Volume 43 Issue 2, February 2011

Volume 43 Issue 2

Cover art by Erin Dewalt

Editorial

  • Editorial |

    As genome sequencing becomes more versatile and easier, the journal prioritizes those genomic sequences that maximize the prospects of harnessing genome variation and understanding evolutionary processes.

News and Views

  • News & Views |

    Two studies illustrate that with the appropriate resources and scale of study, most of the heritability of complex traits in maize is not missing, but can be located within the genome. Given that maize is one of the world's most important crop plants, this has implications for feeding a growing population with minimum carbon footprint as well as for understanding the genetics of complex traits in a range of species.

    • Chris Haley
  • News & Views |

    A new study shows that the piRNA-binding protein Piwi interacts with Hsp90 and suppresses phenotypic variation in Drosophila melanogaster by preventing the expression of hidden epigenetic variation. This suggests that Hsp90 and Piwi function are dampened in times of stress to increase genetic and epigenetic variability, providing a last-ditch mechanism for a species to survive.

    • Douglas M Ruden
  • News & Views |

    Two new studies show that mutations in tartrate-resistant acid phosphatase (TRAP) cause spondyloenchondrodysplasia, a rare recessive disease associated with short stature, brain calcifications and lupus-like autoimmunity. The complex clinical syndrome is probably mediated by impaired dephosphorylation of osteopontin.

    • Timothy W Behrens
    •  & Robert R Graham

Research Highlights

Analysis

  • Analysis |

    Johan Paulsson and Dann Huh report a mathematical modeling analysis proposing that stochastic partitioning errors during cell division contribute to non-genetic heterogeneity between cells in a population. They find that fluctuations arising from such partitioning errors are difficult to suppress and can mimic noise in gene expression.

    • Dann Huh
    •  & Johan Paulsson

Articles

  • Article | | open

    Xavier Argout and colleagues report the draft genome of Theobroma cacao, the tropical crop that is the source of chocolate. The sequence assembly covers approximately 80% of the genome.

    • Xavier Argout
    • , Jerome Salse
    • , Jean-Marc Aury
    • , Mark J Guiltinan
    • , Gaetan Droc
    • , Jerome Gouzy
    • , Mathilde Allegre
    • , Cristian Chaparro
    • , Thierry Legavre
    • , Siela N Maximova
    • , Michael Abrouk
    • , Florent Murat
    • , Olivier Fouet
    • , Julie Poulain
    • , Manuel Ruiz
    • , Yolande Roguet
    • , Maguy Rodier-Goud
    • , Jose Fernandes Barbosa-Neto
    • , Francois Sabot
    • , Dave Kudrna
    • , Jetty Siva S Ammiraju
    • , Stephan C Schuster
    • , John E Carlson
    • , Erika Sallet
    • , Thomas Schiex
    • , Anne Dievart
    • , Melissa Kramer
    • , Laura Gelley
    • , Zi Shi
    • , Aurélie Bérard
    • , Christopher Viot
    • , Michel Boccara
    • , Ange Marie Risterucci
    • , Valentin Guignon
    • , Xavier Sabau
    • , Michael J Axtell
    • , Zhaorong Ma
    • , Yufan Zhang
    • , Spencer Brown
    • , Mickael Bourge
    • , Wolfgang Golser
    • , Xiang Song
    • , Didier Clement
    • , Ronan Rivallan
    • , Mathias Tahi
    • , Joseph Moroh Akaza
    • , Bertrand Pitollat
    • , Karina Gramacho
    • , Angélique D'Hont
    • , Dominique Brunel
    • , Diogenes Infante
    • , Ismael Kebe
    • , Pierre Costet
    • , Rod Wing
    • , W Richard McCombie
    • , Emmanuel Guiderdoni
    • , Francis Quetier
    • , Olivier Panaud
    • , Patrick Wincker
    • , Stephanie Bocs
    •  & Claire Lanaud
  • Article | | open

    The International Strawberry Sequencing Consortium reports the draft genome of the woodland strawberry (Fragaria vesca). The genome of this diploid species should serve as a reference genome for the Fragaria genus, as the cultivated strawberry (Fragaria × ananassa) is an octoploid where F. vesca is predicted to be a subgenome donor.

