当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.

Pedigree-based genome re-sequencing reveals genetic variation patterns of elite backbone varieties during modern rice improvement.

Abstract：

:Rice breeding has achieved great productivity improvements by semi-dwarf varieties and hybrid vigour. Due to poor understanding of genetic basis of elite backbone varieties, the continuous increasing in rice yield still faces great challenges. Here, 52 elite rice varieties from three historical representative pedigrees were re-sequenced with 10.1× depth on average, and ~6.5 million single nucleotide polymorphisms (SNPs) were obtained. We identified thousands of low-diversity genomic regions and 0-diversity genes during breeding. Using pedigree information, we also traced SNP transmission patterns and observed breeding signatures in pedigree. These regions included the larger number of key well-known functional genes. Besides, 35 regions spanning 0.16% of the rice gnome had been differentially selected between conventional and restorer pedigrees. These genes identified here will be useful to the further pedigree breeding. Our study provides insights into the genetic basis of backbone varieties and will have immediate implications for performing genome-wide breeding by design.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Zheng X,Li L,Liang F,Tan C,Tang S,Yu S,Diao Y,Li S,Hu Z

doi

10.1038/s41598-017-00415-1

subject

Has Abstract

pub_date

2017-03-22 00:00:00

pages

292

issue

1

issn

2045-2322

pii

10.1038/s41598-017-00415-1

journal_volume

7

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • OCT-based label-free in vivo lymphangiography within human skin and areola.

    abstract：:Due to the limitations of current imaging techniques, visualization of lymphatic capillaries within tissue in vivo has been challenging. Here, we present a label-free high resolution optical coherence tomography (OCT) based lymphangiography (OLAG) within human skin in vivo. OLAG enables rapid (~seconds) mapping of lym...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep21122

    authors： Baran U,Qin W,Qi X,Kalkan G,Wang RK

    更新日期：2016-02-19 00:00:00

  • Contribution of C1485T mutation in the HBx gene to human and murine hepatocarcinogenesis.

    abstract：:Although Hepatitis B virus (HBV) X gene mutations are frequently detected in HBV-related human hepatocellular carcinoma (HCC) patients, causative HBx mutations in the development of HCC have not yet been determined. We herein identified C1485T and C1653T mutations in the HBx gene as independent risk of HCC for HBV thr...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-10570-0

    authors： Hagiwara S,Nishida N,Park AM,Komeda Y,Sakurai T,Watanabe T,Kudo M

    更新日期：2017-09-05 00:00:00

  • Central transthyretin acts to decrease food intake and body weight.

    abstract：:Transthyretin (TTR) is a blood and cerebrospinal fluid transporter of thyroxine and retinol. Gene expression profiling revealed an elevation of Ttr expression in the dorsomedial hypothalamus (DMH) of rats with exercise-induced anorexia, implying that central TTR may also play a functional role in modulating food intak...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep24238

    authors： Zheng F,Kim YJ,Moran TH,Li H,Bi S

    更新日期：2016-04-07 00:00:00

  • Rigid soles improve balance in beam walking, but improvements do not persist with bare feet.

    abstract：:Maintaining balance while walking on a narrow beam is a challenging motor task. One important factor is that the foot's ability to exert torque on the support surface is limited by the beam width. Still, the feet serve as a critical interface between the body and the external environment, and it is unclear how the mec...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-64035-y

    authors： Huber ME,Chiovetto E,Giese M,Sternad D

    更新日期：2020-05-06 00:00:00

  • Structural characterization of recombinant IAV polymerase reveals a stable complex between viral PA-PB1 heterodimer and host RanBP5.

    abstract：:The genome of influenza A virus (IAV) comprises eight RNA segments (vRNA) which are transcribed and replicated by the heterotrimeric IAV RNA-dependent RNA-polymerase (RdRp). RdRp consists of three subunits (PA, PB1 and PB2) and binds both the highly conserved 3'- and 5'-ends of the vRNA segment. The IAV RdRp is an imp...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep24727

    authors： Swale C,Monod A,Tengo L,Labaronne A,Garzoni F,Bourhis JM,Cusack S,Schoehn G,Berger I,Ruigrok RW,Crépin T

    更新日期：2016-04-20 00:00:00

  • Modelling indirect interactions during failure spreading in a project activity network.

    abstract：:Spreading broadly refers to the notion of an entity propagating throughout a networked system via its interacting components. Evidence of its ubiquity and severity can be seen in a range of phenomena, from disease epidemics to financial systemic risk. In order to understand the dynamics of these critical phenomena, co...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-22770-3

    authors： Ellinas C

    更新日期：2018-03-12 00:00:00

  • Regioisomer-independent quantification of fatty acid oxidation products by HPLC-ESI-MS/MS analysis of sodium adducts.

