Puccinia Triticina Research Articles

Evaluation of the genotypes of the Kazakh-Siberian nursery (KASIB) in the conditions of the Novosibirsk region

The paper presents the results of evaluation of the KASIB-22 nursery soft wheat samples resistance to the main wheat pathogens. The research material was 44 wheat samples obtained from different regions of Russia and Kazakhstan within the framework of the KASIB shuttle breeding program (A.I. Barayev Research and Production Centre for Grain Farming, Omsk State Agrarian University, ICiG SB RAS, Karabalyk AES, Karaganda AES, North-Kazakhstan AES, FSBSI "Omsk ASC", HE SAU of the Northern Trans-Urals, Aktyubinsk AES, Kurgan Research Institute of Agriculture, Pavlodar AES, agrokomplex "Kurgansemena", Samara Research Institute of Agriculture, Chelyabinsk Research Institute of Agriculture). The following breeding lines were identified as highly productive and possessing high and medium resistance to brown rust, powdery mildew and loose smut: Line Pt-311 (Kurgan Research Institute of Agriculture), Lutescens 1462, Lutescens 1486, Line1616ae14 (Samara Research Institute of Agriculture), Lutescens 1356 (ICiG SB RAS). The yield of the selected samples averaged 42.1–51.2 c/ha. Genotypes Novosibirskaya 41, Line 435/12 and Lutescens 1364 are of interest for selection for quality. The gluten content of the nursery genotypes ranged from 24.1 (Line 23/07 in 2022) to 38.0% (variety Astana 2 in 2021), protein ranged from 13.4 (variety Tertia in 2022) to 19.5% (Lutescens 1364 in 2022). Each of the selected lines is of practical value for breeding, and the samples from the KASIB-22 nursery allow to expand the genetic diversity of spring soft wheat by selecting the most resistant forms to local populations of powdery mildew, leaf rust and loose smut pathogens.

Development and Evaluation of a Loop-Mediated Isothermal Amplifcation (LAMP) Assay for Specific and Sensitive Detection of Puccinia melanocephala Causing Brown Rust in Sugarcane

Development and Evaluation of a Loop-Mediated Isothermal Amplifcation (LAMP) Assay for Specific and Sensitive Detection of Puccinia melanocephala Causing Brown Rust in Sugarcane

Biocontrol potential of Acremonium sclerotigenum (Moreau & R. Moreau ex Valenta) W. Gams against wheat and oat rust fungi (Puccinia species)

Biocontrol potential of Acremonium sclerotigenum (Moreau & R. Moreau ex Valenta) W. Gams against wheat and oat rust fungi (Puccinia species)

Response of Durum Wheat (Triticum durum L.) Genotypes to Blended NPSB Fertilizer Rates and Wheat Rust Diseases in Southern Ethiopia

Lack of improved varieties and soil fertility degradation are among the major factors that limit durum wheat (Triticum turgidum L.) production in Ethiopia. The objectives of this study were to determine the response of durum wheat cultivars (i) to nitrogen, phosphorus, sulphur, and boron (NPSB) fertilizer blend; (ii) rust infection; and (iii) partial budget analysis using NPSB fertilizer blend. A 2-location experiment was conducted in 2021 in South Ethiopia to evaluate the response of 4 durum wheat genotypes to blended NPSB fertilizer rates in a randomized complete block design in a 4 × 4 factorial arrangement. The results showed significant (P<0.05) differences due to genotypes (G), rate of NPSB fertilizer (F), and location (E) for all the parameters. The effects due to the G × F × E interaction were significant (P<0.05) for the number of total tillers, number of productive tillers, and grain yield (GY). A significant (P<0.05) G × E interaction was observed for the majority of parameters except days to 50% heading and plant height. Durum wheat genotype S3-213037 produced the highest grain yield of 3689.3 kg·ha−1 when NPSB fertilizer was applied at a rate of 225 kg·ha−1 at Adekoysha. Moreover, partial budget analysis indicated that genotype S3-213037 accrued a maximum benefit of 112,986.50 birr·ha−1 and the highest marginal rate of return of 1356.4% when NPSB fertilizer was applied at a rate of 225 kg·ha−1. Therefore, this study indicated that the application of an NPSB fertilizer rate of 225 kg·ha−1 could be used in the production of durum wheat in the East African region with similar agroecologies to the study area.

