Volume 48 Issue 9, September 2016

Volume 48 Issue 9

Cover Art: Cerealists by Rachel Meyer

Editorial

  • Editorial |

    The coevolution of staple crops and human society can be traced in the relics of ancient genomes and in population genetic signatures that our interdependence has left on our genomes and those of our crop plants. Patterns of geographical adaptation in the genomes of local crop varieties connect millennia of survival strategies of subsistence farmers with future agricultural improvement in the face of challenges from environmental changes.

Correspondence

News and Views

  • News & Views |

    A new analysis has characterized a fundamental building block of complex transcribed loci. Constellations of core promoters can generally be reduced to pairs of divergent transcription units, where the distance between the pairs of transcription units correlates with constraints on genomic context, which in turn contribute to transcript fate.

    • Craig D Kaplan
  • News & Views |

    A genome-wide study in Samoans has identified a protein-altering variant (p.Arg475Gln) in CREBRF as being associated with 1.3-fold increased risk of obesity and, intriguingly, 1.6-fold decreased risk of type 2 diabetes. This variant, which is common among Samoans (minor allele frequency = 26%) but extremely rare in other populations, promotes fat storage and reduces energy use in cellular models.

    • Ruth J F Loos
  • News & Views |

    Study of the Greater Middle East (GME), home to approximately 10% of the world's population, has made invaluable contributions to the characterization of rare genetic disease, especially recessive conditions arising from the tradition of consanguinity and large families with multiple children. A new study now reports 1,111 unrelated exomes from the GME and provides a comprehensive view of genetic variation for enhanced discovery of disease-associated genes.

    • Tayfun Özçelik
    •  & Onur Emre Onat

Analysis

  • Analysis |

    Albert Tenesa and colleagues report an analysis of the heritability of 12 complex diseases in 1,555,906 individuals from the UK Biobank. They find that SNP heritability explains a higher proportion of estimated heritability when shared familial environmental factors are taken into account.

    • María Muñoz
    • , Ricardo Pong-Wong
    • , Oriol Canela-Xandri
    • , Konrad Rawlik
    • , Chris S Haley
    •  & Albert Tenesa
  • Analysis |

    Yun Chen, Albin Sandelin, Torben Heick Jensen and colleagues describe general rules governing the expression of reverse-oriented promoter upstream transcripts (PROMPTs) based on the orientation and proximity of promoter pairs. They characterize how the distance between promoters affects the expression of PROMPTs and the usage of alternate mRNA transcription start sites.

    • Yun Chen
    • , Athma A Pai
    • , Jan Herudek
    • , Michal Lubas
    • , Nicola Meola
    • , Aino I Järvelin
    • , Robin Andersson
    • , Vicent Pelechano
    • , Lars M Steinmetz
    • , Torben Heick Jensen
    •  & Albin Sandelin

Articles

  • Article |

    Jonathan Pritchard, Christopher Garcia and colleagues examine associations between different T cell receptor V genes and MHC alleles by eQTL mapping. They find that there are strong associations between MHC variation and T cell receptor gene usage and map these signals to specific MHC amino acids, many of which physically interact with germline-encoded amino acids on the T cell receptor.

    • Eilon Sharon
    • , Leah V Sibener
    • , Alexis Battle
    • , Hunter B Fraser
    • , K Christopher Garcia
    •  & Jonathan K Pritchard
  • Article |

    Yongfeng Shang and colleagues report that the pioneering factor FOXA1 associates with DNA repair complexes and regulates DNA demethylation at its genomic targets in a DNA polymerase β–dependent manner. They show that FOXA1-associated DNA demethylation is coupled with genomic targeting of estrogen receptor α and estrogen responsiveness in a breast cancer cell line.

