Stripe rust, caused by Puccinia striiformis f. sp. tritici, was observed on bread wheat (Triticum aestivum L.) lines previously considered to be resistant. Specifically, near isogenic lines (NIL) carrying the resistance genes Yr10, Yr24, and Yr26 at the CIMMYT-Toluca research station were observed to be infected with stripe rust in 2015. Several leaves exhibiting stripe rust uredinia and urediniospores were collected from field plots containing the Yr24 (MEX16.04) and Yr26 (MEX16.03) NILs. More than 20 pustules were isolated from the diseased leaves and inoculated onto 12-day-old wheat seedlings of cultivars Morocco and Avocet Yr24. Inoculated plants were incubated in a dew chamber with 100% relative humidity for 20 h in the dark, maintained between 7 and 10°C. After incubation, plants were moved to a greenhouse where each pot was isolated in its own compartment. Greenhouse temperature was maintained at 15 to 18°C, supplemented with 10,000 lx of fluorescent light for 8 h per day. Urediniospores representing each of 24 isolates were collected 12 days after inoculation and maintained at 4°C. Virulence spectra of each isolate were determined by inoculating 30 differential lines that contained known Yr resistance genes. Cultivars Moro (Yr10), Chuanmai 42, and Neimai 836 (Yr24) were also included. Infection types were recorded approximately 2 weeks postinoculation using a 0 to 9 scale (McNeal et al. 1971). A change in the infection types from 1 to 9 for wheat lines containing Yr10 and from 3 to 9 for Yr24 and Yr26 indicated that a mutation for virulence to Yr10 and Yr24 (= Yr26) occurred in a recently identified isolate accessioned and maintained at CIMMYT as MEX14.141. MEX14.141, among others, had caused a severe yellow rust epidemic during 2014 on Mexican cultivars Nana F2007 and Luminaria F2014 (Solis et al. 2016). One of the 20 isolates mentioned, designated as MEX16.04, has the following avirulence/virulence formula: Yr1, 5, 15, Sp/Yr2, 3, 6, 7, 8, 9, 10, (17), 24, 26, 27, 28, 31, 32. MEX16.04 is avirulent onto the most susceptible barley cultivar Kaputar, which allowed us to classify the isolate as P. striiformis f. sp. tritici instead of P. striiformis f. sp. hordei. MEX16.04 belongs to the aggressive race group first identified in North America in 2000 and which became predominant in subsequent years (Milus et al. 2009). Seedling tests using the above mentioned methodology on 12-day-old seedlings of 167 bread wheat, 508 durum, and 460 member set composed of synthetic hexaploid wheats with their respective durum parents from CIMMYT indicated that MEX16.04 does not represent a major threat since a majority of the lines remained resistant to this isolate. Moreover, I is not known to be present in CIMMYT bread wheat germplasm and I occurs in low frequency; however, I is present in combination with other effective gene(s) in durum wheat. Purified urediniospores of MEX16.03 and MEX16.04 isolates are stored in the CIMMYT and INIFAP yellow rust collections.
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Stripe rust is the most important disease of wheat in many wheat growing areas in Iran. Good knowledge of the genetic basis of resistance to stripe rust in commercial bread wheat cultivars and selected elite lines is an important objective in wheat breeding programs. This study aimed to identify resistance genes and modes of inheritance of stripe rust resistance in recently released Iranian commercial wheat cultivars (Aflak, Parsi, Sivand, Uroum, and Pishgam) and elite bread wheat lines (M-84-14 and M-83-6). Crosses were made between these cultivars and elite lines with Avocet S and the F1, F2, and F3 generations were developed. Two F3-derived families (one adult plant stage and one seedling stage), as well as parents and controls, were grown under field and greenhouse conditions and inoculated with stripe rust pathotypes 134E158 A+, 166E150 A+, and 6E150 A+, Yr27. The adult plant responses of parental cultivars Aflak, Uroum, Parsi, Pishgam, Sivand, and elite lines M-84-14 and M-83-6 to stripe rust in the field were 40 MR, 10R, 50 M, 10R, 50 MS, respectively, in 2011, and 60 MR, 5R, 40 MR, 30 MR, and 40 M, respectively, in 2013. Cultivars and elite lines were resistant to stripe rust at the seedling stage test. Avocet S was susceptible at both adult plant and seedling stages. In addition to the seedling resistance responses of the parents, frequencies of F3 lines for each of the crosses in both adult plant and seedling stages conformed well with those expected for segregating for a trait at two loci, indicating that all five cultivars and two elite lines carry two dominant seedling resistance genes that have so far been effective for controlling stripe rust in Iran.
