Genome evolution and diversity of wild and cultivated potatoes

Nature, Journal Year: 2022, Volume and Issue: 606(7914), P. 535 - 541

Published: June 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Language: Английский

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A super pan-genomic landscape of rice

Cell Research, Journal Year: 2022, Volume and Issue: 32(10), P. 878 - 896

Published: July 12, 2022

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting 251-accession panel comprising both cultivated wild species Asian African rice. Our reveals extensive structural variations (SVs) gene presence/absence variations. Additionally, our enables the accurate identification nucleotide-binding leucine-rich repeat genes characterization their inter- intraspecific diversity. Moreover, uncovered grain weight-associated SVs which specify traits by affecting expression nearby genes. We characterized variants associated with submergence tolerance, seed shattering plant architecture found independent selection for common set that drove adaptation domestication in This facilitates pinpointing lineage-specific haplotypes trait-associated provides insights into evolutionary events have shaped various species.

Language: Английский

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The plant immune system: From discovery to deployment

Cell, Journal Year: 2024, Volume and Issue: 187(9), P. 2095 - 2116

Published: April 1, 2024

Plant diseases cause famines, drive human migration, and present challenges to agricultural sustainability as pathogen ranges shift under climate change. breeders discovered Mendelian genetic loci conferring disease resistance specific isolates over 100 years ago. Subsequent breeding for underpins modern agriculture and, along with the emergence focus on model plants genetics genomics research, has provided rich resources molecular biological exploration last 50 years. These studies led identification of extracellular intracellular receptors that convert recognition microbe-encoded patterns or pathogen-delivered virulence effectors into defense activation. receptor systems, downstream responses, define plant immune systems have evolved since migration land ∼500 million Our current understanding provides platform development rational enhancement control many continue plague crop production.

Language: Английский

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Structural basis of NLR activation and innate immune signalling in plants

Immunogenetics, Journal Year: 2022, Volume and Issue: 74(1), P. 5 - 26

Published: Jan. 4, 2022

Abstract Animals and plants have NLRs (nucleotide-binding leucine-rich repeat receptors) that recognize the presence of pathogens initiate innate immune responses. In plants, there are three types distinguished by their N-terminal domain: CC (coiled-coil) domain NLRs, TIR (Toll/interleukin-1 receptor) RPW8 (resistance to powdery mildew 8)-like coiled-coil NLRs. CC-NLRs (CNLs) TIR-NLRs (TNLs) generally act as sensors effectors secreted pathogens, while RPW8-NLRs (RNLs) signal downstream many sensor called helper Recent studies revealed dimensional structures a CNL (ZAR1) including its inactive, intermediate active oligomeric state, well TNLs (RPP1 ROQ1) in states. Furthermore, accumulating evidence suggests members family lipase-like EDS1 (enhanced disease susceptibility 1) proteins, which uniquely found seed play key role providing link between during Here, we summarize implications plant NLR provide insights into distinct mechanisms action different discuss NLR-mediated signalling pathways involving proteins RNLs.

Language: Английский

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Effector‐dependent activation and oligomerization of plant NRC class helper NLRs by sensor NLR immune receptors Rpi‐amr3 and Rpi‐amr1

The EMBO Journal, Journal Year: 2023, Volume and Issue: 42(5)

Published: Jan. 2, 2023

Abstract Plant pathogens compromise crop yields. Plants have evolved robust innate immunity that depends in part on intracellular Nucleotide‐binding, Leucine rich‐Repeat (NLR) immune receptors activate defense responses upon detection of pathogen‐derived effectors. Most “sensor” NLRs detect effectors require the activity “helper” NLRs, but how helper support sensor NLR function is poorly understood. Many Solanaceae NRC (NLR‐Required for Cell death) class NLRs. We show here Rpi‐amr3, a from Solanum americanum , detects AVRamr3 potato late blight pathogen, Phytophthora infestans and activates oligomerization NRC2 NRC4 into high‐molecular‐weight resistosomes. In contrast, recognition P. effector AVRamr1 by another Rpi‐amr1 induces formation only resistosome. The activated oligomer becomes enriched membrane fractions. ATP‐binding motifs both Rpi‐amr3 are required resistosome formation, not interaction with its cognate effector. can be homologs other species. Mechanistic understanding will underpin engineering crops durable disease resistance.

