Plant sciences articles within Nature Reviews Genetics

Featured

  • Review Article |

    Targeted genome modification using CRISPR–Cas genome editing, base editing or prime editing is driving base research in plants and precise molecular breeding. The authors review the technological principles underlying these methods, approaches for their delivery in plants, and emerging crop-breeding strategies based on targeted genome modification.

    • Boshu Li
    • , Chao Sun
    •  & Caixia Gao

  • Review Article |

    Plants have uniquely adapted to manage endoplasmic reticulum stress triggered by protein misfolding. The authors review the dynamics of gene expression regulation underlying the unfolded protein response in plants, highlighting recent insights provided by systems-level approaches and omics data.

    • Dae Kwan Ko
    •  & Federica Brandizzi

  • Review Article |

    Plant pangenomes have had a transformative impact on crop enhancement, biodiversity conservation and evolutionary research. This Review delves into the application of plant pangenomes for understanding trait diversity, aiding breeding, biodiversity classification and monitoring, and illuminating evolutionary innovations.

    • Mona Schreiber
    • , Murukarthick Jayakodi
    •  & Martin Mascher

  • Comment |

    In April 2023, leading experts met with members of US Congress to discuss strategies to ensure global food security. Following on from this, Pamela Ronald emphasizes the role that plant genetics has in achieving these goals.

    • Pamela C. Ronald

  • Journal Club |

    Fay-Wei Li recalls a 1966 paper by Klekowski and Baker, who built on their observation that homosporous pteridophytes have many more chromosomes than heterosporous lineages to generate hypotheses on the evolutionary impact of polyploidy.

    • Fay-Wei Li

  • Perspective |

    Commemorating the 200th birthday of Gregor Mendel, Kim Nasmyth reflects on Mendel’s life and legacy and how his work has shaped and defined the field of modern genetics.

    • Kim Nasmyth

  • In Brief |

    Omary et al. map shoot-borne root development at single-cell resolution in tomato to identify the origin of shoot-borne roots.

    • Linda Koch

  • Journal Club |

    Michael Purugganan reflects on a 100-year-old publication by Nikolai Vavilov, which postulated a new law of genetics from which key evolutionary insights emerged and which guided future molecular genetic investigations.

    • Michael D. Purugganan

  • Review Article |

    In this Review, Zhang et al. summarize our current understanding of the molecular mechanisms underlying the responses of plants to abiotic stresses, and how this knowledge can be used to improve crop resilience through genetic, chemical and microbial approaches.

    • Huiming Zhang
    • , Jianhua Zhu
    •  & Jian-Kang Zhu

  • Review Article |

    The authors review intra-individual and inter-individual plant epigenome variation during development and in response to environmental changes, including stress. They also discuss functions of epigenome plasticity and epigenome editing technologies that will drive future research.

    • James P. B. Lloyd
    •  & Ryan Lister

  • Review Article |

    Omics methods can be used to mine the genomes of diverse organisms, from microorganisms to plants and animals, for the discovery of natural products and their biosynthetic genes. In this Review, the authors review the why, what, where and how of genome mining.

    • Marnix H. Medema
    • , Tristan de Rond
    •  & Bradley S. Moore

  • Research Highlight |

    Two papers in Nature Plants provide evidence that plants, like mammals, regulate gene expression from long-range cis-regulatory elements (CREs). Plant CREs are widespread and have distinct evolutionarily conserved chromatin characteristics that are predictive of their effect on gene expression.

    • Dorothy Clyde

  • Research Highlight |

    An experimental evolution study published in Science demonstrates that non-additive interactions between pollinators (bumblebees) and herbivores (caterpillars) drive rapid evolution in plants.

    • Dorothy Clyde

  • Perspective |

    Using the example of carbon concentrating mechanisms in plants, the authors of this Perspective provide evidence that broad comparative genomic analyses likely overestimate the genetic complexity underlying convergent evolution of complex traits.

    • Karolina Heyduk
    • , Jose J. Moreno-Villena
    •  & Erika J. Edwards

  • Research Highlight |

    Two studies in Science show that cytosine base editors, but not adenine base editors or CRISPR–Cas9, induce notable off-target single-nucleotide variants in rice and in mouse embryos.

    • Katharine H. Wrighton

  • Review Article |

    Genomic technologies are helping researchers to understand the natural genetic variation that exists in wild and cultivated rice populations. Harnessing this genetic variation will be key to developing Green Super Rice varieties with high yield and low environmental costs.

    • Rod A. Wing
    • , Michael D. Purugganan
    •  & Qifa Zhang

  • Review Article |

    Fruit flavour is a complex phenotype that has been adversely affected by human intervention. Recent progress in defining the chemistry of consumer preferences and the availability of high-quality genome sequences are providing a foundation for defining the genetics underlying this trait and could be used for flavour improvement.

