GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture.

Abstract:

:Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture. A genome-wide association study (GWAS) using PC1 as a dependent variable was used to isolate a gene encoding rice, SPINDLY (OsSPY), that activates the gibberellin (GA) signal suppression protein SLR1. The effect of GA signaling on the regulation of rice architecture was confirmed in 9 types of isogenic plant having different levels of GA responsiveness. Further population genetics analysis demonstrated that the functional allele of OsSPY associated with semidwarfism and small panicles was selected in the process of rice breeding. In summary, the use of PCA in GWAS will aid in uncovering genes involved in traits with complex characteristics.

authors

Yano K,Morinaka Y,Wang F,Huang P,Takehara S,Hirai T,Ito A,Koketsu E,Kawamura M,Kotake K,Yoshida S,Endo M,Tamiya G,Kitano H,Ueguchi-Tanaka M,Hirano K,Matsuoka M

doi

10.1073/pnas.1904964116

subject

Has Abstract

pub_date

2019-10-15 00:00:00

pages

21262-21267

issue

42

eissn

0027-8424

issn

1091-6490

pii

1904964116

journal_volume

116

pub_type

杂志文章
  • Correlated protein conformational states and membrane dynamics during attack by pore-forming toxins.

    abstract::Pore-forming toxins (PFTs) are a class of proteins implicated in a wide range of virulent bacterial infections and diseases. These toxins bind to target membranes and subsequently oligomerize to form functional pores that eventually lead to cell lysis. While the protein undergoes large conformational changes on the bi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1821897116

    authors: Ponmalar II,Cheerla R,Ayappa KG,Basu JK

    更新日期:2019-06-25 00:00:00

  • Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.

    abstract::Denaturing gradient gel electrophoresis (DGGE) can be used to distinguish two DNA molecules that differ by as little as a single-base substitution. This method detects approximately 50% of all possible single-base changes in DNA fragments ranging from 50 to approximately 1000 base pairs. To increase the number of sing...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.1.232

    authors: Sheffield VC,Cox DR,Lerman LS,Myers RM

    更新日期:1989-01-01 00:00:00

  • Climate forcing from the transport sectors.

    abstract::Although the transport sector is responsible for a large and growing share of global emissions affecting climate, its overall contribution has not been quantified. We provide a comprehensive analysis of radiative forcing from the road transport, shipping, aviation, and rail subsectors, using both past- and forward-loo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0702958104

    authors: Fuglestvedt J,Berntsen T,Myhre G,Rypdal K,Skeie RB

    更新日期:2008-01-15 00:00:00

  • Membrane fusion protein synexin (annexin VII) as a Ca2+/GTP sensor in exocytotic secretion.

    abstract::Exocytotic membrane fusion and secretion are promoted by the concerted action of GTP and Ca2+, although the precise site(s) of action in the process are not presently known. However, the calcium-dependent membrane fusion reaction driven by synexin (annexin VII) is an in vitro model for this process, which we have now ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.20.10797

    authors: Caohuy H,Srivastava M,Pollard HB

    更新日期:1996-10-01 00:00:00

  • Chromosomal organization of the heavy chain variable region gene segments comprising the human fetal antibody repertoire.

    abstract::The adult repertoire of antibody specificities is acquired in a developmentally programmed fashion that, in mouse and man, parallels the ordered rearrangement of a limited number of germ-line heavy chain variable region (VH) gene segments during development. It has been hypothesized that this developmental bias is a c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.21.10430

    authors: Willems van Dijk K,Milner LA,Sasso EH,Milner EC

    更新日期:1992-11-01 00:00:00

  • Proteins antigenically related to the human erythrocyte glucose transporter in normal and Rous sarcoma virus-transformed chicken embryo fibroblasts.

    abstract::Antibody raised against the purified human erythrocyte glucose transporter specifically precipitated four proteins from normal and Rous sarcoma virus-transformed chicken embryo cells: a major protein of Mr 41,000 and minor proteins of Mr 68,000, 73,000, and 82,000. The Mr 41,000 and 82,000 proteins were found only in ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.5.1540

    authors: Salter DW,Baldwin SA,Lienhard GE,Weber MJ

    更新日期:1982-03-01 00:00:00

  • Distinct coated vesicles labeled for p200 bud from trans-Golgi network membranes.