    abstract：:Despite growing acknowledgement of the role of oxidized fatty acids (oxFA) as cellular signaling molecules and in the pathogenesis of disease, developing methods to measure these species in biological samples has proven challenging. Here we describe a novel method utilizing HPLC-ESI-MS/MS to identify and quantify mult...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-47693-5

    authors： Ahern KW,Serbulea V,Wingrove CL,Palas ZT,Leitinger N,Harris TE

    更新日期：2019-08-01 00:00:00

  • Collision with duplex DNA renders Escherichia coli DNA polymerase III holoenzyme susceptible to DNA polymerase IV-mediated polymerase switching on the sliding clamp.

    abstract：:Organisms possess multiple DNA polymerases (Pols) and use each for a different purpose. One of the five Pols in Escherichia coli, DNA polymerase IV (Pol IV), encoded by the dinB gene, is known to participate in lesion bypass at certain DNA adducts. To understand how cells choose Pols when the replication fork encounte...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-13080-1

    authors： Le TT,Furukohri A,Tatsumi-Akiyama M,Maki H

    更新日期：2017-10-16 00:00:00

  • Magnetically-induced ferroelectricity in the (ND4)2[FeCl5(D2O)] molecular compound.

    abstract：:The number of magnetoelectric multiferroic materials reported to date is scarce, as magnetic structures that break inversion symmetry and induce an improper ferroelectric polarization typically arise through subtle competition between different magnetic interactions. The (NH4)2[FeCl5(H2O)] compound is a rare case wher...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep14475

    authors： Alberto Rodríguez-Velamazán J,Fabelo Ó,Millán Á,Campo J,Johnson RD,Chapon L

    更新日期：2015-09-29 00:00:00

  • Chemical evidence of rare porphyrins in purple shells of Crassostrea gigas oyster.

    abstract：:The colour of oyster shells is a very diverse characteristic morphotype, forming intriguing vivid patterns both on the inside and outside of the shell. In the present study, we have identified for the first time, the presence of several porphyrins as constituents of the shell pigmentation of the Crassostrea gigas oyst...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-69133-5

    authors： Bonnard M,Cantel S,Boury B,Parrot I

    更新日期：2020-07-22 00:00:00

  • Deconvoluting the Photonic and Electronic Response of 2D Materials: The Case of MoS2.

    abstract：:Evaluating and tuning the properties of two-dimensional (2D) materials is a major focus of advancing 2D science and technology. While many claim that the photonic properties of a 2D layer provide evidence that the material is "high quality", this may not be true for electronic performance. In this work, we deconvolute...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-16970-6

    authors： Zhang K,Borys NJ,Bersch BM,Bhimanapati GR,Xu K,Wang B,Wang K,Labella M,Williams TA,Haque MA,Barnard ES,Fullerton-Shirey S,Schuck PJ,Robinson JA

    更新日期：2017-12-05 00:00:00

  • Fatty liver is associated with blood pathways of inflammatory response, immune system activation and prothrombotic state in Young Finns Study.

    abstract：:Fatty liver (FL) disease is the most common type of chronic liver disease. We hypothesized that liver's response to the process where large droplets of triglyceride fat accumulate in liver cells is reflected also in gene pathway expression in blood. Peripheral blood genome wide gene expression analysis and ultrasonic ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-28563-y

    authors： Taipale T,Seppälä I,Raitoharju E,Mononen N,Lyytikäinen LP,Illig T,Waldenberger M,Juonala M,Hutri-Kähönen N,Oksala N,Kähönen M,Raitakari O,Lehtimäki T

    更新日期：2018-07-09 00:00:00

  • Highly sensitive determination of heavy metals in water prior to and after remediation using Citrofortunella Microcarpa.

    abstract：:A highly sensitive bismuth/silver nanoparticles/Nafion-modified screen-printed graphene electrode was fabricated and was utilized for the detection of trace lead (Pb) concentrations in river water samples prior to and after remediation using calamansi (Citrofortunella Microcarpa) rinds in different forms viz., ground ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-80672-9

    authors： Palisoc ST,Vitto RIM,Noel MG,Palisoc KT,Natividad MT

    更新日期：2021-01-14 00:00:00

  • Dietary patterns and the risk of rhinitis in primary school children: a prospective cohort study.

