Plant genetics articles within Nature Communications

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  • Article
    | Open Access

    Phytochromes are red-light photoreceptors in plants that regulate key life cycle processes, yet their evolutionary origins are not well understood. Using transcriptomic and genomic data, Li et al.find that canonical plant phytochromes originated in a common ancestor of land plants and charophyte algae.

    • Fay-Wei Li
    • , Michael Melkonian
    •  & Sarah Mathews

  • Article
    | Open Access

    Kelps are ecologically and economically important seaweeds. Here the authors sequence the genome of Saccharina japonicato gain insights into the evolutionary adaptation of polysaccharide biosynthesis, iodine concentration and antioxidation mechanisms and the population genetics of kelp domestication.

    • Naihao Ye
    • , Xiaowen Zhang
    •  & Fangqing Zhao

  • Article
    | Open Access

    Structural variations in crop genomes are thought to be responsible for significant differences in phenotype and they can be well-represented by a ‘pan-genome’. Here, Lu et al.develop an approach to genetically map pan-genome sequence anchors using 14,129 inbred lines of maize, showing structural variation is a significant source of adaptive variation.

    • Fei Lu
    • , Maria C. Romay
    •  & Edward S. Buckler

  • Article |

    Nitrogen and phosphorous are both major macronutrients and important signalling molecules that regulate plant growth. Here, Medici et al.show that nitrogen and phosphorous signals converge at the HRS1 transcription factor to regulate the root elongation in response to nutrient deficiency.

    • Anna Medici
    • , Amy Marshall-Colon
    •  & Gabriel Krouk

  • Article
    | Open Access

    Cotton fibre is the most important renewable material for textiles, with a huge economic output. Here the authors show that a homeodomain-leucine zipper transcription factor, GhHOX3, transduces a gibberellin signal that in turn promotes fibre cell elongation.

    • Chun-Min Shan
    • , Xiao-Xia Shangguan
    •  & Xiao-Ya Chen

  • Article |

    Haploid production technology has the potential to accelerate genetic research and breeding in plants. Here Ravi et al. describe a suite of genetic methods to demonstrate the effectiveness of haploid technology for basic research in Arabidopsis.

    • Maruthachalam Ravi
    • , Mohan Prem Anand Marimuthu
    •  & Simon W. L. Chan

  • Article
    | Open Access

    Cassava is a major source of food in tropical and subtropical regions. Here the authors sequence the genomes of wild and domesticated cassava varieties and identify genes that have been selected for and against during the evolution and domestication of this economically important crop.

    • Wenquan Wang
    • , Binxiao Feng
    •  & Ming Peng

  • Article |

    Hybrid rice varieties are bred using male-sterile maternal lines, which are unable to self-pollinate. Here, the authors show that mutations of the tms5 gene, which codes for RNase ZS1, result in the accumulation of ubiquitin fusion ribosomal protein mRNAs at high temperature to confer genic male sterility.

    • Hai Zhou
    • , Ming Zhou
    •  & Chuxiong Zhuang

  • Article
    | Open Access

    Rice stripe virus (RSV) causes a disease in rice with significant economic consequences. Here, the authors clone an RSV-resistant gene in rice and suggest that this gene encodes a sulphotransferase that catalyses the conversion of salicylic acid (SA) into sulphonated salicylic acid, leading to increased SA accumulation in RSV-infected plants and inhibition of viral replication.

    • Qi Wang
    • , Yuqiang Liu
    •  & Jianmin Wan

  • Article
    | Open Access

    Fertility in polyploid species relies on pairing and recombination occurring only between true homologues rather than the diverged homoeologous chromosomes also present. Here, Martin et al.show that Ph1 stabilises polyploidy in wheat by promoting homologue pairing and preventing crossovers on paired homoeologues during meiosis.

    • Azahara C. Martín
    • , Peter Shaw
    •  & Graham Moore

  • Article
    | Open Access

    The identification of genes that control economically important traits is an essential step towards crop improvement. Here the authors sequence the genome of the wild soybean and, through a combined genetic and functional approach, identify a new gene affecting salt tolerance in soybean.

    • Xinpeng Qi
    • , Man-Wah Li
    •  & Hon-Ming Lam

  • Article
    | Open Access

    Fruit colour is a trait that affects the harvesting, and therefore oil yield, of the economically important oil palm. Here, the authors identify a gene that may control fruit colour in the oil palm and suggest that selection for this gene during early development could advance the breeding potential of this important crop.

    • Rajinder Singh
    • , Eng-Ti Leslie Low
    •  & Ravigadevi Sambanthamurthi

  • Article
    | Open Access

    Nucleocytoplasmic large DNA viruses, NCLDVs, are eukaryotic viruses with large genomes, known to infect animals and diverse unicellular eukaryotes. Here, Maumus et al. find NCLDV-like sequences in two land plants and show that they are transcriptionally inactive and highly methylated.

    • Florian Maumus
    • , Aline Epert
    •  & Guillaume Blanc

  • Article |

    Selecting for varieties of commercial crops with enhanced nutritional quality is important in agriculture. Here, the authors identify alleles of a gene in tomatoes that give rise to increased levels of vitamin E and find that the promoter of the gene is differentially methylated.

    • Leandro Quadrana
    • , Juliana Almeida
    •  & Fernando Carrari

  • Article
    | Open Access

    Brassica oleracea is plant species comprising economically important vegetable crops. Here, the authors report the draft genome sequence of B. oleracea and, through a comparative analysis with the closely related B. rapa, reveal insights into Brassicaevolution and divergence of interspecific genomes and intraspecific subgenomes.