    abstract::Golgi-associated cytoplasmic proteins, such as the coatomer protein complex, are required for vesicle budding and trafficking. We have previously described a cytoplasmic phosphoprotein, p200, which binds dynamically and specifically to Golgi membranes. The p200 protein is dissociated from Golgi membranes in the presen...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.7.2874

    authors: Narula N,Stow JL

    更新日期:1995-03-28 00:00:00

  • Indirubin derivatives inhibit Stat3 signaling and induce apoptosis in human cancer cells.

    abstract::Stat3 protein has an important role in oncogenesis and is a promising anticancer target. Indirubin, the active component of a traditional Chinese herbal medicine, has been shown previously to inhibit cyclin-dependent kinases, resulting in cell cycle arrest. Here, we show that the indirubin derivatives E564, E728, and ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0409467102

    authors: Nam S,Buettner R,Turkson J,Kim D,Cheng JQ,Muehlbeyer S,Hippe F,Vatter S,Merz KH,Eisenbrand G,Jove R

    更新日期:2005-04-26 00:00:00

  • Hypoxia-activated cytotoxic agent tirapazamine enhances hepatic artery ligation-induced killing of liver tumor in HBx transgenic mice.

    abstract::Transarterial chemoembolization (TACE) is the main treatment for intermediate stage hepatocellular carcinoma (HCC) with Barcelona Clinic Liver Cancer classification because of its exclusive arterial blood supply. Although TACE achieves substantial necrosis of the tumor, complete tumor necrosis is uncommon, and the res...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1613466113

    authors: Lin WH,Yeh SH,Yeh KH,Chen KW,Cheng YW,Su TH,Jao P,Ni LC,Chen PJ,Chen DS

    更新日期:2016-10-18 00:00:00

  • Tracking an embryonic L1 retrotransposition event.

    abstract::Long interspersed nuclear elements 1 (L1) are active retrotransposons that reside in many species, including humans and rodents. L1 elements produce an RNA intermediate that is reverse transcribed to DNA and inserted in a new genomic location. We have tagged an active human L1 element (L1(RP)) with a gene encoding enh...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0337627100

    authors: Prak ET,Dodson AW,Farkash EA,Kazazian HH Jr

    更新日期:2003-02-18 00:00:00

  • Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping.

    abstract::A whole genome cattle-hamster radiation hybrid cell panel was used to construct a map of 54 markers located on bovine chromosome 5 (BTA5). Of the 54 markers, 34 are microsatellites selected from the cattle linkage map and 20 are genes. Among the 20 mapped genes, 10 are new assignments that were made by using the compa...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.050007097

    authors: Ozawa A,Band MR,Larson JH,Donovan J,Green CA,Womack JE,Lewin HA

    更新日期:2000-04-11 00:00:00

  • Insect societies as divided organisms: the complexities of purpose and cross-purpose.

    abstract::Individual organisms are complex in a special way. The organization and function of their parts seem directed toward a purpose: the survival and reproduction of that individual. Groups of organisms are different. They may also be complex, but that is usually because their parts, the individual organisms, are working a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0701285104

    authors: Strassmann JE,Queller DC

    更新日期:2007-05-15 00:00:00

  • Isolation of a diterpenoid substance with potent neuroprotective activity from fetal calf serum.

    abstract::Excess activation of glutamate receptors and production of free radicals including nitric oxide may result in severe and irreversible damage to the mammalian central nervous system (CNS), but endogenous defense systems that protect neurons from these insults are poorly understood. Here, we purified and isolated a neur...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.052693999

    authors: Kume T,Asai N,Nishikawa H,Mano N,Terauchi T,Taguchi R,Shirakawa H,Osakada F,Mori H,Asakawa N,Yonaga M,Nishizawa Y,Sugimoto H,Shimohama S,Katsuki H,Kaneko S,Akaike A

    更新日期:2002-03-05 00:00:00

  • Selenoprotein A of the clostridial glycine reductase complex: purification and amino acid sequence of the selenocysteine-containing peptide.

