Abstract:
:Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Xu X,Liu X,Ge S,Jensen JD,Hu F,Li X,Dong Y,Gutenkunst RN,Fang L,Huang L,Li J,He W,Zhang G,Zheng X,Zhang F,Li Y,Yu C,Kristiansen K,Zhang X,Wang J,Wright M,McCouch S,Nielsen R,Wang J,Wang Wdoi
10.1038/nbt.2050subject
Has Abstractpub_date
2011-12-11 00:00:00pages
105-11issue
1eissn
1087-0156issn
1546-1696pii
nbt.2050journal_volume
30pub_type
杂志文章abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Nature biotechnology
pub_type: 杂志文章,已发布勘误
doi:10.1038/s41587-020-0457-8
更新日期:2020-03-01 00:00:00
abstract::Pluripotent stem cell-derived cardiomyocyte grafts can remuscularize substantial amounts of infarcted myocardium and beat in synchrony with the heart, but in some settings cause ventricular arrhythmias. It is unknown whether human cardiomyocytes can restore cardiac function in a physiologically relevant large animal m...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.4162
更新日期:2018-08-01 00:00:00
abstract::Recombinant adeno-associated viruses (rAAVs) are commonly used vehicles for in vivo gene transfer. However, the tropism repertoire of naturally occurring AAVs is limited, prompting a search for novel AAV capsids with desired characteristics. Here we describe a capsid selection method, called Cre recombination-based AA...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3440
更新日期:2016-02-01 00:00:00
abstract::To construct a mammalian artificial chromosome (MAC), telomere repeats and selectable markers were introduced into a 100 kb yeast artificial chromosome (YAC) containing human centromeric DNA. This YAC, which has a regular repeat structure of alpha-satellite DNA and centromere protein B (CENP-B) boxes, efficiently form...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0598-431
更新日期:1998-05-01 00:00:00
abstract::This report describes the selection of highly efficient antibody catalysts by combining chemical selection from a synthetic library with directed in vitro protein evolution. Evolution started from a naive antibody library displayed on phage made from fully synthetic, antibody-encoding genes (the Human Combinatorial An...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt828
更新日期:2003-06-01 00:00:00
abstract::Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downst...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1404
更新日期:2008-05-01 00:00:00
abstract::Isoflavones have drawn much attention because of their benefits to human health. These compounds, which are produced almost exclusively in legumes, have natural roles in plant defense and root nodulation. Isoflavone synthase catalyzes the first committed step of isoflavone biosynthesis, a branch of the phenylpropanoid...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/72671
更新日期:2000-02-01 00:00:00
abstract::We report the use of an atomic force microscopy (AFM)-based force spectroscopy technique to identify, at the single-molecule level, the components of mixtures of polysaccharides. Previously, we showed that the elasticity of certain types of polysaccharides is governed by force-induced conformational transitions of the...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/85712
更新日期:2001-03-01 00:00:00
abstract::Antisense oligonucleotides are designed to specifically hybridize to a target messenger RNA (mRNA) and interfere with the synthesis of the encoded protein. Uniformly modified oligonucleotides containing N3'-P5' phosphoramidate linkages exhibit (NP) extremely high-affinity binding to single-stranded RNA, do not induce ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/83489
更新日期:2001-01-01 00:00:00
abstract::Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chrom...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2195
更新日期:2012-05-13 00:00:00
abstract::We report a protocol for the rapid identification of DNA-binding proteins. Immobilized DNA probes harboring a specific sequence motif are incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The det...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/12873
更新日期:1999-09-01 00:00:00
abstract::An analysis of US Federal Circuit decisions shows strategies for designing around patents. ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0508-519
更新日期:2008-05-01 00:00:00
abstract::By using an engineered, self-assembling, proteinaceous, 2-nm pore equipped with a metal-actuated switch, a technique to reversibly permeabilize the plasma membrane to small molecules (approximately 1000 Da) has been developed. We have demonstrated the dose-dependent permeabilization of fibroblasts by pores designed to...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0397-278
更新日期:1997-03-01 00:00:00
abstract::Thermostable enzymes combine catalytic specificity with the toughness required to withstand industrial reaction conditions. Stabilized enzymes also provide robust starting points for evolutionary improvement of other protein properties. We recently created a library of at least 2,300 new active chimeras of the biotech...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1333
更新日期:2007-09-01 00:00:00
abstract::Functional genomics and proteomics are identifying many potential drug targets for novel therapeutic proteins, and both rational and combinatorial protein engineering methods are available for creating drug candidates. A central challenge is the definition of the most appropriate design criteria, which will benefit cr...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1064
更新日期:2005-02-01 00:00:00