    • Yu Zhang
    • , Di Zhang
    • , Qian Li
    • , Jing Liang
    • , Luyang Sun
    • , Xia Yi
    • , Zhe Chen
    • , Ruorong Yan
    • , Guojia Xie
    • , Wanjin Li
    • , Shumeng Liu
    • , Bosen Xu
    • , Lei Li
    • , Jianguo Yang
    • , Lin He
    •  & Yongfeng Shang
  • Article |

    Margaret Goodell, Wei Li and colleagues use double-knockout mice for Dnmt3a and Tet2 to model leukemia development. Through epigenetic and transcriptional analyses, they show that loss of DNMT3A and TET2 upregulates lineage-specific transcription factors such as KLF1 in hematopoietic stem cells and accelerates malignancy.

    • Xiaotian Zhang
    • , Jianzhong Su
    • , Mira Jeong
    • , Myunggon Ko
    • , Yun Huang
    • , Hyun Jung Park
    • , Anna Guzman
    • , Yong Lei
    • , Yung-Hsin Huang
    • , Anjana Rao
    • , Wei Li
    •  & Margaret A Goodell
  • Article |

    Robbie Waugh, Nils Stein, Gary Muehlbauer and colleagues report the exome sequencing of 267 landraces and wild accessions of barley from diverse regions to study adaptations to different agricultural environments. They observe correlations of days to heading and height with environment and find that variation in flowering-associated genes has strong geographical structuring.

    • Joanne Russell
    • , Martin Mascher
    • , Ian K Dawson
    • , Stylianos Kyriakidis
    • , Cristiane Calixto
    • , Fabian Freund
    • , Micha Bayer
    • , Iain Milne
    • , Tony Marshall-Griffiths
    • , Shane Heinen
    • , Anna Hofstad
    • , Rajiv Sharma
    • , Axel Himmelbach
    • , Manuela Knauft
    • , Maarten van Zonneveld
    • , John W S Brown
    • , Karl Schmid
    • , Benjamin Kilian
    • , Gary J Muehlbauer
    • , Nils Stein
    •  & Robbie Waugh
  • Article |

    Ashley Winslow, Roy Perlis, David Hinds and colleagues report the identification of 15 genetic loci associated with risk of major depressive disorder in individuals of European descent. They find that several loci are also associated with risk of other psychiatric traits, including schizophrenia and neuroticism.

    • Craig L Hyde
    • , Michael W Nagle
    • , Chao Tian
    • , Xing Chen
    • , Sara A Paciga
    • , Jens R Wendland
    • , Joyce Y Tung
    • , David A Hinds
    • , Roy H Perlis
    •  & Ashley R Winslow

Letters

  • Letter |

    Jan Veldink and colleagues show that loss-of-function variants in NEK1 are associated with susceptibility to amyotrophic lateral sclerosis (ALS). In addition to finding an excess of rare loss-of-function NEK1 variants in ALS cases, they report a significant association between a specific NEK1 missense variant (p.Arg261His) and disease risk.