Virulence phenotypes of Puccinia graminis on barley, wheat and oat in Canada from 2020 to 2022

Stem rust of barley and wheat is caused by the obligate pathogen Puccinia graminis f. sp. tritici (Pgt) and stem rust of oat is caused by P. graminis f. sp. avenae (Pga). Stem rust can be a very destructive disease of cereal crops and, until the development of resistant host varieties, was responsible for millions of dollars of losses to producers. Genetic host resistance is the most common and effective method to control stem rust on cereals. Knowledge of the virulence genes and races present in the pathogen population is important to identify effective host resistance genes for use by cereal plant breeders. The objectives of this study were to determine the incidence and severity of P. graminis in wheat, barley and oat in Manitoba, Canada, and assess the virulence frequencies and races of isolates collected from Manitoba, Saskatchewan and Ontario, Canada during 2020 to 2022. Stem rust incidence and severity was very light in Manitoba in 2020, 2021 and 2022. Virulence was not observed on resistance genes Sr30, Sr24 and Sr31 from Canadian collections of Pgt isolates made during 2020 to 2022. Race QFCSC was the most common race of Pgt in Canada, and races MCCFC and TPMKC were also common in Manitoba in 2022. Virulence to resistance genes Pg6, Pg10 and Pg16 was not observed among Pga isolates. The most common race of Pga from Manitoba and Saskatchewan was TGN, followed by SGB and TJS. The most frequent Pga races were TDJ, TDD and TGN in Ontario.

Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.)

BackgroundWheat 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).ResultsForty-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.ConclusionThe 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.

Winter Durum Wheat Disease Severity Detection with Field Spectroscopy in Phenotyping Experiment at Leaf and Canopy Level

Accurate disease severity assessment is critical for plant breeders, as it directly impacts crop yield. While hyperspectral remote sensing has shown promise for disease severity assessment in breeding experiments, most studies have focused on either leaf or canopy levels, neglecting the valuable insights gained from a combined approach. Moreover, many studies have centered on experiments involving a single disease and a few genotypes. However, this approach needs to accurately represent the challenges encountered in field conditions, where multiple diseases could occur simultaneously. To address these gaps, our current study analyses a combination of diseases, yellow rust, brown rust, and yellow leaf spots, collectively evaluated as the percentage of the diseased leaf area relative to the total leaf area (DA) at both leaf and canopy levels, using hyperspectral data from an ASD field spectrometer. We quantitatively estimate overall disease severity across fifty-two winter durum wheat genotypes categorized into early (medium milk) and late (late milk) groups based on the phenophase. Chlorophyll content (CC) within each group is studied concerning infection response, and a correlation analysis is conducted for each group with nine vegetation indices (VI) known for their sensitivity to rust and leaf spot infection in wheat. Subsequent parametric (linear and polynomial) and nonparametric (partial least squares and kernel ridge) regression analyses were performed using all available spectral bands. We found a significant reduction in Leaf CC (>30%) in the late group and Canopy CC (<10%) for both groups. YROI and LRDSI_1 are the VIs that exhibited notable and strong negative correlations with Leaf CC in the late group, with a Pearson coefficient of −0.73 and −0.72, respectively. Interestingly, spectral signatures between the early and late disease groups at both leaf and canopy levels exhibit opposite trends. The regression analysis showed we could retrieve leaf CC only for the late group, with R2 of 0.63 and 0.42 for the cross-validation and test datasets, respectively. Canopy CC retrieval required separate models for each group: the late group achieved R2 of 0.61 and 0.37 (cross-validation and test), while the early group achieved R2 of 0.48 and 0.50. Similar trends were observed for canopy DA, with separate models for early and late groups achieving comparable R2 values of 0.53 and 0.51 (cross-validation) and 0.35 and 0.36 (test), respectively. All of our models had medium accuracy and tended to overfit. In this study, we analyzed the spectral response mechanism associated with durum wheat diseases, offering a novel crop disease severity assessment approach. Additionally, our findings serve as a foundation for detecting resistant wheat varieties, which is the most economical and environmentally friendly management strategy for wheat leaf diseases on a large scale in the future.

Tackling unbalanced datasets for yellow and brown rust detection in wheat.

