Nature Reviews Genetics

Genetic approaches to crop improvement: responding to environmental and population changes.

Publication Date: 2008 May 13 PMID: 18475268
Authors: Takeda, S. - Matsuoka, M.
Journal: Nat Rev Genet

Crop production is threatened by global climate change, and recent demands for crops to produce bio-fuels have started to affect the worldwide supply of some of the most important foods. How can we support a growing human population in such circumstances? One potential solution is the improvement of crops to increase yield from both irrigated and non-irrigated lands, and to create novel varieties that are more tolerant to environmental stresses. Recent progress has been made in the isolation and functional analyses of genes controlling yield and tolerance to abiotic stresses. In addition, promising new methods are being developed for identifying additional genes and variants of interest and putting these to practical use in crop improvement.

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Use and misuse of the gene ontology annotations.

Publication Date: 2008 May 13 PMID: 18475267
Authors: Yon Rhee, S. - Wood, V. - Dolinski, K. - Draghici, S.
Journal: Nat Rev Genet

The Gene Ontology (GO) project is a collaboration among model organism databases to describe gene products from all organisms using a consistent and computable language. GO produces sets of explicitly defined, structured vocabularies that describe biological processes, molecular functions and cellular components of gene products in both a computer- and human-readable manner. Here we describe key aspects of GO, which, when overlooked, can cause erroneous results, and address how these pitfalls can be avoided.

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Detecting genetic responses to environmental change.

Publication Date: 2008 May 8 PMID: 18463665
Authors: Hoffmann, A. A. - Willi, Y.
Journal: Nat Rev Genet

Changes in environmental conditions can rapidly shift allele frequencies in populations of species with relatively short generation times. Frequency shifts might be detectable in neutral genetic markers when stressful conditions cause a population decline. However, frequency shifts that are diagnostic of specific conditions depend on isolating sets of genes that are involved in adaptive responses. Shifts at candidate loci underlying adaptive responses and DNA regions that control their expression have now been linked to evolutionary responses to pollution, global warming and other changes. Conversely, adaptive constraints, particularly in physiological traits, are recognized through DNA decay in candidate genes. These approaches help researchers and conservation managers understand the power and constraints of evolution.

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DNA methylation landscapes: provocative insights from epigenomics.

Publication Date: 2008 May 8 PMID: 18463664
Authors: Suzuki, M. M. - Bird, A.
Journal: Nat Rev Genet

The genomes of many animals, plants and fungi are tagged by methylation of DNA cytosine. To understand the biological significance of this epigenetic mark it is essential to know where in the genome it is located. New techniques are making it easier to map DNA methylation patterns on a large scale and the results have already provided surprises. In particular, the conventional view that DNA methylation functions predominantly to irreversibly silence transcription is being challenged. Not only is promoter methylation often highly dynamic during development, but many organisms also seem to target DNA methylation specifically to the bodies of active genes.

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Linkage disequilibrium - understanding the evolutionary past and mapping the medical future.

Publication Date: 2008 Apr 22 PMID: 18427557
Authors: Slatkin, M.
Journal: Nat Rev Genet

Linkage disequilibrium - the nonrandom association of alleles at different loci - is a sensitive indicator of the population genetic forces that structure a genome. Because of the explosive growth of methods for assessing genetic variation at a fine scale, evolutionary biologists and human geneticists are increasingly exploiting linkage disequilibrium in order to understand past evolutionary and demographic events, to map genes that are associated with quantitative characters and inherited diseases, and to understand the joint evolution of linked sets of genes. This article introduces linkage disequilibrium, reviews the population genetic processes that affect it and describes some of its uses. At present, linkage disequilibrium is used much more extensively in the study of humans than in non-humans, but that is changing as technological advances make extensive genomic studies feasible in other species.

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A universal classification of eukaryotic transposable elements implemented in Repbase.