    • Kevin P Kenna
    • , Perry T C van Doormaal
    • , Annelot M Dekker
    • , Nicola Ticozzi
    • , Brendan J Kenna
    • , Frank P Diekstra
    • , Wouter van Rheenen
    • , Kristel R van Eijk
    • , Ashley R Jones
    • , Pamela Keagle
    • , Aleksey Shatunov
    • , William Sproviero
    • , Bradley N Smith
    • , Michael A van Es
    • , Simon D Topp
    • , Aoife Kenna
    • , Jack W Miller
    • , Claudia Fallini
    • , Cinzia Tiloca
    • , Russell L McLaughlin
    • , Caroline Vance
    • , Claire Troakes
    • , Claudia Colombrita
    • , Gabriele Mora
    • , Andrea Calvo
    • , Federico Verde
    • , Safa Al-Sarraj
    • , Andrew King
    • , Daniela Calini
    • , Jacqueline de Belleroche
    • , Frank Baas
    • , Anneke J van der Kooi
    • , Marianne de Visser
    • , Anneloor L M A ten Asbroek
    • , Peter C Sapp
    • , Diane McKenna-Yasek
    • , Meraida Polak
    • , Seneshaw Asress
    • , José Luis Muñoz-Blanco
    • , Tim M Strom
    • , Thomas Meitinger
    • , Karen E Morrison
    • , SLAGEN Consortium
    • , Sandra D'Alfonso
    • , Letizia Mazzini
    • , Giacomo P Comi
    • , Roberto Del Bo
    • , Mauro Ceroni
    • , Stella Gagliardi
    • , Giorgia Querin
    • , Cinzia Bertolin
    • , Viviana Pensato
    • , Barbara Castellotti
    • , Stefania Corti
    • , Cristina Cereda
    • , Lucia Corrado
    • , Gianni Sorarù
    • , Giuseppe Lauria
    • , Kelly L Williams
    • , P Nigel Leigh
    • , Garth A Nicholson
    • , Ian P Blair
    • , Claire S Leblond
    • , Patrick A Dion
    • , Guy A Rouleau
    • , Hardev Pall
    • , Pamela J Shaw
    • , Martin R Turner
    • , Kevin Talbot
    • , Franco Taroni
    • , Kevin B Boylan
    • , Marka Van Blitterswijk
    • , Rosa Rademakers
    • , Jesús Esteban-Pérez
    • , Alberto García-Redondo
    • , Phillip Van Damme
    • , Wim Robberecht
    • , Adriano Chio
    • , Cinzia Gellera
    • , Carsten Drepper
    • , Michael Sendtner
    • , Antonia Ratti
    • , Jonathan D Glass
    • , Jesús S Mora
    • , Nazli A Basak
    • , Orla Hardiman
    • , Albert C Ludolph
    • , Peter M Andersen
    • , Jochen H Weishaupt
    • , Robert H Brown Jr
    • , Ammar Al-Chalabi
    • , Vincenzo Silani
    • , Christopher E Shaw
    • , Leonard H van den Berg
    • , Jan H Veldink
    •  & John E Landers
  • Letter |

    Ammar Al-Chalabi, Jan Veldink and colleagues perform a genome-wide association study for amyotrophic lateral sclerosis (ALS) in 15,156 cases and 26,242 controls. They identify three new genome-wide-significant variants and establish ALS as a complex trait with a polygenic architecture, but with a distinct and important role for low-frequency variants.