This study evaluates the efficacy of hyperspectral data for detecting yellow and brown rust in wheat, employing machine learning models and the SMOTE (Synthetic Minority Oversampling Technique) augmentation technique to tackle unbalanced datasets. Artificial Neural Network (ANN), Support Vector Machine (SVM), Random Forest (RF), and Gaussian Naïve Bayes (GNB) models were assessed. Overall, SVM and RF models showed higher accuracies, particularly when utilizing SMOTE-enhanced datasets. The RF model achieved 70% accuracy in detecting yellow rust without data alteration. Conversely, for brown rust, the SVM model outperformed others, reaching 63% accuracy with SMOTE applied to the training set. This study highlights the potential of spectral data and machine learning (ML) techniques in plant disease detection. It emphasizes the need for further research in data processing methodologies, particularly in exploring the impact of techniques like SMOTE on model performance.

Mapping of Leaf Rust Resistance Loci in Two Kenyan Wheats and Development of Linked Markers.

Leaf rust caused by the pathogen Puccinia triticina (Pt) is a destructive fungal disease of wheat that occurs in almost all wheat-growing areas across the globe. Genetic resistance has proven to be the best solution to mitigate the disease. Wheat breeders are continuously seeking new diversified and durable sources of resistance to use in developing new varieties. We developed recombinant inbred line (RIL) populations from two leaf rust-resistant genotypes (Kenya Kudu and AUS12568) introduced from Kenya to identify and characterize resistance to Pt and to develop markers linked closely to the resistance that was found. Our studies detected four QTL conferring adult plant resistance (APR) to leaf rust. Two of these loci are associated with known genes, Lr46 and Lr68, residing on chromosomes 1B and 7B, respectively. The remaining two, QLrKK_2B and QLrAus12568_5A, contributed by Kenya Kudu and AUS12568 respectively, are putatively new loci for Pt resistance. Both QLrKK_2B and QLrAus12568_5A were found to interact additively with Lr46 in significantly reducing the disease severity at adult plant growth stages in the field. We further developed a suite of six closely linked markers within the QLrAus12568_5A locus and four within the QLrKK_2B region. Among these, markers sunKASP_522 and sunKASP_524, flanking QLrAus12568_5A, and sunKASP_536, distal to QLrKK_2B, were identified as the most closely linked and reliable for marker-assisted selection. The markers were validated on a selection of 64 Australian wheat varieties and found to be polymorphic and robust, allowing for clear allelic discrimination. The identified new loci and linked molecular markers will enable rapid adoption by breeders in developing wheat varieties carrying diversified and durable resistance to leaf rust.

Sudogda is a new variety of winter triticale for fodder production

Sudogda is a new variety of winter triticale for fodder production

Integrated genome-wide association and transcriptomic analysis to identify receptor kinase genes to stripe rust resistance in wheat germplasm from southwestern China

Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide. Identification of new and elite Pst-resistance loci or genes has the potential to enhance overall resistance to this pathogen. Here, we conducted an integrated genome-wide association study (GWAS) and transcriptomic analysis to screen for loci associated with resistance to stripe rust in 335 accessions from Yunnan, including 311 landraces and 24 cultivars. Based on the environmental phenotype, we identified 113 protein kinases significantly associated with Pst resistance using mixed linear model (MLM) and generalized linear model (GLM) models. Transcriptomic analysis revealed that 52 of 113 protein kinases identified by GWAS were up and down regulated in response to Pst infection. Among these genes, a total of 15 receptor kinase genes were identified associated with Pst resistance. 11 candidate genes were newly discovered in Yunnan wheat germplasm. Our results revealed that resistance alleles to stripe rust were accumulated in Yunnan wheat germplasm, implying direct or indirect selection for improving stripe rust resistance in elite wheat breeding programs.

The F-box protein encoding genes of the leaf-rust fungi Puccinia triticina: genome-wide identification, characterization and expression dynamics during pathogenesis.