    • Harry J. Klee
    •  & Denise M. Tieman

  • Review Article |

    Disease-resistant crops have the potential to reduce crop losses. This Review discusses how advances in genetic and genomic technologies are contributing to efforts by plant breeders to generate durable, broad-spectrum disease resistance in crop plants.

    • Rebecca Nelson
    • , Tyr Wiesner-Hanks
    •  & Peter Balint-Kurti

  • Review Article |

    To unlock the potential of epigenetic variation for crop improvement, it will be crucial to understand how epigenetic variation is established and how it is stably inherited across generations. Springer and Schmitz review these challenges, the different sources of epigenetic variation in plants, and how epigenome profiling and engineering could help to improve crops.

    • Nathan M. Springer
    •  & Robert J. Schmitz

  • Review Article |

    The plant circadian clock regulates many physiological processes, such as growth, flowering time, abiotic and biotic stress responses, and metabolism. In turn, many of these responses feed back to control the circadian clock. This Review describes the integration of circadian dynamics into the study of plant physiological processes and highlights the importance of incorporating circadian, spatial and temporal information into predictive models to improve crop breeding.

    • Kathleen Greenham
    •  & C. Robertson McClung

  • Review Article |

    Arabidopsis thaliana, a member of the phenotypically diverse Brassicaceae family, has proved to be a key model organism for characterizing plant genome and morphological evolution. This Review outlines how recent comparative and functional genomic studies usingArabidopsisrelatives have further advanced our understanding of plant diversity and evolution.

    • Daniel Koenig
    •  & Detlef Weigel

  • Review Article |

    The rising human population and climate instability are putting unprecedented pressure on global agricultural practices. This Review describes the diverse mechanisms by which plants tolerate various stresses, such as flooding, drought, toxins, salinity and temperature extremes. The authors focus on how the genetic loci that underlie these survival and tolerance traits can be introgressed into current crops to improve yield stability.

    • Michael V. Mickelbart
    • , Paul M. Hasegawa
    •  & Julia Bailey-Serres

  • Review Article |

    DNA and histone modifications undergo extensive reprogramming to reset the epigenomic state between generations. This Review discusses the mechanisms and consequences of epigenetic reprogramming during plant sexual reproduction. Despite various similarities to the equivalent process in mammals, a key difference is the seemingly incomplete reprogramming of plant epigenomes, which has implications for evolution and transgenerational epigenetic inheritance.

    • Tomokazu Kawashima
    •  & Frédéric Berger

  • Review Article |

    RNA-directed DNA methylation (RdDM) is a major mechanism of transcriptional gene silencing in plants that is mediated through small interfering RNAs (siRNAs) and plant-specific RNA polymerases. This Review summarizes our latest understanding of RdDM, including its genomic targets, molecular mechanisms (such as emerging non-canonical pathways) and diverse biological roles.

    • Marjori A. Matzke
    •  & Rebecca A. Mosher

  • Review Article |

    The recent improvement in technologies to identify genetic variants linked with quantitative traits has allowed the identification of variants that are associated with crop domestication. This Review considers these approaches and their application to the study of crop domestication.

    • Rachel S. Meyer
    •  & Michael D. Purugganan

  • Research Highlight |

    • Hannah Stower

  • Review Article |

    This Review considers mechanisms by which information is transmitted over short and long distances during plant development and how different modes of signalling integrate with gene regulatory networks to allow plants to respond to their environment.

    • Erin Sparks
    • , Guy Wachsman
    •  & Philip N. Benfey

  • Review Article |

    Transposable elements are important sources of genetic and epigenetic variation in plant genomes. The author discusses the evidence that this variation has been important for plant evolution and how new genomic resources should allow a systematic assessment of this issue.

    • Damon Lisch

  • Review Article |

    Seasonal cues, such as day length and temperature, influence the developmental programme of plants. Recent genetic research has shed light on the pathways that lead to seasonal responses in flowering. The regulation of these pathways inArabidopsis thaliana, their conservation throughout other species and comparative analysis of annual and perennial plants are considered here.

    • Fernando Andrés
    •  & George Coupland

  • Review Article |

    Genome-wide studies of protein–DNA interactions are helping to provide a more complete picture of the regulation of transcriptional programmes during plant development. Models of regulation have evolved from hierarchies of transcription factors to complex networks that involve these factors and chromatin-modifying proteins.

    • Kerstin Kaufmann
    • , Alice Pajoro
    •  & Gerco C. Angenent

  • Review Article |

    Our understanding of the evolution and molecular basis of plant–pathogen interactions has recently been advanced by bringing together genetic and genomic studies of both plants and pathogens. Insights into the strategies used by plants to recognize pathogens may lead to novel agricultural applications.

    • Peter N. Dodds
    •  & John P. Rathjen

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