abstract::The Human Proteome Organization (HUPO) recently completed the first large-scale collaborative study to characterize the human serum and plasma proteomes. The study was carried out in different locations and used diverse methods and instruments to compare and integrate tandem mass spectrometry (MS/MS) data on aliquots ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1183
更新日期:2006-03-01 00:00:00
abstract::Current tools for targeted RNA editing rely on the delivery of exogenous proteins or chemically modified guide RNAs, which may lead to aberrant effector activity, delivery barrier or immunogenicity. Here, we present an approach, called leveraging endogenous ADAR for programmable editing of RNA (LEAPER), that employs s...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-019-0178-z
更新日期:2019-09-01 00:00:00
abstract::Microbially catalyzed reactions, which occur in the natural sulfur cycle, have been integrated in a microbiological process to remove toxic metals from contaminated soils. Bioleaching using sulfuric acid produced by sulfur-oxidizing bacteria was followed by precipitation of the leachate metals as insoluble sulfides by...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0698-572
更新日期:1998-06-01 00:00:00
abstract::For the past five decades, the need for new antibiotics has been met largely by semisynthetic tailoring of natural product scaffolds discovered in the middle of the 20(th) century. More recently, however, advances in technology have sparked a resurgence in the discovery of natural product antibiotics from bacterial so...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt1266
更新日期:2006-12-01 00:00:00
abstract::Programmable DNA cleavage using CRISPR-Cas9 enables efficient, site-specific genome engineering in single cells and whole organisms. In the research arena, versatile CRISPR-enabled genome editing has been used in various ways, such as controlling transcription, modifying epigenomes, conducting genome-wide screens and ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3659
更新日期:2016-01-01 00:00:00
abstract::We present a technology to screen millions of B cells for natively paired human antibody repertoires. Libraries of natively paired, variable region heavy and light (VH:VL) amplicons are expressed in a yeast display platform that is optimized for human Fab surface expression. Using our method we identify HIV-1 broadly ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.4052
更新日期:2018-02-01 00:00:00
abstract::Tocotrienols are the primary form of vitamin E in seeds of most monocot plants, including cereals such as rice and wheat. As potent antioxidants, tocotrienols contribute to the nutritive value of cereal grains in human and livestock diets. cDNAs encoding homogentisic acid geranylgeranyl transferase (HGGT), which catal...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt853
更新日期:2003-09-01 00:00:00
abstract::Debates on patenting DNA must evolve to reflect the global decline in filings and regional disparities in patenting activity. ...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt0207-185
更新日期:2007-02-01 00:00:00
abstract::CRISPR-Cas9-based genetic screens are a powerful new tool in biology. By simply altering the sequence of the single-guide RNA (sgRNA), one can reprogram Cas9 to target different sites in the genome with relative ease, but the on-target activity and off-target effects of individual sgRNAs can vary widely. Here, we use ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3437
更新日期:2016-02-01 00:00:00
abstract::An approach to the systematic identification and quantification of the proteins contained in the microsomal fraction of cells is described. It consists of three steps: (1) preparation of microsomal fractions from cells or tissues representing different states; (2) covalent tagging of the proteins with isotope-coded af...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1001-946
更新日期:2001-10-01 00:00:00
abstract::Enzymatic removal of blood group ABO antigens to develop universal red blood cells (RBCs) was a pioneering vision originally proposed more than 25 years ago. Although the feasibility of this approach was demonstrated in clinical trials for group B RBCs, a major obstacle in translating this technology to clinical pract...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1298
更新日期:2007-04-01 00:00:00
abstract::Peptide nucleic acids (PNAs) form stable and tight complexes with complementary DNA and/or RNA and would be promising antisense reagents if their cellular delivery could be improved. We show that a 21-mer PNA, complementary to the human galanin receptor type 1 mRNA, coupled to the cellular transporter peptides, transp...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0998-857
更新日期:1998-09-01 00:00:00
abstract::The density and long-term stability of DNA make it an appealing storage medium, particularly for long-term data archiving. Existing DNA storage technologies involve the synthesis and sequencing of multiple nominally identical molecules in parallel, resulting in information redundancy. We report the development of enco...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-019-0240-x
更新日期:2019-10-01 00:00:00
abstract::We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2798
更新日期:2014-02-01 00:00:00
abstract::The specificity of biological regulatory mechanisms relies on selective interactions between different proteins in different cell types and in response to different extracellular signals. We describe a bimolecular fluorescence complementation (BiFC) approach for the simultaneous visualization of multiple protein inter...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt816
更新日期:2003-05-01 00:00:00