The F-box proteins in fungi perform diverse functions including regulation of cell cycle, circadian clock, development, signal transduction and nutrient sensing. Genome-wide analysis revealed 10 F-box genes in Puccinia triticina, the causal organism for the leaf rust disease in wheat and were characterized using in silico approaches for revealing phylogenetic relationships, gene structures, gene ontology, protein properties, sequence analysis and gene expression studies. Domain analysis predicted functional domains like WD40 and LRR at C-terminus along with the obvious presence of F-box motif in N-terminus. MSA showed amino acid replacements, which might be due to nucleotide substitution during replication. Phylogenetic analysis revealed the F-box proteins with similar domains to be clustered together while some sequences were spread out in different clades, which might be due to functional diversity. The clustering of Puccinia triticina GG705409 with Triticum aestivum TaAFB4/TaAFB5 in a single clade suggested the possibilities of horizontal gene transfer during the coevolution of P. triticina and wheat. Gene ontological annotation categorized them into three classes and were functionally involved in protein degradation through the protein ubiquitination pathway. Protein-protein interaction network revealed F-box proteins to interact with other components of the SCF complex involved in protein ubiquitination. Relative expression analysis of five F-box genes in a time course experiment denoted their involvement in leaf rust susceptible wheat plants. This study provides information on structure elucidation of F-box proteins of a basidiomycetes plant pathogenic fungi and their role during pathogenesis.

Physio-Biochemical, Anatomical, and Molecular Analysis of Resistant and Susceptible Wheat Cultivars Infected with TTKSK, TTKST, and TTTSK Novel Puccinia graminis Races.

Stem rust, caused by Puccinia graminis f.sp. tritici, is one of the most dangerous rust diseases on wheat. Through physiological, biochemical, and molecular analysis, the relationship between the change in resistance of 15 wheat cultivars to stem rust disease and the response of 41 stem rust resistance genes (Sr,s) as well as TTKSK, TTKST, and TTTSK races was explained. Some cultivars and Sr genes, such as Gemmeiza-9, Gemmeiza-11, Sids-13, Sakha-94, Misr-1, Misr-2, Sr31, and Sr38, became susceptible to infection. Other new cultivars include Mir-3 and Sakha-95, and Sr genes 13, 37, 40, GT, and FR*2/SRTT3-SRTT3-SR10 remain resistant. Some resistance genes have been identified in these resistant cultivars: Sr2, Sr13, Sr24, Sr36, and Sr40. Sr31 was not detected in any cultivars. Reactive oxygen species such as hydrogen peroxide and superoxide, enzymes activities (catalase, peroxidase, and polyphenoloxidase), and electrolyte leakage were increased in the highly susceptible cultivars, while they decreased in the resistant ones. Anatomical characteristics such as the thickness of the epidermis, ground tissue, phloem tissue and vascular bundle diameter in the midrib were decreased in susceptible cultivars compared with resistant cultivars. Our results indicated that some races (TTKSK, TTKST, and TTTSK) appeared for the first time in Egypt and many other countries, which broke the resistant cultivars. The wheat rust breeding program must rely on land races and pyramiding genes in order to develop new resistance genes that will survive for a very long time.

Registration of ‘CP 10‐1620’ sugarcane

Abstract‘CP 10‐1620’ (Reg. no. CV‐216, PI 693837) sugarcane (a complex hybrid of Saccharum spp.) was developed through cooperative research conducted by the USDA–ARS, the University of Florida, and the Florida Sugar Cane League, Inc. At the June 7, 2018, Florida Sugarcane Variety Committee Meeting, CP 10‐1620 was released to growers for mineral (sand) soils in Florida, and seed was available in September 2018. CP 10‐1620 was selected from a polycross of ‘CP 00‐1100’ × ‘CP 05‐1740’ (Cross no. X07‐1225) made at Canal Point, FL, in December 2007. Neither the female parent, CP 00‐1100, nor the male parent, CP 05‐1740, is a commercial cultivar. Cane yield of CP 10‐1620 on sand soils, averaged across 12 harvests through three crop cycles (plant cane, first ratoon, and second ratoon), was 11.0% higher (P < 0.05) than the combined mean of three checks, ‘CL 88‐4730’, ‘CP 96‐1252’, and ‘CPCL 97‐2730’, which are commercial checks for sand soils. The commercial recoverable sucrose for CP 10‐1620 was not significantly lower than the combined mean of the checks but the higher cane yield resulted in 8.4% higher (P < 0.05) sucrose yield than the combined mean of the checks. CP 10‐1620 was released because of its high cane yields on sand soils, and its acceptable levels of resistance to brown rust (caused by Puccinia melanocephala H. & P. Sydow), leaf scald (caused by Xanthomonas albilineans Ashby, Dowson), Sugarcane mosaic virus strain E (mosaic), smut (caused by Sporisorium scitamineum), Sugarcane yellow leaf virus, and ratoon stunt [caused by Leifsonia xyli subsp. xyli (Davis et al.) Evtushenko]. CP 10‐1620 was moderately susceptible to orange rust (caused by Puccinia kuehnii E. J. Butler), and it has high freeze tolerance. CP 10‐1620 tested positive for the Bru1 locus, which is an indicator of brown rust resistance.

