Wheat cultivation in many regions faces threats by devastating fungal infections. However, wheat cultivar 92R137 shows resistance to Puccinia striiformis infection. To isolate the stripe rust resistance gene Yr26, an integrated transcriptomic and comparative genomics approach was undertaken. Near-isogenic lines of wheat (carrying Yr26 or not) infected with two Puccinia striiformis f. sp. tritici (Pst) (Virulence or avirulence to Yr26) were analysed in a dual detailed time series RNA-seq study. The emerging IWGSC refseq v1.0 genome assembly sequence serves as a valuable template and was also used for comparative genomics studies of the gene candidate region with the genome sequences of close relatives and wheat progenitors. Using bulked segregant analysis (BSA) to identify polymorphic SNPs between parent and resistant DNA (R-bulk) and susceptible DNA (S-bulk), flanking markers for Yr26 were identified. These two markers were mapped to the Chinese spring reference genome sequence, spanning a region of about 250 kb. The synteny analysis of this candidate region in CS chr1B with chr1A, chr1D, Wild Emmer Wheat (Td_chr1A and Td_chr1B) and Barley (chr1H) identified three candidate Yr26 genes. To detect gene candidates a dual time series RNA-seq analysis was performed. Genes differently expressed between rust susceptible (NIL-S) host lines and rust resistant (NIL-R) lines, carrying the Yr26 candidate gene were analysed. Both lines were inoculated with Pst carrying different avirulence factors (Pst-CYR32 and Pst-V26), compatible or incompatible with the corresponding wheat lines. Differential gene expression analysis (DEG) between compatible and incompatible interaction revealed DEGs in the wheat genome and in the Pst genome. From a network analysis of both wheat and Pst genes, we inferred connected co-expressed modules. Resulting modules showed particular enrichments for disease resistance, defense response to fungus and cell wall components.
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Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat in western Canada. Although stripe rust was an issue in southern Alberta for many years, it became important in other parts of the country after a dramatic population shift in 2000, resulting from an invasive race. Sporadic epidemics of the disease are common and cause considerable loss, due to which, an intermediate level of resistance to stripe rust was required for new varietal registrations beginning 2017. Virulence surveys are of key importance in germplasm and cultivar development as they provide breeders and pathologists the information needed to better understand host-pathogen interactions and the effectiveness of Yr genes. Virulence characterization revealed a wide range of virulence phenotypes exhibited by 33 Pst races in western Canada, although only 2-3 races were predominant. The expression of Yr genes may differ between controlled conditions and natural field conditions as previously reported. Thus, stripe rust differentials and wheat cultivars grown in western Canada are also screened at multiple locations in every year. At present, all stage resistance genes Yr1, Yr4, Yr5, Yr15, Yr76, and YrSP are effective against the predominant Pst races, whereas at the adult stage under field conditions, Yr2, Yr17, Yr28, or those carried by Yamhill are also effective. Seedling resistance genes Yr7, Yr10, Yr17, or Yr27 were the most common in Canadian wheat cultivars. Of these, only Yr17 is effective under field conditions. Adult plant resistance genes Yr18 and Yr29 are carried by many cultivars, but are not effective under high disease pressure. The effectiveness of each resistance gene may vary between the eastern and western prairies of western Canada due to differences in virulence. Regular virulence surveys using contemporary and regional cultivars facilitate the development of rust resistant cultivars.
Yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici is the most devastating disease of bread wheat (Triticum aestivum) in the world. A wide range of virulent yellow rust pathotypes is evolving in different regions of the world causing the breakdown of widely utilized sources of resistance in wheat. Hence, the knowledge of virulence factors of pathogen and determining of effective resistance genes in the region will enable breeders to target those useful genes in their breeding programs. During cropping seasons of 2015-2016 and 2016-2017, virulence of the wheat yellow rust was investigated by planting differential cultivars and isogenic lines in a yellow rust trap nursery in Ardabil, northwest of Iran . Results showed stripe rust infections on some cultivars carrying Yr genes such as Yr1, Yr3, and Yrsp previously known to be resistant. The virulence spectrum of race population in Ardabil was identical to the Warrior race or its variants which is different from characterized races in Ardabil by carrying virulence combination for Yr1, Yr3, Yr17, Yr32, and YrSP and is avirulent on Yr8 and Yr27. Except for Yr8, Yr17 and Yr27, the common races in Ardabil are generally avirulent on Yr1, Yr3, and YrSP. This is the first report of race population in Ardabil (Iran) which is similar to the Warrior race or its variants.