    abstract：:This study was to investigate the association between dietary patterns and rhinitis in primary school children. 1,599 students without rhinitis at baseline survey were selected from a primary school children cohort. Information on food consumption, respiratory symptoms, and confounders was collected using questionnair...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep44610

    authors： Liu X,Wong CC,Yu IT,Zhang Z,Tan L,Lau AP,Lee A,Yeoh EK,Lao XQ

    更新日期：2017-03-15 00:00:00

  • Lactoferrin-derived Peptides Active towards Influenza: Identification of Three Potent Tetrapeptide Inhibitors.

    abstract：:Bovine lactoferrin is a biglobular multifunctional iron binding glycoprotein that plays an important role in innate immunity against infections. We have previously demonstrated that selected peptides from bovine lactoferrin C-lobe are able to prevent both Influenza virus hemagglutination and cell infection. To deeper ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-10492-x

    authors： Scala MC,Sala M,Pietrantoni A,Spensiero A,Di Micco S,Agamennone M,Bertamino A,Novellino E,Bifulco G,Gomez-Monterrey IM,Superti F,Campiglia P

    更新日期：2017-09-06 00:00:00

  • TRPV4 regulates calcium homeostasis, cytoskeletal remodeling, conventional outflow and intraocular pressure in the mammalian eye.

    abstract：:An intractable challenge in glaucoma treatment has been to identify druggable targets within the conventional aqueous humor outflow pathway, which is thought to be regulated/dysregulated by elusive mechanosensitive protein(s). Here, biochemical and functional analyses localized the putative mechanosensitive cation cha...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep30583

    authors： Ryskamp DA,Frye AM,Phuong TT,Yarishkin O,Jo AO,Xu Y,Lakk M,Iuso A,Redmon SN,Ambati B,Hageman G,Prestwich GD,Torrejon KY,Križaj D

    更新日期：2016-08-11 00:00:00

  • Establishment of a highly sensitive sandwich ELISA for the N-terminal fragment of titin in urine.

    abstract：:Muscle damage and loss of muscle mass are triggered by immobilization, loss of appetite, dystrophies and chronic wasting diseases. In addition, physical exercise causes muscle damage. In damaged muscle, the N-terminal and C-terminal regions of titin, a giant sarcomere protein, are cleaved by calpain-3, and the resulti...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep39375

    authors： Maruyama N,Asai T,Abe C,Inada A,Kawauchi T,Miyashita K,Maeda M,Matsuo M,Nabeshima YI

    更新日期：2016-12-19 00:00:00

  • The importance of spatial heterogeneity and self-restraint on mutualism stability - a quantitative review.

    abstract：:Understanding the factors that enable mutualisms to evolve and to subsequently remain stable over time, is essential to fully understand patterns of global biodiversity and for evidence based conservation policy. Theoretically, spatial heterogeneity of mutualists, through increased likelihood of fidelity between coope...

    journal_title：Scientific reports

    pub_type： 杂志文章,评审

    doi：10.1038/srep14826

    authors： Wang RW,Dunn DW,Luo J,He JZ,Shi L

    更新日期：2015-10-05 00:00:00

  • Surface plasmon coupling dynamics in InGaN/GaN quantum-well structures and radiative efficiency improvement.

    abstract：:Surface plasmonics from metal nanoparticles have been demonstrated as an effective way of improving the performance of low-efficiency light emitters. However, reducing the inherent losses of the metal nanoparticles remains a challenge. Here we study the enhancement properties by Ag nanoparticles for InGaN/GaN quantum-...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep06392

    authors： Fadil A,Iida D,Chen Y,Ma J,Ou Y,Petersen PM,Ou H

    更新日期：2014-09-22 00:00:00

  • Identification of temozolomide resistance factors in glioblastoma via integrative miRNA/mRNA regulatory network analysis.

    abstract：:Drug resistance is a major issue in the treatment of glioblastoma. Almost all glioblastomas are intrinsically resistant to chemotherapeutic temozolomide (TMZ) or develop resistance during treatment. The interaction networks of microRNAs (miRNAs) and mRNAs likely regulate most biological processes and can be employed t...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep05260

    authors： Hiddingh L,Raktoe RS,Jeuken J,Hulleman E,Noske DP,Kaspers GJ,Vandertop WP,Wesseling P,Wurdinger T

    更新日期：2014-06-11 00:00:00

  • Improving femtosecond laser pulse delivery through a hollow core photonic crystal fiber for temporally focused two-photon endomicroscopy.

    abstract：:In this paper, we present a strategy to improve delivery of femtosecond laser pulses from a regenerative amplifier through a hollow core photonic crystal fiber for temporally focused wide-field two-photon endomicroscopy. For endomicroscope application, wide-field two-photon excitation has the advantage of requiring no...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep06626

    authors： Choi H,So PT

    更新日期：2014-10-15 00:00:00

  • Carrier density effect on recombination in PTB7-based solar cell.

