Plant genetics

  • Article |

    OsTCP19 is a modulator of the tillering response to nitrogen in rice, and introgression of an allele of OsTCP19 associated with a high tillering response into modern rice cultivars markedly improves their nitrogen-use efficiency.

    • Yongqiang Liu
    • , Hongru Wang
    •  & Chengcai Chu
  • Article
    | Open Access

    Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement

    • Murukarthick Jayakodi
    • , Sudharsan Padmarasu
    •  & Nils Stein
  • Article |

    Resequencing analyses of three species of wild sunflower identify large non-recombining haplotype blocks that correlate with ecologically relevant traits, soil and climate characteristics, and that differentiate species ecotypes.

    • Marco Todesco
    • , Gregory L. Owens
    •  & Loren H. Rieseberg
  • Review Article |

    Genetic strategies for improving the yield and sustainability of agricultural crops, and the resilience of crops in the face of biotic and abiotic stresses contingent on projected climate change, are evaluated.

    • Julia Bailey-Serres
    • , Jane E. Parker
    •  & Julian I. Schroeder
  • Letter |

    The yeast one-hybrid network for nitrogen-associated metabolism in Arabidopsis reveals the transcription factors that regulate the architecture of root and shoot systems under conditions of changing nitrogen availability.

    • Allison Gaudinier
    • , Joel Rodriguez-Medina
    •  & Siobhan M. Brady
  • Article
    | Open Access

    Constructing a reference genome for quinoa (Chenopodium quinoa) allows for genetic diversity during the evolution of sub-genomes in quinoa to be characterized and markers that may be used to develop sweet commercial varieties are identified.

    • David E. Jarvis
    • , Yung Shwen Ho
    •  & Mark Tester
  • Letter
    | Open Access

    The genome sequence and genetic diversity of European ash (Fraxinus excelsior) trees reveals the species’ varying susceptibility to ash dieback.

    • Elizabeth S. A. Sollars
    • , Andrea L. Harper
    •  & Richard J. A. Buggs
  • Article |

    Insights into the genomic architecture of heterosis for grain yield in rice are presented, and further mapping of grain yield loci resolves candidate genes that could be useful for breeding.

    • Xuehui Huang
    • , Shihua Yang
    •  & Bin Han
  • Letter |

    Structural, biochemical, mass spectrometry and genetic analyses define Arabidopsis thaliana AtD14 as a non-canonical hormone receptor for strigolactone, which hydrolyses strigolactone into a covalently linked intermediate molecule and undergoes an open-to-closed state transition for interaction with D3 to trigger strigolactone signalling.

    • Ruifeng Yao
    • , Zhenhua Ming
    •  & Daoxin Xie
  • Letter |

    The plant enzyme Rubisco is the main enzyme converting atmospheric carbon dioxide into biological compounds, however, this enzymatic process is inefficient in vascular plants; this study demonstrates that tobacco plants can be engineered to fix carbon with a faster cyanobacterial Rubisco, thus potentially improving plant photosynthesis.

    • Myat T. Lin
    • , Alessandro Occhialini
    •  & Maureen R. Hanson
  • Letter
    | Open Access

    A full genome sequence is presented of sugar beet Beta vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions.

    • Juliane C. Dohm
    • , André E. Minoche
    •  & Heinz Himmelbauer
  • Letter
    | Open Access

    The genome sequence of the African oil palm, the main source of oil production, is used to predict at least 34,802 genes, including oil biosynthesis genes; comparison with the draft sequence of the South American oil palm reveals that the two species may have diverged in the New World and that segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees.

    • Rajinder Singh
    • , Meilina Ong-Abdullah
    •  & Ravigadevi Sambanthamurthi
  • Letter |

    Genetic mapping and whole-genome sequencing studies identify the SHELL gene (a homologue of Arabidopsis SEEDSTICK) as responsible for the three different fruit forms in oil palm (Elaeis guineesis); this has important economic implications for modulating SHELL activity to breed desired fruit forms and enhance oil yields.

    • Rajinder Singh
    • , Eng-Ti Leslie Low
    •  & Robert A. Martienssen
  • Letter |

    In Arabidopsis, RNA-directed DNA methylation is a poorly understood gene silencing pathway in which small interfering RNAs generated by RNA polymerase IV (Pol-IV) target a DNA methyltransferase to its sites of action; here structural and genomic analyses demonstrate that SHH binds chromatin via repressive histone modifications and recruits Pol-IV to enable siRNA production.

    • Julie A. Law
    • , Jiamu Du
    •  & Steven E. Jacobsen
  • Letter
    | Open Access

    The Gossypium genus is used to investigate emergent consequences of polyploidy in cotton species; comparative genomic analyses reveal a complex evolutionary history including interactions among subgenomes that result in genetic novelty in elite cottons and provide insight into the evolution of spinnable fibres.

    • Andrew H. Paterson
    • , Jonathan F. Wendel
    •  & Jeremy Schmutz
  • Article
    | Open Access

    An integrated high-resolution genetic, physical and shotgun sequence assembly of the barley genome, one of the earliest domesticated and most important crops, is described; it will provide a platform for genome-assisted research and future crop improvement.

    • Klaus F. X. Mayer
    • , Robbie Waugh
    •  & Nils Stein
  • Letter |

    Sequencing of the Arabidopsis thaliana root microbiome shows that its composition is strongly influenced by location, inside or outside the root, and by soil type.