    • Vladimir Shulaev
    • , Daniel J Sargent
    • , Ross N Crowhurst
    • , Todd C Mockler
    • , Otto Folkerts
    • , Arthur L Delcher
    • , Pankaj Jaiswal
    • , Keithanne Mockaitis
    • , Aaron Liston
    • , Shrinivasrao P Mane
    • , Paul Burns
    • , Thomas M Davis
    • , Janet P Slovin
    • , Nahla Bassil
    • , Roger P Hellens
    • , Clive Evans
    • , Tim Harkins
    • , Chinnappa Kodira
    • , Brian Desany
    • , Oswald R Crasta
    • , Roderick V Jensen
    • , Andrew C Allan
    • , Todd P Michael
    • , Joao Carlos Setubal
    • , Jean-Marc Celton
    • , D Jasper G Rees
    • , Kelly P Williams
    • , Sarah H Holt
    • , Juan Jairo Ruiz Rojas
    • , Mithu Chatterjee
    • , Bo Liu
    • , Herman Silva
    • , Lee Meisel
    • , Avital Adato
    • , Sergei A Filichkin
    • , Michela Troggio
    • , Roberto Viola
    • , Tia-Lynn Ashman
    • , Hao Wang
    • , Palitha Dharmawardhana
    • , Justin Elser
    • , Rajani Raja
    • , Henry D Priest
    • , Douglas W Bryant Jr
    • , Samuel E Fox
    • , Scott A Givan
    • , Larry J Wilhelm
    • , Sushma Naithani
    • , Alan Christoffels
    • , David Y Salama
    • , Jade Carter
    • , Elena Lopez Girona
    • , Anna Zdepski
    • , Wenqin Wang
    • , Randall A Kerstetter
    • , Wilfried Schwab
    • , Schuyler S Korban
    • , Jahn Davik
    • , Amparo Monfort
    • , Beatrice Denoyes-Rothan
    • , Pere Arus
    • , Ron Mittler
    • , Barry Flinn
    • , Asaph Aharoni
    • , Jeffrey L Bennetzen
    • , Steven L Salzberg
    • , Allan W Dickerman
    • , Riccardo Velasco
    • , Mark Borodovsky
    • , Richard E Veilleux
    •  & Kevin M Folta

Letters

  • Letter |

    Ewan Pearson and colleagues report a genome-wide association study for glycemic response to metformin in individuals with type 2 diabetes. They identify variants near ATM associated with treatment success.

    • The GoDARTS and UKPDS Diabetes Pharmacogenetics Study Group
    • , Kaixin Zhou
    • , Celine Bellenguez
    • , Chris C A Spencer
    • , Amanda J Bennett
    • , Ruth L Coleman
    • , Roger Tavendale
    • , Simon A Hawley
    • , Louise A Donnelly
    • , Chris Schofield
    • , Christopher J Groves
    • , Lindsay Burch
    • , Fiona Carr
    • , Amy Strange
    • , Colin Freeman
    • , Jenefer M Blackwell
    • , Elvira Bramon
    • , Matthew A Brown
    • , Juan P Casas
    • , Aiden Corvin
    • , Nicholas Craddock
    • , Panos Deloukas
    • , Serge Dronov
    • , Audrey Duncanson
    • , Sarah Edkins
    • , Emma Gray
    • , Sarah Hunt
    • , Janusz Jankowski
    • , Cordelia Langford
    • , Hugh S Markus
    • , Christopher G Mathew
    • , Robert Plomin
    • , Anna Rautanen
    • , Stephen J Sawcer
    • , Nilesh J Samani
    • , Richard Trembath
    • , Ananth C Viswanathan
    • , Nicholas W Wood
    • , Lorna W Harries
    • , Andrew T Hattersley
    • , Alex S F Doney
    • , Helen Colhoun
    • , Andrew D Morris
    • , Calum Sutherland
    • , D Grahame Hardie
    • , Leena Peltonen
    • , Mark I McCarthy
    • , Rury R Holman
    • , Colin N A Palmer
    • , Peter Donnelly
    • , Ewan R Pearson
    •  & The Wellcome Trust Case Control Consortium 2
  • Letter |

    Aida Bertoli-Avella and colleagues report the identification of SMAD3 mutations in individuals with a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis. The mutations cause increased aortic expression of components of the TGF-β signaling pathway.