    • Wouter van Rheenen
    • , Aleksey Shatunov
    • , Annelot M Dekker
    • , Russell L McLaughlin
    • , Frank P Diekstra
    • , Sara L Pulit
    • , Rick A A van der Spek
    • , Urmo Võsa
    • , Simone de Jong
    • , Matthew R Robinson
    • , Jian Yang
    • , Isabella Fogh
    • , Perry TC van Doormaal
    • , Gijs H P Tazelaar
    • , Max Koppers
    • , Anna M Blokhuis
    • , William Sproviero
    • , Ashley R Jones
    • , Kevin P Kenna
    • , Kristel R van Eijk
    • , Oliver Harschnitz
    • , Raymond D Schellevis
    • , William J Brands
    • , Jelena Medic
    • , Androniki Menelaou
    • , Alice Vajda
    • , Nicola Ticozzi
    • , Kuang Lin
    • , Boris Rogelj
    • , Katarina Vrabec
    • , Metka Ravnik-Glavač
    • , Blaž Koritnik
    • , Janez Zidar
    • , Lea Leonardis
    • , Leja Dolenc Grošelj
    • , Stéphanie Millecamps
    • , François Salachas
    • , Vincent Meininger
    • , Mamede de Carvalho
    • , Susana Pinto
    • , Jesus S Mora
    • , Ricardo Rojas-García
    • , Meraida Polak
    • , Siddharthan Chandran
    • , Shuna Colville
    • , Robert Swingler
    • , Karen E Morrison
    • , Pamela J Shaw
    • , John Hardy
    • , Richard W Orrell
    • , Alan Pittman
    • , Katie Sidle
    • , Pietro Fratta
    • , Andrea Malaspina
    • , Simon Topp
    • , Susanne Petri
    • , Susanne Abdulla
    • , Carsten Drepper
    • , Michael Sendtner
    • , Thomas Meyer
    • , Roel A Ophoff
    • , Kim A Staats
    • , Martina Wiedau-Pazos
    • , Catherine Lomen-Hoerth
    • , Vivianna M Van Deerlin
    • , John Q Trojanowski
    • , Lauren Elman
    • , Leo McCluskey
    • , A Nazli Basak
    • , Ceren Tunca
    • , Hamid Hamzeiy
    • , Yesim Parman
    • , Thomas Meitinger
    • , Peter Lichtner
    • , Milena Radivojkov-Blagojevic
    • , Christian R Andres
    • , Cindy Maurel
    • , Gilbert Bensimon
    • , Bernhard Landwehrmeyer
    • , Alexis Brice
    • , Christine A M Payan
    • , Safaa Saker-Delye
    • , Alexandra Dürr
    • , Nicholas W Wood
    • , Lukas Tittmann
    • , Wolfgang Lieb
    • , Andre Franke
    • , Marcella Rietschel
    • , Sven Cichon
    • , Markus M Nöthen
    • , Philippe Amouyel
    • , Christophe Tzourio
    • , Jean-François Dartigues
    • , Andre G Uitterlinden
    • , Fernando Rivadeneira
    • , Karol Estrada
    • , Albert Hofman
    • , Charles Curtis
    • , Hylke M Blauw
    • , Anneke J van der Kooi
    • , Marianne de Visser
    • , An Goris
    • , Markus Weber
    • , Christopher E Shaw
    • , Bradley N Smith
    • , Orietta Pansarasa
    • , Cristina Cereda
    • , Roberto Del Bo
    • , Giacomo P Comi
    • , Sandra D'Alfonso
    • , Cinzia Bertolin
    • , Gianni Sorarù
    • , Letizia Mazzini
    • , Viviana Pensato
    • , Cinzia Gellera
    • , Cinzia Tiloca
    • , Antonia Ratti
    • , Andrea Calvo
    • , Cristina Moglia
    • , Maura Brunetti
    • , Simona Arcuti
    • , Rosa Capozzo
    • , Chiara Zecca
    • , Christian Lunetta
    • , Silvana Penco
    • , Nilo Riva
    • , Alessandro Padovani
    • , Massimiliano Filosto
    • , Bernard Muller
    • , Robbert Jan Stuit
    • , PARALS Registry
    • , SLALOM Group
    • , SLAP Registry
    • , FALS Sequencing Consortium
    • , SLAGEN Consortium
    • , NNIPPS Study Group
    • , Ian Blair
    • , Katharine Zhang
    • , Emily P McCann
    • , Jennifer A Fifita
    • , Garth A Nicholson
    • , Dominic B Rowe
    • , Roger Pamphlett
    • , Matthew C Kiernan
    • , Julian Grosskreutz
    • , Otto W Witte
    • , Thomas Ringer
    • , Tino Prell
    • , Beatrice Stubendorff
    • , Ingo Kurth
    • , Christian A Hübner
    • , P Nigel Leigh
    • , Federico Casale
    • , Adriano Chio
    • , Ettore Beghi
    • , Elisabetta Pupillo
    • , Rosanna Tortelli
    • , Giancarlo Logroscino
    • , John Powell
    • , Albert C Ludolph
    • , Jochen H Weishaupt
    • , Wim Robberecht
    • , Philip Van Damme
    • , Lude Franke
    • , Tune H Pers
    • , Robert H Brown
    • , Jonathan D Glass
    • , John E Landers
    • , Orla Hardiman
    • , Peter M Andersen
    • , Philippe Corcia
    • , Patrick Vourc'h
    • , Vincenzo Silani
    • , Naomi R Wray
    • , Peter M Visscher
    • , Paul I W de Bakker
    • , Michael A van Es
    • , R Jeroen Pasterkamp
    • , Cathryn M Lewis
    • , Gerome Breen
    • , Ammar Al-Chalabi
    • , Leonard H van den Berg
    •  & Jan H Veldink
  • Letter |

    Stephen McGarvey and colleagues identify a missense variant in CREBRF strongly associated with body mass index in Samoans. This variant is rare in other populations but is common in Samoans and has a much larger effect size than other known common obesity risk variants, including variation in FTO.

