. The QTL on 6AS also reduced infection type at Njoro, but a similar reduction was not observed at St. Paul suggesting a genotype x environment or genotype x race interaction. The QTL on 2BS was associated with reduced stem rust severity at both Njoro and St. Paul. It is a strong candidate for use in breeding for APR to stem rust.

Department of Plant Pathology, University of Minnesota, USA
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Genetics of stem rust resistance in tetraploid wheats (Triticum turgidum ssp.)

Our research objective is to identify new resistance genes in cultivated and wild tetraploid wheats that are effective against race TTKSK and other Pgt races, and could be utilized in durum breeding. We characterized 7,000 durum and 360 emmer accessions for field resistance at Debre Zeit, Ethiopia, and Saint Paul, Minnesota. Accessions with resistant to moderately resistant responses in multiple field evaluations were characterized at the seedling stage for resistance to races TTKSK, TRTTF, TTTTF, JRCQC, TKTTF, and an additional six representative U.S. races. We identified 208 durum and 28 emmer accessions resistant to moderately resistant in all field and seedling evaluations. A search for resistance through seedling evaluations was also conducted on wild emmer (840 accessions) and four cultivated tetraploids (Persian, Polish, Oriental, and Pollard wheats, 560 accessions). About 20% of the accessions were resistant to race TTKSK. Thirty-six resistant accessions of cultivated and wild tetraploids were selected to investigate the genetics of TTKSK and TRTTF resistance. Results from evaluating F2 and F2:3 generations from biparental crosses revealed that resistance to race TTKSK in various subspecies of T. turgidum was conferred mostly by one or two genes with dominant and recessive actions. Additional resistance genes were identified when populations were evaluated against race TRTTF. A bulk segregant analysis approach is being used to map the resistance genes in selected resistant parents using the 90K SNP platform.

Department of Plant Pathology, University of Minnesota, USA
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SNP discovery and genotyping of wheat-Dasypyrum villosum disomic addition lines by genotyping-by-sequencing (GBS) to facilitate identification and introgression of novel stem rust resistance genes

Most accessions of Dasypyrum villosum (2n = 2x = 14), a tertiary gene pool of wheat, were resistant in previous tests with a collection of Pgt races, including TTKSK. In order to transfer novel resistance genes with minimum linkage drag into wheat, chromosome-specific markers linked to the resistance loci would be useful. However, the currently available SNP and sequence information for D. villosum is very limited. Hence, developing SNP markers and genotyping D. villosum will aid in transferring stem rust resistance genes to wheat. We used genotyping-by-sequencing (GBS) to sequence a complete set of Chinese Spring (CS)-D. villosum addition lines (1V#3 to 7V#3) as well as CS and several D. villosum accessions to map D. villosum SNPs on each chromosome. We have also produced TTKSK-resistant CS-D. villosum amphiploids using other D. villosum accessions assuming they could carry different stem rust resistance genes.

Department of Crop and Soil Sciences, Washington State University, USA
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Re-emergence of stem rust at epidemic levels in Argentina and Uruguay in 2014

Argentina and Uruguay are neighboring countries located in the same rust epidemiological area.  The last significant stem rust epidemic occurred in 1950. Since then, stem rust was frequently observed in experimental fields and off-season nurseries, but was mostly absent in commercial fields. During 2014, 4.6 million ha of wheat were grown, and there was a widespread incidence of stem rust, reaching levels of 80S on susceptible cultivars in both countries. Yield losses of 13 to 21% were estimated in experimental trials in Argentina. The epidemic was probably caused by the increasingly widespread cultivation of highly susceptible, but high yielding French cultivars during the last decade. In Argentina 42.3% of the commercial cultivars were susceptible to stem rust, and in Uruguay 23.0% were susceptible, 6.8% moderately susceptible and 20.3% were intermediate in reaction. However, the actual area sown to susceptible cultivars in Uruguay has continued to increase, from 22% of the wheat area in 2009 to 53.3% in 2014. Conductive weather conditions of high rainfall and warmer than average temperatures during the winter and spring, favored early infection. Cultivars with resistance genes Sr31 and Sr24 continue to be resistant in the region and are believed to be the most important genes currently providing resistance. Some Argentinean and Uruguayan cultivars that do not carry Sr31 and/or Sr24 were susceptible in 2011, but resistant in 2014, indicating a narrower range of virulence in 2014 compared to 2011. Both countries are working to improve resistance to local races and to the Ug99 race group. Disease modeling would be useful for understanding and predicting the occurrence and severity of this disease.

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National Institute of Agricultural Technology (INTA), Argentina
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