Language: Английский

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NLR receptors in plant immunity: making sense of the alphabet soup

EMBO Reports, Journal Year: 2023, Volume and Issue: 24(10)

Published: Aug. 21, 2023

Plants coordinately use cell-surface and intracellular immune receptors to perceive pathogens mount an response. Intracellular events of pathogen recognition are largely mediated by the nucleotide binding leucine rich-repeat (NLR) classes. Upon perception, NLRs trigger a potent broad-spectrum reaction, usually accompanied form programmed cell death termed hypersensitive Some plant act as multifunctional singleton which combine detection signaling. However, can also function in higher order pairs networks functionally specialized interconnected receptors. In this article, we cover basic aspects NLR biology with emphasis on networks. We highlight some recent advances structure, function, activation discuss emerging topics such modulator NLRs, suppression bioengineering. Multi-disciplinary approaches required disentangle how these receptor evolve. Answering questions holds potential deepen our understanding system unlock new era disease resistance breeding.

Language: Английский

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Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Plant Communications, Journal Year: 2023, Volume and Issue: 5(1), P. 100646 - 100646

Published: July 6, 2023

Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks the of powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional approach was not effective due to suppressed recombination. Chromosome sorting compromised by insufficient purity. physical map, constructed assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. single candidate NLR identified anchoring RNASeq reads susceptible mutants ONT contigs and validated virus-induced silencing. is likely newly evolved NLR, which discovered only one location across WEW distribution range Israel. successfully introgressed into cultivated wheat, diagnostic molecular marker used accelerate its deployment pyramiding other R-genes.

Language: Английский

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Plant NLR immunity activation and execution: a biochemical perspective

Open Biology, Journal Year: 2024, Volume and Issue: 14(1)

Published: Jan. 1, 2024

Plants deploy cell-surface and intracellular receptors to detect pathogen attack trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as sensors or downstream mediators defence outputs cell death, which prevent disease. Established genetic underpinnings NLR-mediated immunity revealed various strategies plants adopt combat rapidly evolving microbial pathogens. The molecular mechanisms NLR activation signal transmission components controlling execution were less clear. Here, we review recent protein structural biochemical insights plant sensor signalling functions. When put together, the data show how different families, whether transducers, converge on nucleotide-based second messengers cellular calcium confer immunity. Although pathogen-activated NLRs in engage plant-specific machineries promote defence, comparisons with mammalian receptor counterparts highlight some shared working principles for across kingdoms.

Language: Английский

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Future of Bacterial Disease Management in Crop Production

Annual Review of Phytopathology, Journal Year: 2022, Volume and Issue: 60(1), P. 259 - 282

Published: July 6, 2022

Bacterial diseases are a constant threat to crop production globally. Current management strategies rely on an array of tactics, including improved cultural practices; application bactericides, plant activators, and biocontrol agents; use resistant varieties when available. However, effective remains challenge, as the longevity deployed tactics is threatened by constantly changing bacterial populations. Increased scrutiny impact pesticides human environmental health underscores need for alternative solutions that durable, sustainable, accessible farmers, environmentally friendly. In this review, we discuss strengths shortcomings existing practices dissect recent advances may shape future disease management. We conclude resistance through genome modification be most arsenal against diseases. Nonetheless, more research necessary developing novel meet food demand growing global population.

Language: Английский

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From plant immunity to crop disease resistance

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2022, Volume and Issue: 49(8), P. 693 - 703

Published: June 18, 2022

Plant diseases caused by diverse pathogens lead to a serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective sustainable approach control diseases. In last decade, our understanding at both molecular genomic levels has improved greatly. Combined with advances biotechnologies, particularly clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing, we can now rapidly identify new resistance genes engineer disease-resistance plants like never before. this review, summarize current knowledge outline existing strategies for disease plants. We also discuss challenges field suggest directions future studies.

Language: Английский

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