    • Ryan L Minster
    • , Nicola L Hawley
    • , Chi-Ting Su
    • , Guangyun Sun
    • , Erin E Kershaw
    • , Hong Cheng
    • , Olive D Buhule
    • , Jerome Lin
    • , Muagututi'a Sefuiva Reupena
    • , Satupa'itea Viali
    • , John Tuitele
    • , Take Naseri
    • , Zsolt Urban
    • , Ranjan Deka
    • , Daniel E Weeks
    •  & Stephen T McGarvey
  • Letter |

    Ewan Pearson, Kathleen Giacomini and the Metformin Genetics Consortium perform a genome-wide association study for glycemic response to the antidiabetic drug metformin. They find an intronic allele of the GLUT2 glucose transporter gene that associates with greater metformin action, an effect that is more pronounced in obese individuals.

    • Kaixin Zhou
    • , Sook Wah Yee
    • , Eric L Seiser
    • , Nienke van Leeuwen
    • , Roger Tavendale
    • , Amanda J Bennett
    • , Christopher J Groves
    • , Ruth L Coleman
    • , Amber A van der Heijden
    • , Joline W Beulens
    • , Catherine E de Keyser
    • , Linda Zaharenko
    • , Daniel M Rotroff
    • , Mattijs Out
    • , Kathleen A Jablonski
    • , Ling Chen
    • , Martin Javorský
    • , Jozef Židzik
    • , Albert M Levin
    • , L Keoki Williams
    • , Tanja Dujic
    • , Sabina Semiz
    • , Michiaki Kubo
    • , Huan-Chieh Chien
    • , Shiro Maeda
    • , John S Witte
    • , Longyang Wu
    • , Ivan Tkáč
    • , Adriaan Kooy
    • , Ron H N van Schaik
    • , Coen D A Stehouwer
    • , Lisa Logie
    • , MetGen Investigators
    • , DPP Investigators
    • , ACCORD Investigators
    • , Calum Sutherland
    • , Janis Klovins
    • , Valdis Pirags
    • , Albert Hofman
    • , Bruno H Stricker
    • , Alison A Motsinger-Reif
    • , Michael J Wagner
    • , Federico Innocenti
    • , Leen M 't Hart
    • , Rury R Holman
    • , Mark I McCarthy
    • , Monique M Hedderson
    • , Colin N A Palmer
    • , Jose C Florez
    • , Kathleen M Giacomini
    •  & Ewan R Pearson
  • Letter |

    Matthew Hurles and colleagues report exome sequencing of 1,891 individuals with syndromic or nonsyndromic congenital heart defects (CHD). They found that nonsyndromic CHD patients were enriched for protein-truncating variants in CHD-associated genes inherited from unaffected parents and identified three new syndromic CHD disorders caused by de novo mutations.