Wheat is an important food security crop in central Asia but frequently suffers severe damage and yield losses from insect pests, pathogens, and weeds. With funding from the United States Agency for International Development, a team of scientists from three U.S. land-grant universities in collaboration with the International Center for Agricultural Research in Dry Areas and local institutions implemented an integrated pest management (IPM) demonstration program in three regions of Tajikistan from 2011 to 2014. An IPM package was developed and demonstrated in farmer fields using a combination of crop and pest management techniques including cultural practices, host plant resistance, biological control, and chemical approaches. The results from four years of demonstration/research indicated that the IPM package plots almost universally had lower pest abundance and damage and higher yields and were more profitable than the farmer practice plots. Wheat stripe rust infestation ranged from 30% to over 80% in farmer practice plots, while generally remaining below 10% in the IPM package plots. Overall yield varied among sites and years but was always at least 30% to as much as 69% greater in IPM package plots. More than 1,500 local farmers—40% women—were trained through farmer field schools and field days held at the IPM demonstration sites. In addition, students from local agricultural universities participated in on-site data collection. The IPM information generated by the project was widely disseminated to stakeholders through peer-reviewed scientific publications, bulletins and pamphlets in local languages, and via Tajik national television.
An isolate of the fungus Puccinia striiformis, causing yellow (stripe) rust on cereals and grasses, was selfed on the alternate (sexual) host, Berberis vulgaris. This enabled us to investigate genetic variability of progeny isolates within and among aecia. Nine aecial clusters each consisting of an aecium (single aecial cup) and nine clusters containing multiple aecial cups were selected from 18 B. vulgaris leaves. Aeciospores from each cluster were inoculated on susceptible wheat seedlings and 64 progeny isolates were recovered. Molecular genotyping using 37 simple sequence repeat markers confirmed the parental origin of all progeny isolates. Thirteen molecular markers, which were heterozygous in the parental isolate, were used to analyse genetic diversity within and among aecial cups. The 64 progeny isolates resulted in 22 unique recombinant multilocus genotypes and none of them were resampled in different aecial clusters. Isolates derived from a single cup were always of the same genotype whereas isolates originating from clusters containing up to nine aecial cups revealed one to three genotypes per cluster. These results implied that each aecium was the result of a successful fertilization in a corresponding pycnium and that an aecium consisted of genetically identical aeciospores probably multiplied via repetitive mitotic divisions. Furthermore, the results suggested that aecia within a cluster were the result of independent fertilization events often involving genetically different pycniospores. The application of molecular markers represented a major advance in comparison to previous studies depending on phenotypic responses on host plants. The study allowed significant conclusions about fundamental aspects of the biology and genetics of an important cereal rust fungus.
We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009–2015 revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales.
The widely effective and genetically linked rust resistance genes Yr47 and Lr52 have previously been mapped in the short arm of chromosome 5B in two F3 populations (Aus28183/Aus27229 and Aus28187/Aus27229). The Aus28183/Aus27229 F3 population was advanced to generate an F6 recombinant inbred line (RIL) population to identify markers closely linked with Yr47 and Lr52. Diverse genomic resources including flow-sorted chromosome survey sequence contigs representing the orthologous region in Brachypodium distachyon, the physical map of chromosome arm 5BS, expressed sequence tags (ESTs) located in the 5BS6-0.81-1.00 deletion bin and resistance gene analog contigs of chromosome arm 5BS were used to develop markers to saturate the target region. Selective genotyping was also performed using the iSelect 90 K Infinium wheat SNP assay. A set of SSR, STS, gene-based and SNP markers were developed and genotyped on the Aus28183/Aus27229 RIL population. Yr47 and Lr52 are genetically distinct genes that mapped 0.4 cM apart in the RIL population. The SSR marker sun180 co-segregated with Lr52 and mapped 0.4 cM distal to Yr47. In a high resolution mapping population of 600 F2 genotypes Yr47 and Lr52 mapped 0.2 cM apart and marker sun180 was placed 0.4 cM distal to Lr52. The amplification of a different sun180 amplicon (195 bp) than that linked with Yr47 and Lr52 (200 bp) in 204 diverse wheat genotypes demonstrated its robustness for marker-assisted selection of these genes.