    abstract::A selenium-containing protein, selenoprotein A, is an essential component of the clostridial glycine reductase complex. This enzyme complex catalyzes the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP. Sequence information was obtained by au...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.2.368

    authors: Sliwkowski MX,Stadtman TC

    更新日期:1988-01-01 00:00:00

  • Break-induced replication occurs by conservative DNA synthesis.

    abstract::Break-induced replication (BIR) refers to recombination-dependent DNA synthesis initiated from one end of a DNA double-strand break and can extend for more than 100 kb. BIR initiates by Rad51-catalyzed strand invasion, but the mechanism for DNA synthesis is not known. Here, we used BrdU incorporation to track DNA synt...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1309800110

    authors: Donnianni RA,Symington LS

    更新日期:2013-08-13 00:00:00

  • Anthrax toxin triggers the activation of src-like kinases to mediate its own uptake.

    abstract::AB-type toxins, like other bacterial toxins, are notably opportunistic molecules. They rely on target cell receptors to reach the appropriate location within the target cell where translocation of their enzymatic subunits occurs. The anthrax toxin, however, times its own uptake, suggesting that toxin binding triggers ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0910782107

    authors: Abrami L,Kunz B,van der Goot FG

    更新日期:2010-01-26 00:00:00

  • Cell differentiation in Dictyostelium under submerged conditions.

    abstract::Hitherto it has not been possible to obtain spore and stalk cell differentiation of the cellular slime molds in submerged cultures. It is shown here that cells, when placed in roller tubes under an atmosphere of oxygen, will form clumps and differentiate in 48-72 hr into mature spores and stalk cells. Although differe...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.74.1.268

    authors: Sternfeld J,Bonner JT

    更新日期:1977-01-01 00:00:00

  • Sleep deprivation impairs precision of waggle dance signaling in honey bees.

    abstract::Sleep is essential for basic survival, and insufficient sleep leads to a variety of dysfunctions. In humans, one of the most profound consequences of sleep deprivation is imprecise or irrational communication, demonstrated by degradation in signaling as well as in receiving information. Communication in nonhuman anima...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1009439108

    authors: Klein BA,Klein A,Wray MK,Mueller UG,Seeley TD

    更新日期:2010-12-28 00:00:00

  • Pituitary adenylate cyclase-activating polypeptide protects rat cerebellar granule neurons against ethanol-induced apoptotic cell death.

    abstract::Alcohol exposure during development can cause brain malformations and neurobehavioral abnormalities. In view of the teratogenicity of ethanol, identification of molecules that could counteract the neurotoxic effects of alcohol deserves high priority. Here, we report that pituitary adenylate cyclase-activating polypept...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.082112699

    authors: Vaudry D,Rousselle C,Basille M,Falluel-Morel A,Pamantung TF,Fontaine M,Fournier A,Vaudry H,Gonzalez BJ

    更新日期:2002-04-30 00:00:00

  • Nucleoporin MOS7/Nup88 is required for mitosis in gametogenesis and seed development in Arabidopsis.

    abstract::Angiosperm reproduction is characterized by alternate diploid sporophytic and haploid gametophytic generations. Gametogenesis shares similarities with that of animals except for the formation of the gametophyte, whereby haploid cells undergo several rounds of postmeiotic mitosis to form gametes and the accessory cells...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1421911112

    authors: Park GT,Frost JM,Park JS,Kim TH,Lee JS,Oh SA,Twell D,Brooks JS,Fischer RL,Choi Y

    更新日期:2014-12-23 00:00:00

  • gamma-Aminobutyric acid antagonists decrease junctional communication between L-horizontal cells of the retina.

    abstract::The antagonists of gamma-aminobutyric acid, bicuculline and picrotoxin, were found to narrow the receptive field profile of the large field horizontal cell (L1HC) in the turtle retina when added to the perfusion medium in micromolar concentrations. The coupling resistance between neighboring L1HCs was increased by bic...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.11.3671

    authors: Piccolino M,Neyton J,Witkovsky P,Gerschenfeld HM

    更新日期:1982-06-01 00:00:00

  • Internal fluid pressure influences muscle contractile force.