    • Alejandro Sifrim
    • , Marc-Phillip Hitz
    • , Anna Wilsdon
    • , Jeroen Breckpot
    • , Saeed H Al Turki
    • , Bernard Thienpont
    • , Jeremy McRae
    • , Tomas W Fitzgerald
    • , Tarjinder Singh
    • , Ganesh Jawahar Swaminathan
    • , Elena Prigmore
    • , Diana Rajan
    • , Hashim Abdul-Khaliq
    • , Siddharth Banka
    • , Ulrike M M Bauer
    • , Jamie Bentham
    • , Felix Berger
    • , Shoumo Bhattacharya
    • , Frances Bu'Lock
    • , Natalie Canham
    • , Irina-Gabriela Colgiu
    • , Catherine Cosgrove
    • , Helen Cox
    • , Ingo Daehnert
    • , Allan Daly
    • , John Danesh
    • , Alan Fryer
    • , Marc Gewillig
    • , Emma Hobson
    • , Kirstin Hoff
    • , Tessa Homfray
    • , the INTERVAL Study
    • , Anne-Karin Kahlert
    • , Ami Ketley
    • , Hans-Heiner Kramer
    • , Katherine Lachlan
    • , Anne Katrin Lampe
    • , Jacoba J Louw
    • , Ashok Kumar Manickara
    • , Dorin Manase
    • , Karen P McCarthy
    • , Kay Metcalfe
    • , Carmel Moore
    • , Ruth Newbury-Ecob
    • , Seham Osman Omer
    • , Willem H Ouwehand
    • , Soo-Mi Park
    • , Michael J Parker
    • , Thomas Pickardt
    • , Martin O Pollard
    • , Leema Robert
    • , David J Roberts
    • , Jennifer Sambrook
    • , Kerry Setchfield
    • , Brigitte Stiller
    • , Chris Thornborough
    • , Okan Toka
    • , Hugh Watkins
    • , Denise Williams
    • , Michael Wright
    • , Seema Mital
    • , Piers E F Daubeney
    • , Bernard Keavney
    • , Judith Goodship
    • , the UK10K Consortium
    • , Riyadh Mahdi Abu-Sulaiman
    • , Sabine Klaassen
    • , Caroline F Wright
    • , Helen V Firth
    • , Jeffrey C Barrett
    • , Koenraad Devriendt
    • , David R FitzPatrick
    • , J David Brook
    • , the Deciphering Developmental Disorders Study
    •  & Matthew E Hurles
  • Letter |

    Jaume Bertranpetit, Partha Majumder and colleagues analyze whole-genome sequences from Andamanese individuals and compare them to sequences from mainland Indian and other geographically diverse populations. They find evidence of ancestry from an unknown extinct hominin in South Asian populations and show that distinct Andamanese characteristics derive from strong natural selection.

    • Mayukh Mondal
    • , Ferran Casals
    • , Tina Xu
    • , Giovanni M Dall'Olio
    • , Marc Pybus
    • , Mihai G Netea
    • , David Comas
    • , Hafid Laayouni
    • , Qibin Li
    • , Partha P Majumder
    •  & Jaume Bertranpetit
  • Letter |

    Joseph Gleeson and colleagues report whole-exome sequencing of a cohort of over 1,000 individuals from the Greater Middle East, characterizing common and rare variants. They find evidence of subregional diversity and historical migrations and use the GME Variome to identify disease-causing mutations.