Registration of ‘CP 13‐1954’ sugarcane for Florida organic soils

Abstract‘CP 13‐1954’ (Reg. no. CV‐218, PI 704104) sugarcane (Saccharum spp. hybrid) was developed through cooperative research conducted by the USDA–ARS, the University of Florida, and the Florida Sugar Cane League, Inc., and released to growers for organic (muck) soils in Florida in June 2020. The parentage of CP 13‐1954 is ‘CP 85‐1491’ × Poly 09‐24. Based on the results of three crops (plant cane, first ratoon, and second ratoon) in field trials conducted at five locations, CP 13‐1954 had higher cane yield (16.2%), sucrose yield (15.6%), and economic index (29.7%) at P < .05 compared with the reference cultivar, ‘CP 96‐1252’. CP 13‐1954 stalks are usually taller than the reference cultivar, ‘CP 00‐1101’, with small‐to‐medium diameter, and exhibits resistance to ratoon stunting disease, Sugarcane mosaic virus strain E, brown rust, orange rust, and smut and moderate resistance to leaf scald on muck soils in Florida. CP 13‐1954 has Bru1 locus that provides resistance against brown rust. CP 13‐1954 showed moderate cold tolerance among all the tested cultivars.

Registration of ‘CP 15‐1407’ sugarcane for muck soils

AbstractThe complex hybrid sugarcane (Saccharum spp.) cultivar ‘CP 15‐1407’ (Reg. no. CV‐217; PI 704105) was made available to growers in June 2022 for cultivation on muck soils in Florida. This development took 10 years thanks to collaborative research by the USDA–ARS, the Florida Sugar Cane League Inc., and the University of Florida. It started at Canal Point (CP) as a bi‐parental cross between ‘CP 08‐1110’ (female) and CP 05‐1616 (male). Due to its high stalk weight, adequate disease resistance, higher recoverable sugar, and equivalent cane yield to best check ‘CP 96‐1252’ on muck soils, the Florida Sugarcane Variety Committee recommended releasing CP 15‐1407. It has demonstrated resistance to brown rust, orange rust, sugarcane mosaic, smut, leaf scald, and ratoon stunt and is moderately susceptible to yellow leaf. In late‐stage, on‐farm yield trials, CP 15‐1407 stalk weights were 27.8% heavier than that of CP 96‐1252, while cane yields and economic index (EI) did not differ from CP 96‐1252. Florida sugarcane output and crop sustainability are predicted to benefit from CP 15‐1407's sustained cane production capacity and proven disease resistance.

Effectiveness of Rhodococcus erythropolis strain OPI-01 on the fungal development in winter wheat

Abstract. Behzad A, Diakite S, Astarkhanova TS, Pakina EN, Allen D, Mohammadi PM, Diarra O, Saquee FS. 2024. Effectiveness of Rhodococcus erythropolis strain OPI-01 on the fungal development in winter wheat. Biodiversitas 25: 1063-1070. One of the means of sustainable wheat production is using bacterial pesticides, which can synthesize phytohormonal substances with antibacterial and antifungal action. Therefore, the work aimed to study the effect of different doses of a new growth regulator Restart, ZH (Rhodococcus erythropolis D strain OPI-01) on winter wheat yield. The findings of field experiments on the effect of plant growth regulator R. erythropolis strain OPI-01 method of pre-sowing treatment of seeds (at 0.1 L/t and 0.2 L/t), and soil spraying just before sowing (-0.5 l/ha) revealed that on average, during the 2020-2021 and 2021-2022 seasons, the number of productive stems increased by a margin of 23-30, the number of grains in 1 ear increased in the experimental units by 16.2-19.4%, and the length of the ear by 0.3-0.7cm, gluten varied from 32.3 to 33.8%, yield increased from 27.8-33.0% relative to the control. Disease severity and incidence of powdery mildew, brown rust and Septoria disease in plots amended withR. erythropolis strain OPI-01 was 2-fold less than in the control plots. Research trials show the efficacy of R. erythropolis strain OPI-01 under field conditions as a plant growth regulator and a potential microbial fungicide against some foliar diseases of winter wheat. It would be exciting to study the mechanism of R. erythropolis on wheat pathogens in vitro and in planta which are still less developed in the literature.