    • Ingrid M B H van de Laar
    • , Rogier A Oldenburg
    • , Gerard Pals
    • , Jolien W Roos-Hesselink
    • , Bianca M de Graaf
    • , Judith M A Verhagen
    • , Yvonne M Hoedemaekers
    • , Rob Willemsen
    • , Lies-Anne Severijnen
    • , Hanka Venselaar
    • , Gert Vriend
    • , Peter M Pattynama
    • , Margriet Collée
    • , Danielle Majoor-Krakauer
    • , Don Poldermans
    • , Ingrid M E Frohn-Mulder
    • , Dimitra Micha
    • , Janneke Timmermans
    • , Yvonne Hilhorst-Hofstee
    • , Sita M Bierma-Zeinstra
    • , Patrick J Willems
    • , Johan M Kros
    • , Edwin H G Oei
    • , Ben A Oostra
    • , Marja W Wessels
    •  & Aida M Bertoli-Avella
  • Letter |

    Yanick Crow and colleagues show that mutations in ACP5, which encodes tartrate-resistant acid phosphatase, cause spondyloenchondrodysplasia, a bone dysplasia with autoimmunity. The affected individuals had elevated serum interferon alpha activity.

    • Tracy A Briggs
    • , Gillian I Rice
    • , Sarah Daly
    • , Jill Urquhart
    • , Hannah Gornall
    • , Brigitte Bader-Meunier
    • , Kannan Baskar
    • , Shankar Baskar
    • , Veronique Baudouin
    • , Michael W Beresford
    • , Graeme C M Black
    • , Rebecca J Dearman
    • , Francis de Zegher
    • , Emily S Foster
    • , Camille Francès
    • , Alison R Hayman
    • , Emma Hilton
    • , Chantal Job-Deslandre
    • , Muralidhar L Kulkarni
    • , Martine Le Merrer
    • , Agnes Linglart
    • , Simon C Lovell
    • , Kathrin Maurer
    • , Lucile Musset
    • , Vincent Navarro
    • , Capucine Picard
    • , Anne Puel
    • , Frederic Rieux-Laucat
    • , Chaim M Roifman
    • , Sabine Scholl-Bürgi
    • , Nigel Smith
    • , Marcin Szynkiewicz
    • , Alice Wiedeman
    • , Carine Wouters
    • , Leo A H Zeef
    • , Jean-Laurent Casanova
    • , Keith B Elkon
    • , Anthony Janckila
    • , Pierre Lebon
    •  & Yanick J Crow
  • Letter |

    Andrea Superti-Furga and colleagues report that mutations in ACP5, which encodes tartrate-resistant phosphatase, cause spondyloenchondrodysplasia, a syndrome of skeletal dysplasia, cerebral calcifications and autoimmunity. The affected individuals had elevated levels of phosphorylated osteopontin.

    • Ekkehart Lausch
    • , Andreas Janecke
    • , Matthias Bros
    • , Stefanie Trojandt
    • , Yasemin Alanay
    • , Corinne De Laet
    • , Christian A Hübner
    • , Peter Meinecke
    • , Gen Nishimura
    • , Mari Matsuo
    • , Yoshiko Hirano
    • , Sylvie Tenoutasse
    • , Andrea Kiss
    • , Rafael Fabiano Machado Rosa
    • , Sharon L Unger
    • , Raffaele Renella
    • , Luisa Bonafé
    • , Jürgen Spranger
    • , Sheila Unger
    • , Bernhard Zabel
    •  & Andrea Superti-Furga
  • Letter |

    Johan P de Winter and colleagues report the identification of mutations in SLX4 in a new Fanconi anemia subtype. SLX4 regulates structure-specific endonucleases, important enzymes in the DNA damage response.