    abstract：:Organic solar cells (OSCs) are promising alternatives to the conventional inorganic solar cells due to their low-cost processing and compatibility with flexible substrates. The development of low band-gap polymer, e.g., poly-[[4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl] [3-fluoro-2-[(2-ethylhexy...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep13648

    authors： Moritomo Y,Yonezawa K,Yasuda T

    更新日期：2015-09-01 00:00:00

  • Comparison of Individual Retinal Layer Thicknesses between Highly Myopic Eyes and Normal Control Eyes Using Retinal Layer Segmentation Analysis.

    abstract：:The incidence of myopia is increasing worldwide, and the investigation on pathophysiology of myopia is becoming more important. This retrospective study aimed to compare the thicknesses of individual retinal layers between high-myopic and control eyes, and to evaluate the effects of age and sex on each retinal layer t...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-50306-w

    authors： Kim JH,Lee SH,Han JY,Kang HG,Byeon SH,Kim SS,Koh HJ,Lee SC,Kim M

    更新日期：2019-09-30 00:00:00

  • Bacterial communities of Aphis gossypii and Myzus persicae (Hemiptera: Aphididae) from pepper crops (Capsicum sp.).

    abstract：:Insects harbor a wide variety of microorganisms that form complex and changing communities and play an important role in the biology and evolution of their hosts. Aphids have been used as model organisms to study microorganism-insect interactions. Almost all aphids are infected with the obligate endosymbiont Buchnera ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-42232-8

    authors： Gallo-Franco JJ,Duque-Gamboa DN,Toro-Perea N

    更新日期：2019-04-08 00:00:00

  • A structural-chemical explanation of fungal laccase activity.

    abstract：:Fungal laccases (EC 1.10.3.2) are multi-copper oxidases that oxidize a wide variety of substrates. Despite extensive studies, the molecular basis for their diverse activity is unclear. Notably, there is no current way to rationally predict the activity of a laccase toward a given substrate. Such knowledge would greatl...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-35633-8

    authors： Mehra R,Muschiol J,Meyer AS,Kepp KP

    更新日期：2018-11-23 00:00:00

  • Diversity hotspot and unique community structure of foraminifera in the world's deepest marine blue hole - Sansha Yongle Blue Hole.

    abstract：:Marine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-67221-0

    authors： Li Q,Lei Y,Morard R,Li T,Wang B

    更新日期：2020-06-24 00:00:00

  • Contextual experience modifies functional connectome indices of topological strength and efficiency.

    abstract：:Stimuli presented at short temporal delays before functional magnetic resonance imaging (fMRI) can have a robust impact on the organization of synchronous activity in resting state networks. This presents an opportunity to investigate how sensory, affective and cognitive stimuli alter functional connectivity in rodent...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-76935-0

    authors： Pompilus M,Colon-Perez LM,Grudny MM,Febo M

    更新日期：2020-11-16 00:00:00

  • Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii.

    abstract：:Cold environments dominate the Earth's biosphere and the resident microorganisms play critical roles in fulfilling global biogeochemical cycles. However, only few studies have examined the molecular basis of thermosensing; an ability that microorganisms must possess in order to respond to environmental temperature and...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep24278

    authors： Najnin T,Siddiqui KS,Taha T,Elkaid N,Kornfeld G,Curmi PM,Cavicchioli R

    更新日期：2016-04-07 00:00:00

  • Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon.

    abstract：:Little research on coronaviruses has been conducted on wild animals in Africa. Here, we screened a wide range of wild animals collected in six provinces and five caves of Gabon between 2009 and 2015. We collected a total of 1867 animal samples (cave-dwelling bats, rodents, non-human primates and other wild animals). W...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-64159-1

    authors： Maganga GD,Pinto A,Mombo IM,Madjitobaye M,Mbeang Beyeme AM,Boundenga L,Ar Gouilh M,N'Dilimabaka N,Drexler JF,Drosten C,Leroy EM

    更新日期：2020-04-30 00:00:00

  • All-Materials-Inclusive Flash Spark Plasma Sintering.

    abstract：:A new flash (ultra-rapid) spark plasma sintering method applicable to various materials systems, regardless of their electrical resistivity, is developed. A number of powders ranging from metals to electrically insulative ceramics have been successfully densified resulting in homogeneous microstructures within sinteri...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-15365-x

    authors： Manière C,Lee G,Olevsky EA

    更新日期：2017-11-08 00:00:00