    • Eric M Scott
    • , Anason Halees
    • , Yuval Itan
    • , Emily G Spencer
    • , Yupeng He
    • , Mostafa Abdellateef Azab
    • , Stacey B Gabriel
    • , Aziz Belkadi
    • , Bertrand Boisson
    • , Laurent Abel
    • , Andrew G Clark
    • , Greater Middle East Variome Consortium
    • , Sohair Abdel Rahim
    • , Sawsan Abdel-Hadi
    • , Ghada Abdel-Salam
    • , Ekram Abdel-Salam
    • , Mohammed Abdou
    • , Avinash Abhytankar
    • , Parisa Adimi
    • , Jamil Ahmad
    • , Mustafa Akcakus
    • , Guside Aksu
    • , Sami Al Hajjar
    • , Suliman Al Juamaah
    • , Saleh Al Muhsen
    • , Nouriya Al Sannaa
    • , Salem Al Tameni
    • , Jumana Al-Aama
    • , Nasir Al-Allawi
    • , Raidah Al-Baradie
    • , Lihadh Al-Gazali
    • , Amal Al-Hashem
    • , Waleed Al-Herz
    • , Deema Al-Jeaid
    • , Asma Al-Tawari
    • , Abdullah Alangari
    • , Alexandre Alcais
    • , Tariq S AlFawaz
    • , Zobaida Alsum
    • , Aomar Ammar-Khodja
    • , Sepideh Amouian
    • , Cigdem Arikan
    • , Omid Aryani
    • , Ayca Aslanger
    • , Cigdem Aydogmus
    • , Caner Aytekin
    • , Matloob Azam
    • , Boglarka Bansagi
    • , Mohamed-Rhida Barbouche
    • , Laila Bastaki
    • , Tawfeg Ben-Omran
    • , Parayil Sankaran Bindu
    • , Lizbeth Blancas
    • , Stéphanie Boisson-Dupuis
    • , Damien Bonnet
    • , Omar Boudghene Stambouli
    • , Aziz Bousfiha
    • , Lobna Boussafara
    • , Jeannette Boutros
    • , Jacinta Bustamante
    • , Huseyin Caksen
    • , Yildiz Camcioglu
    • , Emilie Catherinot
    • , Fatma C Celik
    • , Michael Ciancanelli
    • , Funda E Cipe
    • , Gary Clark
    • , Aurélie Cobat
    • , Sinan Comu
    • , Angela Condie
    • , Antonio Condino-Neto
    • , Mukesh Desai
    • , William Dobyns
    • , Figen Dogu
    • , Mohamed Domaia
    • , Meltem Dorum
    • , Odul Egritas
    • , Safa El Azbaoui
    • , Jamila El Baghdadi
    • , Mona El Ruby
    • , Ashraf El-Harouni
    • , Reem A Elfeky
    • , Gehad Elghazali
    • , Eissa Faqeih
    • , Elif Fenerci
    • , Claire Fieschi
    • , Cipe Funda
    • , Iman Gamal
    • , Umit Gelik
    • , Fetah Genel
    • , Alper Gezdirici
    • , Katta M Girisha
    • , Amy Goldstein
    • , Padraic Grattan-Smith
    • , Neerja Gupta
    • , Jin Hahn
    • , Nevin Hatipoglu
    • , Raoul Hennekam
    • , Massoud Houshmand
    • , Philippe Ichai
    • , Aydan Ikinciogullari
    • , Samira Ismail
    • , Chaim Jalas
    • , Emmanuelle Jouanguy
    • , Madhulika Kabra
    • , Göknur Kalkan
    • , Majdi Kara
    • , Neslihan Karaca
    • , Kadri Karaer
    • , Ariana Kariminejad
    • , Hulya Kayserili
    • , Melike Keser-Emiroglu
    • , Sara S Kilic
    • , Najib Kissani
    • , Cristina Kokron
    • , Roshan Koul
    • , Necil Kutukculer
    • , Fanny Lanternier
    • , Alireza Mahdaviani
    • , Nizar Mahlaoui
    • , Lobna Mansour
    • , Davood Mansouri
    • , Lucia Margari
    • , Enza Maria Valente
    • , Naima Marzouki
    • , Amira Masri
    • , Amina Megahed
    • , Hisham Megahed
    • , Najla Mekki
    • , Mehrnaz Mesdaghi
    • , Mohd Mikati
    • , Faezeh Mojahedi
    • , John Mulley
    • , Sheela Nampoothiri
    • , Carmen Navarrete
    • , Tarek Omar
    • , Azza Oraby
    • , Ayse Pandaluz
    • , Nima Parvaneh
    • , Turkan Patiroglu
    • , Zeynep Peker Koc
    • , Isabelle Pellier
    • , Capucine Picard
    • , Anne Puel
    • , Annick Raas-Rothschild
    • , Anna Rajab
    • , Didier Raoult
    • , Ismail Reisli
    • , Nima Rezaei
    • , Ayoub Sabri
    • , Yasin Sahin
    • , Laila Saleem
    • , Fadia Salem
    • , Najla Sameer AlSediq
    • , Ozden Sanal
    • , Terry Sanger
    • , Hanan Shakankiry
    • , Lei Shang
    • , Nabil Shehata
    • , Nuri Shembesh
    • , Vared Shkalim
    • , Ameen Softah
    • , Sameera Sogaty
    • , Neveen Soliman
    • , Fatma Sonmez-Aunaci
    • , Laszlo Sztriha
    • , Lynda Taibi-Berrah
    • , Samia Temtamy
    • , Hasan Tonekaboni
    • , Doris Trauner
    • , Beyhan Tuysuz
    • , Beyhan Tuysuz
    • , Ali Varan
    • , Guillaume Vogt
    • , Christopher Walsh
    • , Geoffrey Woods
    • , Gozde Yesil
    • , Alisan Yildiran
    • , Basak Yildiz
    • , Adnan Yuksel
    • , Maha Zaki
    • , Shen-Ying Zhang
    • , Fowzan S Alkuraya
    • , Jean-Laurent Casanova
    •  & Joseph G Gleeson
  • Letter | | open