This is the first genetic study reporting on the interaction and molecular mapping of resistance to the barley grass stripe rust pathogen (Puccinia striiformis f. sp. pseudo-hordei, Psph) in common wheat. Seedlings of 638 wheat accessions were tested and it was determined that wheat is a near-nonhost to Psph based on rare susceptibility observed in <2% of commercial cultivars and <5% of wheat landraces. As previously observed for P. striiformis f. sp. tritici (Pst), the Australian cultivar Teal was highly susceptible to Psph. In contrast, a selection of cv. Avocet carrying complementary resistance genes Yr73 and Yr74 (Avocet R; AvR) was resistant. The Teal × AvR (T/A) doubled haploid (DH) population was used to map resistance in AvR to Psph. Infection types on the T/A DH lines inoculated with Psph and Pst indicated that all DH lines carrying both Yr73 and Yr74 were also resistant to Psph; however, fewer DH lines were susceptible to Psph than expected, suggesting the resistance was more complex. QTL analysis using 9053 DArT-Seq markers determined that resistance to Psph was polygenically inherited and mapped to chromosomes 3A, 3D, 4A and 5B. The 3DL and 5BL markers co-located with Yr73 and Yr74, suggesting an overlap between host and non-host resistance mechanisms.
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.
Stripe rust (Puccinia striiformis Westend f. sp. tritici) is a devastating disease for wheat (Triticum aestivum L.) production worldwide. Yr5 is a race-specific resistance gene, effective to all races that have been identified in the United States. Therefore, it has been increasingly used for US cultivar development. The goal of this study was to identify and validate single-nucleotide polymorphism (SNP) markers tightly linked with Yr5, evaluate their usefulness with a diverse set of wheat materials, and dissect the Yr5 region to search for candidate genes using a comparative genomic approach. Competitive allele-specific polymerase chain reaction (KASP) markers based on Illumina iSelect 9000 SNP loci IWA6121 and IWA4096 were identified as flanking markers for Yr5 in two spring wheat recombinant inbred line populations that were developed from crosses between moderately susceptible line ‘WA8149’ and Yr5 donors ‘S0900317’ and ‘S0900163.’ These markers were closer to the gene than previously reported markers. Haplotype analysis based on loci of these KASP markers in a set of the Pacific Northwest spring and winter wheat lines and a worldwide spring wheat core collection showed that the combined haplotype for these markers is nearly diagnostic for the presence of Yr5. The Yr5-syntenic regions in Brachypodium and rice (Oryza sativa L.) contained a putative gene encoding a nucleotide binding site–leucine-rich repeat disease resistance protein. Wheat gene Traes_2BL_B5FC3BC9E showed high similarity with these Brachypodium and rice genes, and a marker designed from this gene was mapped closest to Yr5 in the recombinant inbred line populations. This study provides useful SNP markers for Yr5 in wheat breeding programs and resources for potential map-based cloning of Yr5.
Leaf rust and stripe rust are devastating wheat diseases, causing significant yield losses in many regions of the world. The use of resistant varieties is the most efficient way to protect wheat crops from these diseases. Sharon goatgrass (Aegilops sharonensis or AES), which is a diploid wild relative of wheat, exhibits a high frequency of leaf and stripe rust resistance. We used the resistant AES accession TH548 and induced homoeologous recombination by the ph1b allele to obtain resistant wheat recombinant lines carrying AES chromosome segments in the genetic background of the spring wheat cv. Galil. The gametocidal effect from AES was overcome by using an "anti-gametocidal" wheat mutant. These recombinant lines were found resistant to highly virulent races of the leaf and stripe rust pathogens in Israel and the United States. Molecular DArT analysis of the different recombinant lines revealed different lengths of AES segments on wheat chromosome 6B, which indicates the location of both resistance genes.