    • Shengyi Liu
    • , Yumei Liu
    •  & Andrew H Paterson

  • Article
    | Open Access

    Common tobacco (Nicotiana tabacum) is a widely cultivated and economically important non-food crop. Here, the authors report the draft genome sequences for three of the most common tobacco varieties and provide insights into the evolution of tobacco through a comparative analysis with closely related species.

    • Nicolas Sierro
    • , James N.D. Battey
    •  & Nikolai V. Ivanov

  • Article
    | Open Access

    Plants produce a variety of metabolites that have a critical role in growth and development. Here, the authors carry out a genome-wide association analysis of metabolites and metabolite features in maize and identify candidate genes involved in secondary metabolism, and a potential biomarker for the genetic improvement of the crop.

    • Weiwei Wen
    • , Dong Li
    •  & Jianbing Yan

  • Article
    | Open Access

    Hybrids often show poorer performance than their parents due to conflict between parental genes, but the underlying mechanisms are not well understood. Here, Chen et al. identify three genes that activate immune responses and hinder hybrids growth in rice, a finding that may help rice breeding.

    • Chen Chen
    • , Hao Chen
    •  & Hong-Xuan Lin

  • Article |

    Determining the link between gene polymorphisms and phenotypic traits is the subject of intense research in agricultural plant science. In this study, Fu et al. conduct RNA sequencing in maize kernels to determine gene polymorphisms, which may aid future research aiming to improve the nutritional value of maize.

    • Junjie Fu
    • , Yanbing Cheng
    •  & Guoying Wang

  • Article |

    FLOWERING LOCUS T is an important mobile signal that regulates plant development and flowering. In this study, Lee et al. demonstrate that multiple FLOWERING LOCUS Tgenes are involved in onion flowering and bulb formation.

    • Robyn Lee
    • , Samantha Baldwin
    •  & Richard Macknight

  • Article |

    MADS-box genes regulate flowering plant development, but their evolutionary origins are unclear. Here, Ruelens et al.show that three major, apparently flowering plant-specific, MADS-box gene clades are derived from a single ancestral tandem duplication, and identify FLOWERING LOCUS C-like genes in cereals.

    • Philip Ruelens
    • , Ruud A. de Maagd
    •  & Kerstin Kaufmann

  • Article
    | Open Access

    The date palm is one of the most economically important plants of the palm family. Here, the authors present a high-quality genome assembly of the date palm Phoenix dactylifera, and reveal insights into the unique sugar metabolism underlying fruit ripening.

    • Ibrahim S. Al-Mssallem
    • , Songnian Hu
    •  & Jun Yu

  • Article
    | Open Access

    Transition from a spread panicle typical of ancestral wild rice to the compact panicle of present cultivars was a crucial event in rice domestication. Here the authors show that this panicle architecture is controlled by the transcription factor OsLG1 and that a mutation in its regulatory region led to the compact panicle phenotype.

    • Zuofeng Zhu
    • , Lubin Tan
    •  & Chuanqing Sun

  • Article
    | Open Access

    Quantitative trait loci mapping has traditionally been used to discover desirable alleles in plants. In this study, Lyu et al. use a comparative genome approach to identify an allele that is prevalent in upland rice varieties and alters the function of a protein involved in abscisic acid biosynthesis.

    • Jun Lyu
    • , Shilai Zhang
    •  & Wen Wang

  • Article
    | Open Access

    The wild rice species can be used as germplasm resources for this crop’s genetic improvement. Here Chen and colleagues report the de novo sequencing of the O. brachyanthagenome, and identify the origin of genome size variation, the role of gene movement and its implications on heterochromatin evolution in the rice genome.

    • Jinfeng Chen
    • , Quanfei Huang
    •  & Mingsheng Chen

  • Article
    | Open Access

    Sorghum is a drought-adapted cereal, but the grains have lower digestibility than other cereal crops. This work shows that a low-frequency allele type in the starch metabolic gene pullulanase is associated with increased digestibility, which may help improve sorghum yield and therefore food security.

    • Edward K. Gilding
    • , Celine H. Frère
    •  & Ian D. Godwin

  • Article |

    Plants such asArabidopsishave evolved genetic adaptations to their geographic location. Here, a network-based approach is applied to study the link between geographic location and heterogeneous molecular phenotypes, revealing a pattern of isolation by distance in genotypic variability, flowering and metabolic phenotypes.

    • Sabrina Kleessen
    • , Carla Antonio
    •  & Zoran Nikoloski

  • Article
    | Open Access

    The Prunus mume was domesticated in China over 3,000 years ago and is an important ornamental plant and fruit. Here Qixiang Zhang et al.obtain the first assembly of its genome with a combination of next-generation sequencing, whole-genome mapping and restriction-site-associated DNA.

    • Qixiang Zhang
    • , Wenbin Chen
    •  & Jun Wang

  • Article |

    Epigenetic modifications are thought to affect the accessibility of DNA, but it is not clear whether this is a universal effect. These authors map DNA accessibility inArabidopsis thalianaand find that, in contrast to fruitflies, H3K9 dimethylation reduces accessibility in a DNA methylation-dependent manner.

    • Huan Shu
    • , Thomas Wildhaber
    •  & Lars Hennig

  • Article
    | Open Access

    Although horizontal gene transfer is prevalent in microorganisms, such sharing of genetic information is thought to be rare in land plants. Focusing on the sequenced moss species,Physcomitrella patens, these authors report genes acquired from microorganisms, which might have facilitated early evolution of land plants.

    • Jipei Yue
    • , Xiangyang Hu
    •  & Jinling Huang

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