In India, wheat crop is a major contributor to the agricultural economy of India, occupying 30.7 mha area with 98.38 mt production. Stripe or yellow rust is a constraint to wheat production on about 12.0 m ha in the Northern Hills and North Western region of India. Varieties resistant at the time of release become susceptible usually within a few years due to new pathogen races. The present study conducted in 2015-16 was undertaken to identify stripe rust resistant genotypes among a set of 146 advanced breeding lines and popular cultivars. All genotypes were planted in two replications in northern India at ten locations viz., Karnal, Hisar (Haryana), Ludhiana, Gurdaspur (Punjab), Malan, Bajoura, Dhaulakuan (Himachal Pradesh), Pantnagar (Uttarakhand), Durgapura (Rajasthan), Jammu (J & K) and Delhi. After every 20 genotypes, infector (susceptible cultivar to both pathotypes) was planted. All genotypes were inoculated with mixture of prevalent Pst races 78S84 (Yr 27 virulence) and 46S119 (Yr 9 virulence) at Karnal. Out of 58 released cultivars grown in different zones of the country, fifteen lines (HS 507, DBW 90, HD 3086, WH 1080, WH 1124, WH 1142, HD 4728, HI 8498, HI 8737, MPO 1215 (D), NIDW 295 (d), UAS 428 (D), UAS 446 (D), DBW 71, KRL 210) showed stripe rust ACI < 10.00 (average coefficient of infection). But among advance 88 wheat lines, there was good level of resistance in 50 lines (ACI <10.00). Lines having AUDPC values <20% of those of the susceptible checks (maximum AUDPC value 2500 on susceptible check) were considered to be slow rusters. In present study, some of the wheat varieties (DBW 93, HS 490, PBW 723, PBW 644, VL 829, VL 892, WH 1105, WR 544 ) grown at present in northern India were identified as slow ruster lines. The information generated can be utilized in improving the stripe rust resistance of popular cultivars.
Following the introduction of wheat stripe rust into Australia in 1979, an uncharacterized resistance (YrA) was identified in both Australian and International spring wheats. Genetic analyses of YrA indicated it was a pair of complementary genes, which were mapped to chromosomes 3DL and 5BL and designated Yr73 and Yr74, respectively. While selection Avocet 'R' carries both genes, selection Avocet 'S' carries Yr73 only. P. triticina pathotype (pt.) 104-1,2,3,(6),(7),11 +Lr37 ("104-VPM"), first detected in Australia in 2002, most likely arose via mutation from pt. 104-1,2,3,(6),(7),11 ("104"), with added virulence for Lr37. Interestingly, while both pathotypes are avirulent on Lr13, 104-VPM shows a much lower Infection Type (IT, ";1") than pt. 104 ("X++3") on several genotypes carrying Lr13 (e.g.Avocet 'R', Avocet 'S'). Other Lr13 genotypes (e.g. cv. Hereward) respond similarly to both pts ("X++3"). Genetic analyses of 4 doubled haploid (DH) populations based on intercrosses between Avocet 'R' and genotypes lacking Lr13 segregated in a 1:7 ratio to pt. 104-VPM (";1" : all other ITs). Two populations fixed for Lr13 (viz. Hereward/ Avocet 'R' and Estica/Avocet 'R') segregated 1:3 to pt. 104-VPM (";1" : all other ITs). This segregation pattern fitted a model where two complementary genes interact with Lr13 to generate the low (IT ";1") IT. Mapping of a Teal/Avocet 'R' DH population using 92 lines and 9,035 DArT-Seq markers identified three QTLs: chromosome 2BS (Lr13); chromosome 3DL (co-located with Yr73); chromosome 1DS. These results suggest that Yr73 acts in a complementary manner with a gene on chromosome 1DS to confer leaf rust resistance (IT "X"), and that these complementary genes are additive with Lr13. It appears that Yr73 is a modifier of two independent genes in wheat, one conferring resistance to stripe rust (Yr74 on chromosome 5BL), and one conferring resistance to leaf rust (LrAv on chromosome 1DS).