Publication Date: 2008 May PMID: 18421312
Authors: Kapitonov, V. V. - Jurka, J.
Journal: Nat Rev Genet

MeSH Categories: Animals, DNA Transposable Elements/*genetics, Databases, Genetic, *Databases, Nucleic Acid, Eukaryotic Cells/*physiology, *Terminology as Topic

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Segmental patterning of the vertebrate embryonic axis.

Publication Date: 2008 May PMID: 18414404
Authors: Dequeant, M. L. - Pourquie, O.
Journal: Nat Rev Genet

The body axis of vertebrates is composed of a serial repetition of similar anatomical modules that are called segments or metameres. This particular mode of organization is especially conspicuous at the level of the periodic arrangement of vertebrae in the spine. The segmental pattern is established during embryogenesis when the somites--the embryonic segments of vertebrates--are rhythmically produced from the paraxial mesoderm. This process involves the segmentation clock, which is a travelling oscillator that interacts with a maturation wave called the wavefront to produce the periodic series of somites. Here, we review our current understanding of the segmentation process in vertebrates.

MeSH Categories: Animals, Biological Clocks/*physiology, Body Patterning/*physiology, Humans, Mesoderm/*embryology, Somites/*embryology, Spine/*embryology, Vertebrates/*embryology/genetics

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Advances in autism genetics: on the threshold of a new neurobiology.

Publication Date: 2008 May PMID: 18414403
Authors: Abrahams, B. S. - Geschwind, D. H.
Journal: Nat Rev Genet

Autism is a heterogeneous syndrome defined by impairments in three core domains: social interaction, language and range of interests. Recent work has led to the identification of several autism susceptibility genes and an increased appreciation of the contribution of de novo and inherited copy number variation. Promising strategies are also being applied to identify common genetic risk variants. Systems biology approaches, including array-based expression profiling, are poised to provide additional insights into this group of disorders, in which heterogeneity, both genetic and phenotypic, is emerging as a dominant theme.

MeSH Categories: Animals, Autistic Disorder/*genetics, *Gene Dosage, *Gene Expression Profiling, *Gene Expression Regulation, *Genetic Predisposition to Disease, Humans, *Oligonucleotide Array Sequence Analysis, Phenotype, Systems Biology/methods/trends

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Genetic programming of liver and pancreas progenitors: lessons for stem-cell differentiation.

Publication Date: 2008 May PMID: 18398419
Authors: Zaret, K. S.
Journal: Nat Rev Genet

The liver and pancreas arise from a common multipotent population of endoderm cells and share many aspects of their early development. Yet each tissue originates from multiple spatial domains of the endoderm, under the influence of different genes and inductive cues, and obtains different regenerative capacities. Emerging genetic evidence is illuminating the ability of newly specified hepatic and pancreatic progenitors to reverse their course and develop into gut progenitors. Understanding how tissue programming can be reversed and how intrinsic regenerative capacities are determined should facilitate the discovery of the basis of cellular plasticity and aid in the targeted programming and growth of stem cells.

MeSH Categories: Animals, Cell Dedifferentiation/*physiology, Cell Differentiation/*physiology, Humans, Intestines/cytology/physiology, Liver/cytology/*physiology, Pancreas/cytology/*physiology, Regeneration/*physiology, Stem Cells/cytology/*physiology

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Genome-wide association studies for complex traits: consensus, uncertainty and challenges.

Publication Date: 2008 May PMID: 18398418
Authors: McCarthy, M. I. - Abecasis, G. R. - Cardon, L. R. - Goldstein, D. B. - Little, J. - Ioannidis, J. P. - Hirschhorn, J. N.
Journal: Nat Rev Genet

The past year has witnessed substantial advances in understanding the genetic basis of many common phenotypes of biomedical importance. These advances have been the result of systematic, well-powered, genome-wide surveys exploring the relationships between common sequence variation and disease predisposition. This approach has revealed over 50 disease-susceptibility loci and has provided insights into the allelic architecture of multifactorial traits. At the same time, much has been learned about the successful prosecution of association studies on such a scale. This Review highlights the knowledge gained, defines areas of emerging consensus, and describes the challenges that remain as researchers seek to obtain more complete descriptions of the susceptibility architecture of biomedical traits of interest and to translate the information gathered into improvements in clinical management.