    • Derek S. Lundberg
    • , Sarah L. Lebeis
    •  & Jeffery L. Dangl
  • Letter
    | Open Access

    This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum.

    • Shusei Sato
    • , Satoshi Tabata
    •  & René M. Klein Lankhorst
  • Letter |

    The diffusion limited stereospecific enzyme chalcone isomerase represents the adaptive evolution of a catalytically perfected enzyme from non-catalytic, fatty-acid-binding proteins (FAPs) with contemporary roles in plant fatty-acid metabolism as evidenced by altered fatty acid content and marked reproductive defects in Arabidopsis thaliana plants bearing FAP knockouts.

    • Micheline N. Ngaki
    • , Gordon V. Louie
    •  & Joseph P. Noel
  • Letter |

    The transcription of repetitive elements such as retrotransposons is normally repressed, to prevent their unchecked dissemination throughout the genome. This study shows that heat stress induces the transcription of the ONSEN retroelement. The accumulation of ONSEN is suppressed by small interfering RNAs. When siRNAs were absent, new ONSEN insertions were found in the progeny of heat-stressed plants, having transposed during differentiation. These results imply a memory of stress that can be counteracted by siRNAs.

    • Hidetaka Ito
    • , Hervé Gaubert
    •  & Jerzy Paszkowski
  • Letter |

    Circadian rhythms regulate a wide variety of developmental and metabolic processes resulting in enhanced fitness. In this study, a link is made between plant immune responses and the circadian clock. Plant defence against a fungal pathogen which causes downy mildew disease in Arabidopsis is studied, and it is shown that a novel set of defence genes are regulated by the circadian regulator CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1). The mechanism allows plants to 'anticipate' infection at dawn when the pathogen normally disperses its spores. Such a cross-talk mechanism reveals an important strategy for plants to time immune responses against pathogens.

    • Wei Wang
    • , Jinyoung Yang Barnaby
    •  & Xinnian Dong
  • Letter |

    Here, a combination of forward genetics and genome-wide association analyses has been used to show that variation at a single genetic locus in Arabidopsis thaliana underlies phenotypic variation in vegetative growth as well as resistance to infection. The strong enhancement of resistance mediated by one of the alleles at this locus explains the allele's persistence in natural populations throughout the world, even though it drastically reduces the production of new leaves.

    • Marco Todesco
    • , Sureshkumar Balasubramanian
    •  & Detlef Weigel
  • Letter |

    Nucleosomes are composed of around 147 bases of DNA wrapped around an octamer of histone proteins. Here, a genome-wide analysis of nucleosome positioning in Arabidopsis thaliana has been combined with profiles of DNA methylation at single base resolution, revealing 10-base periodicities in the DNA methylation status of nucleosome-bound DNA. The results indicate that nucleosome positioning influences the pattern of DNA methylation throughout the genome.

    • Ramakrishna K. Chodavarapu
    • , Suhua Feng
    •  & Matteo Pellegrini
  • Letter |

    DNA methylation is an important epigenetic mark in many eukaryotes. In Arabidopsis plants, small interfering RNAs bound to the Argonaute 4 (AGO4) protein can direct de novo DNA methylation and consequent gene silencing. Here, a new regulator of RNA-directed DNA methylation has been discovered. This protein, RDM1, is proposed to bind to methylated DNA and to function in the AGO4 effector complex.

    • Zhihuan Gao
    • , Hai-Liang Liu
    •  & Jian-Kang Zhu
  • Article |

    A fundamental question in developmental biology is how cells communicate positional information to pattern the tissues of an organ. Here, the patterning of a plant's xylem tubes, which transport water and solutes from root to shoot, is studied. A new bidirectional signalling pathway is discovered, whereby a transcription factor moves from cell to cell in one direction, and microRNAs move in the other direction. The result is a differential distribution of target mRNA in the vascular cylinder, determining xylem cell types.

    • Annelie Carlsbecker
    • , Ji-Young Lee
    •  & Philip N. Benfey
  • Letter |

    Making haploid plants — which inherit chromosomes from only one parent — is useful for genetic research and also, crucially, for plant breeding. A new method for generating haploid Arabidopsis plants is now described, involving the manipulation of a single centromeric protein, CENH3. When cenh3 null plants are crossed with wild-type plants, the mutant chromosomes are eliminated, producing haploid progeny.

    • Maruthachalam Ravi
    •  & Simon W. L. Chan
  • Letter |

    Here, large-scale genome-wide association studies were carried out with the naturally occurring inbred lines of Arabidopsis thaliana, which can be genotyped once and phenotyped repeatedly. The results range from significant associations, usually corresponding to single genes, to findings that are more difficult to interpret, because confounding by complex genetics and population structure makes it hard to distinguish true associations from false.

    • Susanna Atwell
    • , Yu S. Huang
    •  & Magnus Nordborg
  • Article
    | Open Access

    Soybean is an important crop plant, providing seed protein and oil and fixing atmospheric nitrogen through symbioses with soil-borne microorganisms. Using a whole-genome shotgun approach, its 1.1-gigabase genome is now sequenced and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly.

    • Jeremy Schmutz
    • , Steven B. Cannon
    •  & Scott A. Jackson