Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations ...under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR).
Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype.
The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.
Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their ...lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
Wheat is one of the most important staple foods on earth. Leaf rust, stem rust and stripe rust, caused by
Puccini triticina
,
Puccinia
f. sp.
graminis
and
Puccinia
f. sp.
striiformis
, respectively, ...continue to threaten wheat production worldwide. Utilization of resistant cultivars is the most effective and chemical-free strategy to control rust diseases. Convectional and molecular biology techniques identified more than 200 resistance genes and their associated markers from common wheat and wheat wild relatives, which can be used by breeders in resistance breeding programmes. However, there is continuous emergence of new races of rust pathogens with novel degrees of virulence, thus rendering wheat resistance genes ineffective. An integration of genomic selection, genome editing, molecular breeding and marker-assisted selection, and phenotypic evaluations is required in developing high quality wheat varieties with resistance to multiple pathogens. Although host genotype resistance and application of fungicides are the most generally utilized approaches for controlling wheat rusts, effective agronomic methods are required to reduce disease management costs and increase wheat production sustainability. This review gives a critical overview of the current knowledge of rust resistance, particularly race-specific and non-race specific resistance, the role of pathogenesis-related proteins, non-coding RNAs, and transcription factors in rust resistance, and the molecular basis of interactions between wheat and rust pathogens. It will also discuss the new advances on how integrated rust management methods can assist in developing more durable resistant cultivars in these pathosystems.
•Thekopsora areolata incidence varied greatly among years in Finnish Norway spruce seed orchards.•Amount of rainfall in May-June explained the annual T. areolata incidences on Prunus padus.•Rainfall, ...temperature, time and their interactions were significant variables in a disease model.•To control T. areolata the number of overwintering diseased Prunus leaves should be minimized.•Control of C. pirolata should concentrate on Pyrola in early May and on P. abies in late May.
Cone rusts Thekopsora areolata and Chrysomyxa pirolata are widely distributed in northern hemisphere. In Fennoscandia, these rusts cause severe damage and great economical losses especially in seed orchards specialized to produce high quality seeds. The aim of this study was to investigate sporulation of cone rusts and factors affecting epidemics to develop new control practices against these rusts. Natural sporulation of T. areolata was investigated in Finnish Norway spruce seed orchards on Prunus padus and the effect of environmental variables on rust sporulation in 2018–19. A sample of Prunus leaves was collected from which the coverage and number of T. areolata pustules were estimated. The frequency of cones with cone rusts, T. areolata, Chrysomyxa pirolata and C. ledi, was also estimated in Picea abies cones and the sporulation of C. pirolata on Pyrola sp. leaves in the seed orchards. The T. areolata incidence on Prunus was modelled with temperature sum, rainfall, seed orchard and time of estimation.
The T. areolata disease incidence was low (<30%) in seed orchards in 2018, but it exceeded 100% in 2019. T. areolata pustules covered less than 10% of the leaves in 2018 and 10–40% in 2019. An ascomycete, Phloeosporella padi, was common in all Prunus leaves in 2018–19. Low rainfall in May-June explained the low disease rate on Prunus in 2018, while high rainfall explained the high disease rate in May-June in 2019. Cumulative rainfall, temperature sum, time and their interactions were all significant variables in a disease model explaining the disease incidence, while seed orchard was a non-significant variable. Cone rust frequency was low in P. abies cones in the seed orchards in 2019. Telia with basidia of C. pirolata were rare in May-June on Pyrola due to low rainfall in 2018, but frequent due to high rainfall in 2019. Rust control of T. areolata is recommended to concentrate on Prunus to reduce the number of overwintering diseased leaves in the seed orchards. Old infected cones should be removed from seed orchards to reduce aeciospore dissemination to Prunus in May-June. Control of C. pirolata is recommended to concentrate on Pyrola in early May.
Key message
In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant ...cultivars.
Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the ‘Breeders’ MQTLs’. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.
Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent ...pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.
s
Wheat leaf rust and stripe rust are important diseases worldwide. Breeding resistant cultivars is an effective means to control wheat leaf and stripe rust. Wheat line L224-3 currently has high ...resistance to wheat leaf and stripe rust at the field. In this study, 166 recombinant inbred lines (RILs) derived from the L224-3 × Zhengzhou 5389 cross were used to map quantitative trait locus (QTL) for leaf and stripe rust resistance. The RILs and two parents were phenotyped for leaf rust severity at Baoding in Hebei province and Zhoukou in Henan province in the 2015/2016 and 2016/2017 cropping seasons, and for stripe rust severity at Baoding in Hebei Province and Mianyang in Sichuan Province in the 2015/2016 and 2016/2017 growth seasons. All the RILs and parents were also genotyped with the 660 K SNP array and simple sequence repeat (SSR) markers to screen for potential polymorphic markers associated with rust resistance. Four QTLs on chromosomes 1A, 2A, 4B and 7B, were detected using inclusive composite interval mapping (IciMapping).
QLr.hbau-1A
/
QYr.hbau-1A
, derived from susceptible parent Zhengzhou 5389, was pleiotropic for both leaf rust and stripe rust resistance and maybe a novel QTL. The second QTL,
QLr.hbau-2A
/
QYr.hbau-2A
derived from L224-3 for leaf rust and stripe rust resistance is possibly
Lr37
/
Yr17
.
QLr.hbau-4B
/
QYr.hbau-4B
might be a new locus for leaf rust and stripe rust resistance. The fourth QTL,
QYr.hbau-7B
is possibly a new QTL. The QTL identified in the present study with their flanking markers might be used for candidate gene mining and marker-assisted selection (MAS) in wheat breeding programs for rust resistance.
Rust diseases continue to cause significant losses to wheat production worldwide. Although the life of effective race-specific resistance genes can be prolonged by using gene combinations, an ...alternative approach is to deploy varieties that posses adult plant resistance (APR) based on combinations of minor, slow rusting genes. When present alone, APR genes do not confer adequate resistance especially under high disease pressure; however, combinations of 4–5 such genes usually result in “near-immunity” or a high level of resistance. Although high diversity for APR occurs for all three rusts in improved germplasm, relatively few genes are characterized in detail. Breeding for APR to leaf rust and stripe rust in CIMMYT spring wheats was initiated in the early 1970s by crossing slow rusting parents that lacked effective race-specific resistance genes to prevalent pathogen populations and selecting plants in segregating populations under high disease pressure in field nurseries. Consequently most of the wheat germplasm distributed worldwide now possesses near-immunity or adequate levels of resistance. Some semidwarf wheats such as Kingbird, Pavon 76, Kiritati and Parula show high levels of APR to stem rust race Ug99 and its derivatives based on the
Sr2
-complex, or a combination of
Sr2
with other uncharacterized slow rusting genes. These parents are being utilized in our crossing program and a Mexico-Kenya shuttle breeding scheme is used for selecting resistance to Ug99. High frequencies of lines with near-immunity to moderate levels of resistance are now emerging from these activities. After further yield trials and quality assessments these lines will be distributed internationally through the CIMMYT nursery system.
The global spread of invasive plant pathogens is increasing, putting natural forests and ecosystem services under threat. Spatial data can quantify range non‐overlap between invasive pathogens and ...their hosts to identify existing and potentially restorable refugia to enable ‘escape’ from the pathogen.
In 2017, myrtle rust Austropuccinia psidii was detected in New Zealand. New Zealand has 27 native woody and liana species in the plant family susceptible to the disease (Myrtaceae), many of which are ecosystem dominants and economically important. Spatial methods were used to compare the current New Zealand distribution of myrtle rust with the modelled distributions of its potential native hosts. To guide management and set priorities for conservation of at‐risk species, areas of potential refugia where a Myrtaceae species is predicted to occur outside the pathogen range were identified under two myrtle rust distribution scenarios.
Myrtle rust will thrive in New Zealand's warmer regions. Many native Myrtaceae are distributed within this area, but several species occur extensively outside the core range of the disease. Species distributed in cooler southern regions will be best placed to persist in refugia.
Myrtaceae species with specific habitat requirements and narrow geographical ranges in warmer (northern) areas are likely to require ex situ or active in situ management. Even widely distributed species will benefit from the restoration of suitable habitat that supports multiple species outside the myrtle rust range.
Synthesis and applications. Spatial data can be used to identify refugia and restoration opportunities, and thus inform landscape‐level management responses to invasive pathogens. This approach can guide decisions over where to implement in situ (e.g. fungicide spraying) versus ex situ (e.g. seed banking, botanic gardens) management efforts.
