A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Feb. 24, 2023

Abstract Human activity impacts the evolutionary trajectories of many species worldwide. Global trade agricultural goods contributes to dispersal pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how surmount control strategies cope with new climates is crucial predicting future impact crop pathogens. Here, we address this by assembling a global thousand-genome panel Zymoseptoria tritici , major fungal pathogen wheat reported in all production areas We identify invasion routes ongoing exchange among wheat-growing regions. find that expansion was accompanied increased transposable elements weakened genomic defenses. Finally, significant standing variation adaptation encountered during spread. Our work shows large population panels enable deep insights into trajectory pathogen.

Language: Английский

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Important wheat diseases in the US and their management in the 21st century

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 12, 2023

Wheat is a crop of historical significance, as it marks the turning point human civilization 10,000 years ago with its domestication. Due to rapid increase in population, wheat production needs be increased by 50% 2050 and this growth will mainly based on yield increases, there strong competition for scarce productive arable land from other sectors. This increasing demand can further achieved using sustainable approaches including integrated disease pest management, adaption warmer climates, less use water resources frequency abiotic stress tolerances. Out 200 diseases wheat, 50 cause economic losses are widely distributed. Each year, about 20% lost due diseases. Some major rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria powdery mildew, blast, several viral, nematode, bacterial These badly impact mortality plants. review focuses important present United States, comprehensive information causal organism, damage, symptoms host range, favorable conditions, management strategies. Furthermore, genetic breeding efforts control manage these discussed. A detailed description all QTLs, genes reported cloned provided review. study utmost importance programs throughout world breed resistance under changing environmental conditions.

Language: Английский

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Fungal impacts on Earth’s ecosystems

Nature, Journal Year: 2025, Volume and Issue: 638(8049), P. 49 - 57

Published: Feb. 5, 2025

Language: Английский

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Population genomics of Marchantia polymorpha subsp. ruderalis reveals evidence of climate adaptation

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Sexual reproduction results in the development of haploid and diploid cell states during life cycle. In bryophytes, dominant multicellular phase produces motile sperm that swim through water to egg effect fertilization from which a relatively small develops. angiosperms, reduced non-motile is delivered pollen tube These different cycle characteristics are likely impact distribution genetic variation among populations. However, little known about wild populations bryophytes. To investigate how distributed bryophyte establish foundation for population genetics research we described diversity collections Marchantia polymorpha subsp. ruderalis, cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) total 209 sequenced accessions collected 37 sites Europe Japan. There was no detectable structure European but significant differentiation between Japanese By associating across genome with global climate data, showed temperature precipitation influence frequency potentially adaptive alleles. This collection establishes core an experimental platform exploits natural answer diverse questions biology.

Language: Английский

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Migration of wheat stripe rust from the primary oversummering region to neighboring regions in China

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 3, 2025

Abstract Changing climate and changes in cropping systems have greatly affected outbreaks of plant diseases. Wheat stripe rust is a disease posing threat to global wheat production, caused by Puccinia striiformis f. sp. tritici ( Pst ). oversummering regions play crucial role the emergence new races China. To unveil migration pattern adjacent regions, we develop set KASP-SNP marker from 28 whole-genome sequences investigate population structure its regions. A 19 Chinese differentials used characterize virulence patterns 308 sampled isolates. By integrating characterization, genetic analysis, air trajectory simulation field monitoring, two main dispersal routes are identified. Inocula Eastern Qinghai dispersed Western Liupan Mountain, reach Guanzhong Plain. The second route originates Middle Gansu, then through Longnan, reaches Plain via Mountain. Both result inoculum spreading Huang-Huai-Hai region, wheat-growing region proposed can be management strategies at regional national scale.

Language: Английский

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Long‐term and rapid evolution in powdery mildew fungi

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(10)

Published: March 2, 2023

The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 hosts. In this review, we discuss the long- and short-term evolution these obligate biotrophic outline their diversity respect to morphology, lifestyle, host range. We highlight remarkable ability rapidly overcome immunity, evolve fungicide resistance, broaden range, for example, through adaptation hybridization. Recent advances in genomics proteomics, particularly cereal mildews (genus Blumeria), provided first insights into mechanisms genomic fungi. Transposable elements play key roles shaping genomes, where even close relatives exhibit diversified patterns recent ongoing transposon activity. These transposons ubiquitously resulting highly adaptive genome architecture lacking obvious regions conserved gene space. Transposons can also be neofunctionalized encode novel virulence factors, candidate secreted effector proteins, which may undermine immune system. cereals like barley wheat, some effectors recognized by receptors encoded resistance genes numerous allelic variants. determine incompatibility ("avirulence") sequence diversification copy number variation. Altogether, possess plastic genomes that enable fast evolutionary towards overcoming barriers, chemical stress such as fungicides, foreshadowing future outbreaks, shifts expansions well potential pandemics pathogens.