Wheat rusts, notably yellow rust, are amongst the most damaging diseases on wheat in Morocco. The objective of this survey was to assess the incidence and severity of wheat rust diseases across Morocco. The survey was carried out during April-May 2017 where growth stage of wheat ranged from anthesis to physiological maturity. The severity and response rating for the adult plant field reaction to rusts were based on the modified Cobb scale. A total of 117 bread wheat fields were inspected. The survey revealed that the most prevalent disease was yellow rust (96 out of 117 fields). Leaf rust, SLD (Septoria Like Diseases) and to some extent root rot complex were less prevalent. Leaf rust was only observed in 8 out of 117 inspected fields and exhibited low severity. Stem rust was observed in only one field. Following the drought of 2016, the 2017 growing season was an epidemic year for yellow rust in Morocco. It was detected across all regions and 50% of inspected fields were highly infected. Those that were lightly or not infected were sprayed with fungicides up to two times. Almost all commercial bread wheat cultivars in Morocco are highly susceptible to yellow rust. Appearance of new virulent races is leading to the breakdown of resistance in major cultivars e.g., Arrihan, which had very few pustules of yellow rust in 2013 was highly susceptible in the last three years. Samples of yellow rust from 2016 revealed a new virulent race in all samples, temporarily designated Pst (new) [virulence pattern: [Yr-,2,3,-,-,6,7,8,9,-,-,17,-,25,-,32,Sp,AvS,-]. Thirty-four samples submitted to GRRC in 2017 were all of the same genotype, identical to the new race already detected in 2016. The results demonstrate that surveillance and genotyping/race phenotyping of samples may be important for early-warning and anticipatory breeding strategies.
Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is one of the most important pathogens of wheat. Attempts have been made in the past to characterize the worldwide genetic structure of Pst populations, excluding Canada. Characterization of 59 isolates identified 33 races with three most common races representing half of the population and subtle differences in races of eastern and western prairies. For molecular characterization, 48 isolates were sequenced to obtain SNPs and genotyped with Pst-specific SSR markers. Isolates that were suspected of recombination based on SNP data were examined for their telia production ability as a proxy for sexual recombination. The study revealed that the majority of the population was clonal, however, not exclusively clonal, with the existence of four genetic lineages. Two lineages previously reported were identified: PstS0, representing an old northwestern-European and PstS1, an invasive warmer-temperature adapted lineage. Additionally, two new lineages, PstPr and PstS1-related, were detected that have not been reported previously. The PstPr and PstS1-related lineages produced more telia than the other lineages and had double the number of unique recombination events compared to PstS0 and PstS1. PstPr was concluded to be a sexual recombinant and an exotic incursion, which was closely associated with PstS5, PstS7 (Warrior), and PstS8 (Kranich) lineages, all of which arose by sexual recombination in the center of diversity - the Himalayan region. The total phenotypic variation in the population could not be explained solely by molecular genotypes, and a hypothesis on existence of epigenetic machinery in the Pst genome was tested. Homologs of the DNMTases class (DNMT1) were identified, providing compelling evidence of a role for DNA methylation. As a first report of DNA methylation, an average of ~5%, 5-methyl cytosine (5-hmC) in the Puccinia epigenome indicated the possibility of epigenetic regulation, which merits further investigation.
