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Volume 48 Issue 6, June 2016

Carrot canang sari by Rachel Meyer


  • The genetics of plant breeding cannot by itself end hunger and malnutrition nor ensure sustainable food production. However, driven by genomics, it provides tools with which to raise the research profile and standards of two related fields that together will do so: agronomy, as it relates to crop ecology and evolution, and nutritional natural products research.



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News & Views

  • Studies of the Y chromosome over the past few decades have opened a window into the history of our species, through the reconstruction and exploitation of a patrilineal (Y-genealogical) tree based on several hundred single-nucleotide variants (SNVs). A new study validates, refines and extends this tree by incorporating >65,000 Y-linked variants identified in 1,244 men representing worldwide diversity.

    • Jennifer F Hughes
    • David C Page
    News & Views
  • The genome sequence of carrot (Daucus carota L.) is the first completed for an Apiaceae species, furthering knowledge of the evolution of the important euasterid II clade. Analyzing the whole-genome sequence allowed for the identification of a gene that may regulate the accumulation of carotenoids in the root.

    • Jordi Garcia-Mas
    • Manuel Rodriguez-Concepcion
    News & Views
  • How epigenetic regulators find their specific targets remains a challenging question. Two parallel studies show that REF6, a plant H3K27me3 demethylase, binds a specific DNA motif via its zinc-finger domains and recruits the SWI/SNF-type ATPase BRAHMA, demonstrating a sequence-specific recruitment mechanism for a chromatin-modifying complex.

    • Iva Mozgova
    • Claudia Köhler
    News & Views
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  • Matthew Meyerson, Ramaswamy Govindan and colleagues examine the exome sequences and copy number profiles of 660 lung adenocarcinoma and 484 lung squamous cell carcinoma tumors. They identify novel significantly mutated genes and amplification peaks and find that around half of the tumors have at least five predicted neoepitopes.

    • Joshua D Campbell
    • Anton Alexandrov
    • Matthew Meyerson
  • John Perry, Ken Ong and colleagues perform a genome-wide association study for reproductive ability, behavior and success to determine underlying genetic factors. They find 38 variants associated with age of first sexual intercourse and show that both physical and neurobehavioral traits influence the onset of reproductive activity.

    • Felix R Day
    • Hannes Helgason
    • John R B Perry
  • Daniel Benjamin, Meike Bartels, Philipp Koellinger and colleagues report a genome-wide association meta-analysis of subjective well-being, depressive symptoms and neuroticism. The study leverages a large sample size together with genetic correlations between the phenotypes to identify, with high confidence, loci associated with each phenotype.

    • Aysu Okbay
    • Bart M L Baselmans
    • David Cesarini
  • Kari Stefansson and colleagues report discovery of 13 variants with large effects on non-HDL cholesterol, LDL cholesterol, HDL cholesterol or triglyceride lipid fractions. They further show that, among these lipid fractions, the non-HDL cholesterol genetic risk score associates most strongly with coronary disease and confers risk beyond that of LDL cholesterol and that, after accounting for non-HDL cholesterol, neither HDL cholesterol nor triglyceride genetic risk scores associate with coronary disease.

    • Anna Helgadottir
    • Solveig Gretarsdottir
    • Kari Stefansson
  • Zhenglin Yang and colleagues use whole-exome sequencing to identify a rare variant in the FGD6 gene that is associated with the polypoidal choroidal vasculopathy subtype of wet age-related macular degeneration. They show that FGD6 regulates proangiogenic effects together with VEGF and that the mutation results in abnormal retinal vessel development.

    • Lulin Huang
    • Houbin Zhang
    • Zhenglin Yang
  • John Wallingford and colleagues combine proteomics, in vivo imaging and genetic analyses to identify a new ciliopathy-associated protein module, which they call CPLANE. They show that CPLANE proteins, which include Fuzzy, Inturned and Wdpcp, interact with Jbts17 at basal bodies, where they act to recruit a specific subset of intraflagellar transport proteins.

    • Michinori Toriyama
    • Chanjae Lee
    • John B Wallingford
  • Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further insights into asterid genome evolution, including characterization of two new polyploidization events.

    • Massimo Iorizzo
    • Shelby Ellison
    • Philipp Simon
    Article Open Access
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  • Amanda Spurdle, Ian Tomlinson, Douglas Easton and colleagues conduct a GWAS meta-analysis and identify five new risk loci for endometrial cancer. Functional studies show that one risk-associated SNP is located in an active chromatin region that interacts with the KLF5 promoter.

    • Timothy H T Cheng
    • Deborah J Thompson
    • Amanda B Spurdle
  • Yu Chen and colleagues describe a new constitutively activating mutation in the G-protein-coupled receptor CYSLTR2 in patients with uveal melanoma lacking mutations in the G-protein-encoding genes GNAQ and GNA11. They find that expression of the mutant leads to increased expression of melanocyte-lineage signature genes and promotes tumorigenesis in vivo.

    • Amanda R Moore
    • Emilie Ceraudo
    • Yu Chen
  • Wendy Bickmore, Madapura Pradeepa and colleagues identify a new class of active enhancers marked by histones with modifications on residues in the globular domain. They find that H3K64ac and H3K122ac are markers for active promoters and enhancers in embryonic stem cells and human cancer cell lines.

    • Madapura M Pradeepa
    • Graeme R Grimes
    • Wendy A Bickmore
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