Modern Approaches to Enhancing Rust Resistance in Wheat Leading to Global Food Security

Rust diseases pose significant threats to wheat production. The deployment of wheat cultivars endowed with rust resistance stands as the most potent strategy for effective rust management. This resistance is primarily inherited through Mendelian principles discovered in 1905, but traditional breeding methods are time-consuming. Modern strategies have emerged to develop rust-resistant wheat varieties efficiently. Marker-Assisted Selection (MAS) accelerates the breeding process through precise screening, bringing about a revolution in the creation of rust-resistant wheat varieties. Genetic engineering techniques allow the transfer of resistance genes from other species into susceptible crops, but GMO use remains controversial and regulated. Gene editing, especially with CRISPR-Cas9, is a game-changer, enabling the introduction of natural variations or inactivation of critical genes in rust pathogens, enhancing plant resistance. RNA interference (RNAi) is another promising strategy, using small RNA molecules to inhibit rust pathogen gene expression, reducing disease severity. Induced Systemic Resistance (ISR) primes plant immune systems by treating them with beneficial microorganisms or compounds, fortifying them against subsequent rust infections. Eco-friendly biofungicides with antagonistic microorganisms suppress rust infections as alternatives to chemical fungicides. The development of climate-resilient wheat varieties is essential, as they indirectly enhance rust resistance, ensuring stable production amid changing climate conditions. These efforts to improve wheat productivity and rust resistance are crucial for feeding the growing global population. Integrating modern methods with traditional breeding is key to effectively combatting rust diseases and enhancing food security.

The complex polyploid genome architecture of sugarcane

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Unraveling the role of microRNA-like RNAs in enhancing Puccinia triticina pathogenicity in wheat by high-throughput sequencing data

Wheat (Triticum aestivum L.), a staple crop cultivated across an estimated 215 million hectares worldwide, encounters significant yield reductions due to the leaf rust disease, instigated by the fungus Puccinia triticina (Pt). Control strategies for this pathogen are limited. Research on wheat-leaf rust interaction in the past few years has mainly focused on characterizing and modulating the performance of resistance (R) and other defense genes of the host plant, but rarely targeted to decipher the network of molecular strategies employed by the pathogen except secretome analysis. In wheat plants, pathogen may induce a greater diversity of small RNAs (sRNAs) to manipulate the host's gene expression and suppress defense responses. In the present study, Pt microRNA-like-RNAs (milRNAs) were screened and identified from sRNA libraries prepared from leaf rust pathogen-infected leaves of wheat near isogenic lines (NILs). Pathogenesis engendering Pt target genes were validated through degradome libraries. Our study indicates that milRNAs enter the host system to suppress its immunity and promote symbiosis-like association to maintain a longer virulence span. Through RT‒qPCR expression analysis, it was suggested that milRNAs create an environment to enhance symbiosis via cross-kingdom silencing of host disease resistance gene encoding proteins. We found that seven out of eight milRNAs effectively regulate pathogenesis-related genes and repressed the disease-resistance genes in host wheat. Functional annotation of target genes of Pt reveals regulation of vesicle synthesis, transport, and fusion, which represents cross-kingdom vesicle-mediated export of milRNAs. Our results also manifest an integrative view of how virulence-associated milRNAs endeavor to stamp out PTI (PAMP-triggered immunity) and ETI (Effector-triggered immunity) to increase susceptibility of the host. This study epitomizes one of the tactics developed by Pt employing milRNAs in regulating virulence during leaf rust infection and will usher to design strategies to manage pathogenesis to protect wheat immunity against leaf rust disease.