Stripe (yellow) rust, caused by the fungus Puccinia striiformis f. sp. tritici (PST), is a major global wheat disease. New PST strains that show higher infection rates and rapid adaptation to less favourable environmental conditions have been observed over the last 15 years. It has also continued to spread to areas where it was not previously recorded. In South Africa, stripe rust was first detected in 1996. In subsequent years three more PST races were observed, with what seemed to be a step-wise virulence gain. A better understanding of the South African PST pathotypes and how they fit in the global context is needed. We aimed to address this by sequencing the genomes of four historical PST isolates displaying the four distinct virulence profiles. This allowed us to characterise the genetic diversity between these stripe rust races and develop diagnostic markers to easily genotype current detections. We also placed the South African PST isolates in context with global PST isolates where sequence data was available. This analysis illustrates that the South African PST races are more closely related to PST from other African countries when compared to isolates from Africa, Europe and Asia. Through pairwise comparison of isolates, we identified 27 candidate effector genes showing specific polymorphisms between the four isolates that could be related to their distinct virulence profiles. We are currently undertaking gene expression profiling of these candidates to determine if these effectors are specifically upregulated during infection–a key characteristic of effector genes. This study has shed new light on the potential origin and adaptation of stripe rust in South Africa and provides tools for rapid genotypic classification of infections in the field.
We will present an update on the BBSRC-funded SCPRID project “Maximizing the potential for sustainable and durable resistance to the wheat yellow rust pathogen”. This aims to understand the molecular basis of Puccinia striiformis f. sp. tritici (PST) pathogenicity and exploit this information to design effective breeding strategies that maximize the potential for durable disease resistance in the field. We have established a PST genomics platform through sequencing of PST genomes (UK, European, African, and Indian races) and analysis of expression time courses during infection (Cantu et al 2013). Using this platform we have characterised the PST effector complement, identified putative candidates and have begun their validation. The latest results of this will be presented. We have also evaluated a collection of hexaploid wheat landraces for resistance to PST across continents and have initiated single seed descent mapping populations and initial characterisation in F2:3 populations. We will exemplify the use of new genomic technologies to develop closely linked markers to enable deployment of resistance loci in breeding programmes (Ramirez-Gonzalez et al 2014). We will also provide an update of a new technique, called Field Pathogenomics (Hubbard et al 2015). This method uses transcriptome sequencing of PST-infected wheat leaves to describe pathogen diversity and also identify the host variety. This analysis uncovered a dramatic shift in the PST population in the UK and suggests a recent introduction of a diverse set of exotic PST lineages that may have displaced previous PST populations.
Recent events in worldwide populations of the fungal pathogen Puccinnia striiformis, which causes the yellow rust disease on wheat and other cereals, have suggested that other factors than shifts in virulence can lead to epidemic events. For instance, the spread of two strains across four continents that has occurred within the last 10-15 years seems to be a result of high temperature adaptation combined with a relatively short latent period (Hovmøller et al. 2008; Milus et al. 2009). Variation for quantitative traits like latent period has often been hypothesized to play a significant role in population shift but only very few experimental data have been generated. Here we report difference for components of aggressiveness which included latent period and lesion growth for 17 isolates derived from a selfing of an aggressive isolate using Berberis vulgaris. A group of offspring isolates had a significantly longer latent period and higher lesion growth than the parental isolate. Interestingly, the two traits were found to be positively correlated where a long latent period was correlated with a higher lesion growth rate. This may suggest a trade-off between latent period and lesion growth. All isolates were assessed on seedlings of two highly susceptible host varieties and the two hosts gave similar results. In a previous study the progeny isolates showed segregation for virulence/avirulence and SSR markers (Rodriguez-Algaba et al. 2014). In conclusion, this study demonstrates genetically inheritable variability for latent period and lesion growth in P. striiformis, even within a single parental isolate. The results contribute to a better understanding of the ability of P. striiformis to adapt to new host varieties and changing environments at the quantitative level.