    abstract::Fluid fills intracellular, extracellular, and capillary spaces within muscle. During normal physiological activity, intramuscular fluid pressures develop as muscle exerts a portion of its developed force internally. These pressures, typically ranging between 10 and 250 mmHg, are rarely considered in mechanical models ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1914433117

    authors: Sleboda DA,Roberts TJ

    更新日期:2020-01-21 00:00:00

  • A nonparametric view of network models and Newman-Girvan and other modularities.

    abstract::Prompted by the increasing interest in networks in many fields, we present an attempt at unifying points of view and analyses of these objects coming from the social sciences, statistics, probability and physics communities. We apply our approach to the Newman-Girvan modularity, widely used for "community" detection, ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0907096106

    authors: Bickel PJ,Chen A

    更新日期:2009-12-15 00:00:00

  • Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations.

    abstract::A central tenet of evolutionary social science holds that behaviors, such as those associated with social dominance, produce fitness effects that are subject to cultural selection. However, evidence for such selection is inconclusive because it is based on short-term statistical associations between behavior and ferti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0710158105

    authors: Lansing JS,Watkins JC,Hallmark B,Cox MP,Karafet TM,Sudoyo H,Hammer MF

    更新日期:2008-08-19 00:00:00

  • Minimum size limit for useful locomotion by free-swimming microbes.

    abstract::Formulas are derived for the effect of size on a free-swimming microbe's ability to follow chemical, light, or temperature stimuli or to disperse in random directions. The four main assumptions are as follows: (i) the organisms can be modeled as spheres, (ii) the power available to the organism for swimming is proport...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.20.10949

    authors: Dusenbery DB

    更新日期:1997-09-30 00:00:00

  • Microparadigms: chains of collective reasoning in publications about molecular interactions.

    abstract::We analyzed a very large set of molecular interactions that had been derived automatically from biological texts. We found that published statements, regardless of their verity, tend to interfere with interpretation of the subsequent experiments and, therefore, can act as scientific "microparadigms," similar to domina...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0600591103

    authors: Rzhetsky A,Iossifov I,Loh JM,White KP

    更新日期:2006-03-28 00:00:00

  • Purification of replication protein C, a cellular protein involved in the initial stages of simian virus 40 DNA replication in vitro.

    abstract::The replication of simian virus 40 (SV40) DNA is dependent upon a single viral protein [tumor (T) antigen] and multiple cellular proteins. To define the required cellular proteins, we have made use of a cell-free system that supports the replication of plasmid DNA molecules containing the SV40 origin of replication. W...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.10.3584

    authors: Virshup DM,Kelly TJ

    更新日期:1989-05-01 00:00:00

  • Tritium suicide selection of mammalian cell mutants defective in the transport of neutral amino acids.

    abstract::Mouse lymphocytic cells of the established line GF-14 were allowed to accumulate intracellular 3H-labeled aminoisobutyric acid (AIB), frozen, and stored over liquid N2. After internal radiation had reduced survival to 1 in 10(4), survivors were plated and tested for their ability to transport AIB. Out of 200 clones te...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.74.10.4549

    authors: Finkelstein MC,Slayman CW,Adelberg EA

    更新日期:1977-10-01 00:00:00

  • Classification of charge density waves based on their nature.

    abstract::The concept of a charge density wave (CDW) permeates much of condensed matter physics and chemistry. CDWs have their origin rooted in the instability of a one-dimensional system described by Peierls. The extension of this concept to reduced dimensional systems has led to the concept of Fermi surface nesting (FSN), whi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1424791112

    authors: Zhu X,Cao Y,Zhang J,Plummer EW,Guo J

    更新日期:2015-02-24 00:00:00

  • The product of a thyroid hormone-responsive gene interacts with thyroid hormone receptors.

    abstract::Thyroid hormone is a critical mediator of central nervous system (CNS) development, acting through nuclear receptors to modulate the expression of specific genes. Transcription of the rat hairless (hr) gene is highly up-regulated by thyroid hormone in the developing CNS; we show here that hr is directly induced by thy...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.16.8527

    authors: Thompson CC,Bottcher MC

    更新日期:1997-08-05 00:00:00