    Magnus Nordborg and colleagues report a genomic analysis of all 27 known species in the genus Arabidopsis. They find evidence for a complex speciation history that is not accurately reflected by a traditional bifurcating species tree and identify widespread shared polymorphisms between species.

    • Polina Yu Novikova
    • , Nora Hohmann
    • , Viktoria Nizhynska
    • , Takashi Tsuchimatsu
    • , Jamshaid Ali
    • , Graham Muir
    • , Alessia Guggisberg
    • , Tim Paape
    • , Karl Schmid
    • , Olga M Fedorenko
    • , Svante Holm
    • , Torbjörn Säll
    • , Christian Schlötterer
    • , Karol Marhold
    • , Alex Widmer
    • , Jun Sese
    • , Kentaro K Shimizu
    • , Detlef Weigel
    • , Ute Krämer
    • , Marcus A Koch
    •  & Magnus Nordborg
  • Letter |

    Rachel Meyer and colleagues use whole-genome resequencing of 93 African rice landraces to generate a SNP map used for population analysis and a genome-wide association study for salt tolerance traits. They find 11 significant loci, some with signatures of positive selection, and evidence for a population bottleneck beginning around 15,000 years ago.

    • Rachel S Meyer
    • , Jae Young Choi
    • , Michelle Sanches
    • , Anne Plessis
    • , Jonathan M Flowers
    • , Junrey Amas
    • , Katherine Dorph
    • , Annie Barretto
    • , Briana Gross
    • , Dorian Q Fuller
    • , Isaac Kofi Bimpong
    • , Marie-Noelle Ndjiondjop
    • , Khaled M Hazzouri
    • , Glenn B Gregorio
    •  & Michael D Purugganan
  • Letter |

    Nils Stein, Ehud Weiss, Tzion Fahima, Johannes Krause and colleagues report the genome sequences of 6,000-year-old barley grains obtained from desert caves in Israel. They compare these to whole-exome sequences of a modern barley diversity panel to explore domestication and migration patterns, finding evidence for prehistoric gene flow between wild and cultivated populations.

    • Martin Mascher
    • , Verena J Schuenemann
    • , Uri Davidovich
    • , Nimrod Marom
    • , Axel Himmelbach
    • , Sariel Hübner
    • , Abraham Korol
    • , Michal David
    • , Ella Reiter
    • , Simone Riehl
    • , Mona Schreiber
    • , Samuel H Vohr
    • , Richard E Green
    • , Ian K Dawson
    • , Joanne Russell
    • , Benjamin Kilian
    • , Gary J Muehlbauer
    • , Robbie Waugh
    • , Tzion Fahima
    • , Johannes Krause
    • , Ehud Weiss
    •  & Nils Stein

Technical Report

  • Technical Report |

    Victoria Hore, Jonathan Marchini and colleagues present a method for multiple-tissue gene expression studies aimed at uncovering gene networks linked to genetic variation. They apply their method to RNA sequencing data from adipose, skin and lymphoblastoid cell lines and identify several biologically relevant gene networks with a genetic basis.

    • Victoria Hore
    • , Ana Viñuela
    • , Alfonso Buil
    • , Julian Knight
    • , Mark I McCarthy
    • , Kerrin Small
    •  & Jonathan Marchini