Tuhinga
Kua piki te hora o ngā tukumate puāwai whakaeke, huri noa i te ao, he mea whakararu i ngā ngahere māori, i ngā ratonga taiao rauropi hoki. Mā te raraunga mokowā e ine te rahi o te inaki‐kore i waenga i ngā tukumate me ō rātou kaihautū hei tautohu i ngā punanga o nāianei tonu, otirā, ērā anō hoki e taea ai te haumanu kia pai ai te karo i te tukumate.
Nō te 2017, i kitea te waikura ramarama Austropuccinia psidiii Aotearoa. E 27 ngā momo kākoa, aka māori hoki i te hekenga puāwai e noho mōrearea ana ki te mate (Ramarama), he nui tonu ngā momo puāwai matua i te taiao rauropi, he mea nui hoki ā‐ōhanga. I whakamahia ngā tikanga mokowā ki te taurite i te hora whānui o nāianei i Aotearoa o te waikura ramarama ki te hora whānui o ōna momo kaieke māori. Hei ārahi i te whakahaeretanga, me te whakarite kaupapa atawhai mātāmua o ngā momo e noho mōrearea ana, i tautohua ngā wāhi e tika ana mō ngā punanga e whakapaetia ana ka puta mai he momo Ramarama i waho i te whātorotanga atu o ngā tukumate i raro i ngā momo āhuatanga hora whānui o ngā kaupapa waikura ramarama e rua.
Ka momoho te tipu a te waikura ramarama i ngā rohe mahana ake puta i Aotearoa. He whānui te hora o ngā Ramarama māori i roto i wāhi nei, heoi anō, ka tipu anake ētahi momo puāwai i waho i te whānui matua o te mate. Ka nui ake ngā hua ka puta ki ngā momo kua horahia ki ngā rohe kōangiangi ki te tonga ka nui ake ngā punanga ora.
He nui ake te tūpono ka whai mahi haumanu, kaupapa haumanu rānei ngā momo Ramarama kua waia anake ki ngā tētahi momo taiao, momo mahana hoki ki ngā rohe mahana ake (ki te raki). Ka whai hua anō hoki ngā momo kua horahia whānuitia i te haumanu o tētahi taiao hāngai he mea taunaki i ngā momo puāwai i waho atu i te whātoronga o te mate waikura ramarama.
Te kōtuitanga me ōna whakamahinga. E taea ai te whakamahi te raraunga mokowā ki te tautohu i ngā punanga me ngā momo wā, wāhi haumanu, mā konei e whakamōhio i ngā urupare whakahaere tirohanga‐whānui ki ngā tukumate urutomo. Mā tēnei tū mahi e ārahi ngā whakatau, arā, ngā tūāhuatanga whakahaere, he mahi haumanu (hei tauira, te whakawainehu kōpura whetū) he kaupapa haumanu rānei (hei tauira, te pēke kākano, he kāri huaota).
Spatial data can be used to identify refugia and restoration opportunities, and thus inform landscape‐level management responses to invasive pathogens. This approach can guide decisions over where to implement in situ (e.g. fungicide spraying) versus ex situ (e.g. seed banking, botanic gardens) management efforts.
This study establishes a method to detect and distinguish between brown rust and yellow rust on wheat leaves based on hyperspectral imaging at the leaf scale under controlled laboratory conditions. A ...major problem at this scale is the generation of representative and correctly labelled training data, as only mixed spectra comprising plant and fungal material are observed. For this purpose, the pure spectra of rust spores of Puccinia triticina and P. striiformis, causal agents of brown and yellow rust, respectively, were used to serve as a spectral fingerprint for the detection of a specific leaf rust disease. A least‐squares factorization was used on hyperspectral images to unveil the presence of the spectral signal of rust spores in mixed spectra on wheat leaves. A quantification of yellow and brown rust, chlorosis and healthy tissue was verified in time series experiments on inoculated plants. The detection of fungal crop diseases by hyperspectral imaging was enabled without pixel‐wise labelling at the leaf scale by using reference spectra from spore‐scale observations. For the first time, this study shows an interpretable decomposition of the spectral reflectance mixture during pathogenesis. This novel approach will support a more sophisticated and precise detection of foliar diseases of wheat by hyperspectral imaging.
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