MeSH Categories: Alleles, Animals, Genetic Diseases, Inborn/*genetics, *Genetic Predisposition to Disease, *Genome, Human, Humans, *Quantitative Trait Loci, *Quantitative Trait, Heritable, *Variation (Genetics)

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From genetic privacy to open consent.

Publication Date: 2008 May PMID: 18379574
Authors: Lunshof, J. E. - Chadwick, R. - Vorhaus, D. B. - Church, G. M.
Journal: Nat Rev Genet

Recent advances in high-throughput genomic technologies are showing concrete results in the form of an increasing number of genome-wide association studies and in the publication of comprehensive individual genome-phenome data sets. As a consequence of this flood of information the established concepts of research ethics are stretched to their limits, and issues of privacy, confidentiality and consent for research are being re-examined. Here, we show the feasibility of the co-development of scientific innovation and ethics, using the open-consent framework that was implemented in the Personal Genome Project as an example.

MeSH Categories: *Bioethics/trends, Databases, Nucleic Acid/*ethics/trends, *Genome, Human, Genomics/*ethics/trends, Humans

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Transposable elements and the evolution of regulatory networks.

Publication Date: 2008 May PMID: 18368054
Authors: Feschotte, C.
Journal: Nat Rev Genet

The control and coordination of eukaryotic gene expression rely on transcriptional and post-transcriptional regulatory networks. Although progress has been made in mapping the components and deciphering the function of these networks, the mechanisms by which such intricate circuits originate and evolve remain poorly understood. Here I revisit and expand earlier models and propose that genomic repeats, and in particular transposable elements, have been a rich source of material for the assembly and tinkering of eukaryotic gene regulatory systems.

MeSH Categories: Animals, Chromosome Mapping, DNA Transposable Elements/*physiology, Eukaryotic Cells/*physiology, Gene Expression Regulation/*physiology, Genome/*physiology, Humans

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Coordination of gene expression between organellar and nuclear genomes.

Publication Date: 2008 May PMID: 18368053
Authors: Woodson, J. D. - Chory, J.
Journal: Nat Rev Genet

Following the acquisition of chloroplasts and mitochondria by eukaryotic cells during endosymbiotic evolution, most of the genes in these organelles were either lost or transferred to the nucleus. Encoding organelle-destined proteins in the nucleus allows for host control of the organelle. In return, organelles send signals to the nucleus to coordinate nuclear and organellar activities. In photosynthetic eukaryotes, additional interactions exist between mitochondria and chloroplasts. Here we review recent advances in elucidating the intracellular signalling pathways that coordinate gene expression between organelles and the nucleus, with a focus on photosynthetic plants.

MeSH Categories: Cell Nucleus/*genetics/metabolism, Chloroplasts/*genetics/metabolism, Eukaryotic Cells/physiology, *Evolution, Molecular, Gene Expression Regulation, Plant/*physiology, Genome, Chloroplast/*physiology, Genome, Mitochondrial/*physiology, Genome, Plant/*physiology, Plant Proteins/biosynthesis/genetics, Plants/*genetics/metabolism, Signal Transduction/physiology

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LCN DNA: proof beyond reasonable doubt?

Publication Date: 2008 May PMID: 18347594
Authors: McCartney, C.
Journal: Nat Rev Genet

MeSH Categories: *DNA, DNA Fingerprinting/ethics/*legislation & jurisprudence, False Positive Reactions, Forensic Genetics/ethics/*legislation & jurisprudence, Humans, Northern Ireland, *Polymerase Chain Reaction/ethics, *Specimen Handling/ethics

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