    • Chantal Stoepker
    • , Karolina Hain
    • , Beatrice Schuster
    • , Yvonne Hilhorst-Hofstee
    • , Martin A Rooimans
    • , Jurgen Steltenpool
    • , Anneke B Oostra
    • , Katharina Eirich
    • , Elisabeth T Korthof
    • , Aggie W M Nieuwint
    • , Nicolaas G J Jaspers
    • , Thomas Bettecken
    • , Hans Joenje
    • , Detlev Schindler
    • , John Rouse
    •  & Johan P de Winter
  • Letter |

    Agata Smogorzewska and colleagues report mutations in SLX4 in a new subtype of Fanconi anemia. SLX4 is an endonuclease involved in DNA maintenance and repair.

    • Yonghwan Kim
    • , Francis P Lach
    • , Rohini Desetty
    • , Helmut Hanenberg
    • , Arleen D Auerbach
    •  & Agata Smogorzewska
  • Letter |

    Ketan Patel and colleagues report a new mouse model of Fanconi anemia. The authors show that mice deficient in Btbd12, the mouse ortholog of SLX4 (a new Fanconi anemia gene), phenocopy the human disease.

    • Gerry P Crossan
    • , Louise van der Weyden
    • , Ivan V Rosado
    • , Frederic Langevin
    • , Pierre-Henri L Gaillard
    • , Rebecca E McIntyre
    • , Sanger Mouse Genetics Project
    • , Ferdia Gallagher
    • , Mikko I Kettunen
    • , David Y Lewis
    • , Kevin Brindle
    • , Mark J Arends
    • , David J Adams
    •  & Ketan J Patel
  • Letter |

    Haifan Lin and colleagues report the identification in Drosophila of a protein complex composed of Hsp90 Piwi, and the Hsp70/Hsp90 Organizing Protein Homolog (Hop) and demonstrate the function of this complex in buffering against morphological changes in a sensitized background.

    • Vamsi K Gangaraju
    • , Hang Yin
    • , Molly M Weiner
    • , Jianquan Wang
    • , Xiao A Huang
    •  & Haifan Lin
  • Letter |

    Ed Buckler and colleagues report a genome-wide association study for leaf architecture in the maize nested association mapping population. Genetic variation at the ligueless genes is associated with leaf angle, an important agronomic trait.

    • Feng Tian
    • , Peter J Bradbury
    • , Patrick J Brown
    • , Hsiaoyi Hung
    • , Qi Sun
    • , Sherry Flint-Garcia
    • , Torbert R Rocheford
    • , Michael D McMullen
    • , James B Holland
    •  & Edward S Buckler
  • Letter |

    James Holland and colleagues report a genome-wide association study for resistance to Southern Leaf Blight (SLB) in the maize nested association mapping population. Linkage mapping identified 32 QTLs linked to SLB resistance, and association tests showed that 51 SNPs, many located within the QTL intervals, are significantly associated with SLB resistance.

    • Kristen L Kump
    • , Peter J Bradbury
    • , Randall J Wisser
    • , Edward S Buckler
    • , Araby R Belcher
    • , Marco A Oropeza-Rosas
    • , John C Zwonitzer
    • , Stephen Kresovich
    • , Michael D McMullen
    • , Doreen Ware
    • , Peter J Balint-Kurti
    •  & James B Holland
  • Letter |

    Robbie Waugh and colleagues show that INTERMEDIUM-C, a locus that modifies spikelet fertility in barley, is encoded by an orthologue of the maize domestication gene TEOSINTE BRANCHED 1. Differences in spikelet fertility contributed to barley domestication.

    • Luke Ramsay
    • , Jordi Comadran
    • , Arnis Druka
    • , David F Marshall
    • , William T B Thomas
    • , Malcolm Macaulay
    • , Katrin MacKenzie
    • , Craig Simpson
    • , John Fuller
    • , Nicola Bonar
    • , Patrick M Hayes
    • , Udda Lundqvist
    • , Jerome D Franckowiak
    • , Timothy J Close
    • , Gary J Muehlbauer
    •  & Robbie Waugh