Experimental organisms articles within Nature Genetics

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  • News & Views |

    Three new studies report large-scale resequencing and comparative genomic analysis of diverse maize varieties. The authors conducted a comprehensive characterization of sequence variation in maize genomes and identified signals of selection in maize domestication and breeding.

    • Xuehui Huang
    •  & Bin Han

  • Letter |

    Xiangdong Fu and colleagues map variants in OsSPL16 that influence grain width and yield in a cross between a slender-grain Basmati and a wide-grain indica variety of rice. The authors show that higher expression of OsSPL16 promotes cell division and grain filling and can lead to improvements in grain quality and yield.

    • Shaokui Wang
    • , Kun Wu
    •  & Xiangdong Fu

  • Technical Report |

    Magnus Nordborg and colleagues report a multi-locus mixed-model method (MLMM) for genome-wide association studies in structured populations. Their simulations show that MLMM offers increased power and a reduced false discovery rate, and applications to both human and Arabidopsis thaliana data sets identify new associations and allelic heterogeneity.

    • Vincent Segura
    • , Bjarni J Vilhjálmsson
    •  & Magnus Nordborg

  • Letter |

    Jinsheng Lai and colleagues report the resequencing of 278 inbred maize lines and perform a genome-wide analysis of genetic changes during modern breeding. Using SNP imputation, the authors also perform a genome-wide association study for cob color, silk color and date to anthesis. The authors identified association signals with significant P values near known targets.

    • Yinping Jiao
    • , Hainan Zhao
    •  & Jinsheng Lai

  • Letter |

    The nucleotide diversity present in maize exceeds that in humans by an order of magnitude, and it has been challenging to characterize the high levels of diversity in this important crop. Doreen Ware and colleagues have identified 55 million SNPs in 103 domesticated and pre-domestication Zea mays varieties, as well as in a representative from the sister genus Tripsacum.

    • Jer-Ming Chia
    • , Chi Song
    •  & Doreen Ware

  • Editorial |

    Animal experimentation in scientific research is a good thing: important, increasing and often irreplaceable. Careful experimental design and reporting are at least as important as attention to welfare in ensuring that the knowledge we gain justifies using live animals as experimental tools.

  • Article |

    Eran Segal and colleagues measure the promoter activities of 70 different constructed promoter variants and find that poly(dA:dT) tracts significantly affect transcriptional outcome. They suggest that this is mediated by altering nucleosome organization and that these sequences can be manipulated to fine tune regulation of gene expression.

    • Tali Raveh-Sadka
    • , Michal Levo
    •  & Eran Segal

  • Technical Report |

    To take advantage of hybrid vigor, most crop plants are grown with hybrid seeds, which are produced afresh by crossing elite inbred lines. Here, Erik Wijnker and colleagues demonstrate the feasibility of reverse breeding, a method that enables the generation of homozygous parental lines from a hybrid individual in the plant model organism Arabidopsis thaliana. Homozygous parents can be maintained indefinitely, better facilitating future improvements.

    • Erik Wijnker
    • , Kees van Dun
    •  & Rob Dirks

  • Article |

    David Mitchell, Hannah Mitchison and colleagues identify a new Chlamydomonas protein required for the preassembly of axonemal dyneins before their transport into cilia. They further show that mutations in the homologous gene in humans result in primary ciliary dyskinesia accompanied by defects in the assembly of inner and outer dynein arms.

    • Hannah M Mitchison
    • , Miriam Schmidts
    •  & David R Mitchell

  • News & Views |

    A new study reports a comprehensive survey of genetic diversity in natural populations of the nematode Caenorhabditis elegans. Their analyses suggest that recent chromosome-scale selective sweeps have reduced C. elegans genetic diversity worldwide and strongly structured genetic variation across its genome.

    • Patrick C Phillips

  • Article |

    Leonid Kruglyak and colleagues report high-throughput selective sequencing of a worldwide collection of 200 wild C. elegans strains, providing a comprehensive characterization of genetic variation in this species. They find that chromosome-scale selective sweeps have acted to reduce genetic variation and shape the C. elegans population structure in recent history.

    • Erik C Andersen
    • , Justin P Gerke
    •  & Leonid Kruglyak

  • News & Views |

    A new study reports SNP genotypes of over 1,300 Arabidopsis thaliana accessions from throughout Eurasia, providing a resource for genome-wide association studies and studies of local adaptation. The extensive data are also used to identify targets of natural selection and to describe genome-wide patterns of recombination.

    • Brandon Gaut

  • Letter |

    Albrecht Melchinger and colleagues report a complementary approach to phenotype-based screening for hybrid maize. The new approach accurately predicts the combining abilities of agronomical traits based on genomic and metabolomic information comprising 56,110 SNPs and 130 metabolite measurements.

    • Christian Riedelsheimer
    • , Angelika Czedik-Eysenberg
    •  & Albrecht E Melchinger

  • Letter |

    Joy Bergelson and colleagues characterize genome-wide patterns of genetic variation in a collection of 1,307 worldwide Arabidopsis thaliana accessions from the Regional Mapping (RegMap) panel, a publicly available genomic resource that includes large regional panels. They characterize signatures of selection and patterns of recombination and identify an enrichment of hotspots in intergenic regions and in repetitive DNA.

    • Matthew W Horton
    • , Angela M Hancock
    •  & Joy Bergelson

  • Article |

    Fernando Pardo-Manuel de Villena, Gary Churchill and colleagues provide a high-resolution phylogenetic map of mouse inbred strains based on comparisons to wild-caught mice. They show that the genomes of classical strains are overwhelmingly derived from Mus musculus domesticus whereas wild-derived laboratory strains include a broad sampling of diversity from multiple subspecies with pervasive introgression. The subspecific origin, haplotype diversity and identity-by-descent map of laboratory strains can be visualized at http://msub.csbio.unc.edu/PhylogenyTool.html.

    • Hyuna Yang
    • , Jeremy R Wang
    •  & Fernando Pardo-Manuel de Villena

  • Article |

    Michael Weber and colleagues present profiles of DNA methylation during early development of the mouse embryonic lineage in vivo. They profile 10% of the mouse genome covering all known gene promoters. They show that DNA methylation is targeted to specific gene promoters and is required to maintain gene repression.

    • Julie Borgel
    • , Sylvain Guibert
    •  & Michael Weber

  • Article |

    Bin Han and colleagues performed low-coverage sequencing of 517 rice landraces and constructed a high-density haplotype map of the rice genome. They have used this resource to carry out genome-wide association studies for 14 agronomic traits and identify 80 loci with strong association signals.

    • Xuehui Huang
    • , Xinghua Wei
    •  & Bin Han

  • News & Views |

    The virulence of Candida albicans, a major human fungal pathogen, has been considered dependent on the ability to transition between different morphologies. A new study reports a screen of C. albicans mutants that demonstrates that pathogenesis can be dissociated from morphological switching and in vitro growth rate.

    • P T Magee

  • Letter |

    Takeshi Izawa and colleagues report that the rice florigen gene Hd3a, which triggers photoperiodic flowering, is toggled by a 30-minute change in day length. They report that Hd3a transcription is controlled by two gating mechanisms involving the floral promoter Ehd1 and the floral repressor Ghd7.

    • Hironori Itoh
    • , Yasunori Nonoue
    •  & Takeshi Izawa

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