Language: Английский

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The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: Feb. 8, 2023

Abstract Background Worldwide wheat production is under constant threat by fast-evolving fungal pathogens. In the last decades, breeding for disease resistance heavily relied on introgression of chromosomal segments from related species as genetic sources new resistance. The Pm8 gene against powdery mildew has been introgressed rye into part a large 1BL.1RS translocation encompassing multiple genes and yield components. Due to its high agronomic value, this seen continuous global use since 1960s growth areas, even after was overcome pathogen. long-term at scale provided unique opportunity study consequences such extensive application pathogen evolution. Results Using genome-wide association studies in population isolates, we identified avirulence effector AvrPm8 specifically recognized . Haplovariant mining covering all major growing areas world revealed 17 virulent haplotypes that grouped two functional categories. first one comprised amino acid polymorphisms single position along protein, which confirmed be crucial recognition Pm8. second category consisted numerous destructive mutations open reading frame disruptions start codon, truncations, deletions, interference with mRNA splicing. With exception single, likely ancient, gain-of-virulence mutation found isolates around world, virulence were geographically restricted regions, indicating they occurred recently consequence frequent use. Conclusions study, show broad prolonged worldwide resulted multitude mechanisms affecting Based our findings, conclude both standing variation well locally occurring contributed breakdown introgression.

Language: Английский

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Avirulence depletion assay: Combining R gene-mediated selection with bulk sequencing for rapid avirulence gene identification in wheat powdery mildew

PLoS Pathogens, Journal Year: 2025, Volume and Issue: 21(1), P. e1012799 - e1012799

Published: Jan. 7, 2025

Wheat production is threatened by multiple fungal pathogens, such as the wheat powdery mildew fungus ( Blumeria graminis f. sp. tritici , Bgt ). resistance breeding frequently relies on use of R ) genes that encode diverse immune receptors which detect specific avirulence AVR effectors and subsequently induce an response. While gene cloning has accelerated recently, identification in many pathogens including lags behind, preventing pathogen-informed deployment sources. Here we describe a new “avirulence depletion (AD) assay” for rapid . This assay selection segregating, haploid F1 progeny population resistant host, followed bulk sequencing, thereby allowing candidate with high mapping resolution. In proof-of-concept experiment mapped component receptor Pm3a to 25 kb genomic interval harboring single effector, previously described AvrPm3 a2/f2 Subsequently, applied AD map unknown effector recognized Pm60 receptor. We show AvrPm60 encoded three tandemly arrayed, nearly identical trigger response upon co-expression its alleles Pm60a Pm60b furthermore provide evidence outperforms through more efficient recognition effectors, suggesting it should be prioritized breeding. Finally, virulence towards caused simultaneous deletion all paralogs isolates lacking are especially prevalent US limiting potential this region. The powerful tool inexpensive contribute decisions novel regionally tailored deployment.

Language: Английский

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Genomic analysis, trajectory tracking, and field surveys reveal sources and long-distance dispersal routes of wheat stripe rust pathogen in China

Plant Communications, Journal Year: 2023, Volume and Issue: 4(4), P. 100563 - 100563

Published: Feb. 21, 2023

Identifying sources of phytopathogen inoculum and determining their contributions to disease outbreaks are essential for predicting development establishing control strategies. Puccinia striiformis f. sp. tritici (Pst), the causal agent wheat stripe rust, is an airborne fungal pathogen with rapid virulence variation that threatens production through its long-distance migration. Because wide in geographic features, climatic conditions, systems, Pst related dispersal routes China largely unclear. In present study, we performed genomic analyses 154 isolates from all major wheat-growing regions determine population structure diversity. Through trajectory tracking, historical migration studies, genetic introgression analyses, field surveys, investigated rust epidemics. We identified Longnan, Himalayan region, Guizhou Plateau, which contain highest diversities, as China. Longnan disseminates mainly eastern Liupan Mountain, Sichuan Basin, Qinghai; region spreads Basin Plateau migrates Central Plain. These findings improve our current understanding epidemics emphasize need managing on a national scale.

Language: Английский

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A kinase fusion protein from Aegilops longissima confers resistance to wheat powdery mildew

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 2, 2024

Many disease resistance genes have been introgressed into wheat from its wild relatives. However, reduced recombination within the segments hinders cloning of genes. Here, we cloned powdery mildew gene Pm13, which is Aegilops longissima, using a method that combines physical mapping with radiation-induced chromosomal aberrations and transcriptome sequencing analysis ethyl methanesulfonate (EMS)-induced loss-of-function mutants. Pm13 encodes kinase fusion protein, designated MLKL-K, an N-terminal domain mixed lineage domain-like protein (MLKL_NTD domain) C-terminal serine/threonine bridged by brace. The function validated through transient stable transgenic complementation assays. Transient over-expression analyses in Nicotiana benthamiana leaves protoplasts reveal fragment Brace-Kinase122-476 MLKL-K capable inducing cell death, dependent on functional three α-helices brace region close to N-terminus domain. was longissima. authors report it MLKL_NTD domain-containing kinase.

Language: Английский

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