Haplotype variation at Badh2, the gene determining fragrance in rice.

Abstract:

:Fragrance is an important component of end-use quality in rice. A set of 516 fragrant rice accessions were genotyped and over 80% of them carried the badh2.7 allele. A subset of 144 mostly fragrant accessions, including nine of Oryza rufipogon, was then subjected to a detailed diversity and haplotype analysis. The level of linkage disequilibrium in the Badh2 region was higher among the fragrant accessions. Re-sequencing in the Badh2 region showed that badh2.7, badh2.2 and badh2.4-5 all arose in the japonica genepool, and spread later into the indica genepool as a result of deliberate crossing. However, loss-of-function alleles of Badh2 are also found in the indica genepools, and then transferred into japonica. Evidence for three new possible FNPs was obtained from the Badh2 sequence of 62 fragrant accessions. Based on these data, we have elaborated a model for the evolution of Badh2 and its participation in the rice domestication process.

journal_name

Genomics

journal_title

Genomics

authors

Shao G,Tang S,Chen M,Wei X,He J,Luo J,Jiao G,Hu Y,Xie L,Hu P

doi

10.1016/j.ygeno.2012.11.010

subject

Has Abstract

pub_date

2013-02-01 00:00:00

pages

157-62

issue

2

eissn

0888-7543

issn

1089-8646

pii

S0888-7543(12)00230-3

journal_volume

101

pub_type

杂志文章

相关文献

GENOMICS文献大全
  • Structure of the gene for the testis-specific proprotein convertase 4 and of its alternate messenger RNA isoforms.

    abstract::Proprotein convertase 4 (PC4) is a mammalian secretory serine endoproteinase similar to the yeast KEX2 gene product and specifically expressed in testicular germs cells. PC4 mRNA isoforms that vary in size and 3' coding sequence have been reported (N. G. Seitah, R. Day, J. Hamelin, A. Gaspar, M. W. Collard, and M. Chr...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1158

    authors: Mbikay M,Raffin-Sanson ML,Tadros H,Sirois F,Seidah NG,Chretien M

    更新日期:1994-03-15 00:00:00

  • Structure of the mouse arylsulfatase A gene and cDNA.

    abstract::The murine arylsulfatase A (ARSA) gene and cDNA have been cloned and sequenced. The gene is 3.8 kb long and contains eight exons. All intron/exon splice junctions conform to the GT/AG consensus sequence. The genomic structure is similar to that of the human gene. One major RNA species of 3.2 kb is transcribed. This RN...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1055

    authors: Kreysing J,Polten A,Hess B,von Figura K,Menz K,Steiner F,Gieselmann V

    更新日期:1994-01-15 00:00:00

  • Temporal correlation between transcriptional changes and increased synthesis of hyaluronan in experimental cardiac hypertrophy.

    abstract::The role of hyaluronan in cardiac growth has become evident, previously shown by increased myocardial levels of hyaluronan in a rat model of cardiac hypertrophy. To further investigate the role of hyaluronan and regulation of its synthesis in cardiac hypertrophy, quantitative measurements of myocardial hyaluronan conc...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2010.04.003

    authors: Hellman U,Mörner S,Engström-Laurent A,Samuel JL,Waldenström A

    更新日期:2010-08-01 00:00:00

  • Protective protein for beta-galactosidase, Ppgb, maps to the distal imprinting region of mouse chromosome 2 but is not imprinted.

    abstract::Human chromosome 20 is conserved as a single segment on distal mouse chromosome (Chr) 2. PPGB, protective protein for beta-galactosidase, maps to human chromosome 20q13.1, and from linkage analysis of two interspecific crosses incorporating the mouse reciprocal translocations, T(2;8)2Wa (T2Wa) and T(2;16)28H (T28H), w...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1373

    authors: Williamson CM,Dutton ER,Beechey CV,Peters J

    更新日期:1994-07-01 00:00:00

  • Deletion mapping of the medulloblastoma locus on chromosome 17p.

    abstract::Isochromosome 17q has previously been observed consistently in cytogenetic studies of medulloblastoma, the most common posterior fossa neoplasm in children. We performed a restriction fragment length polymorphism (RFLP) investigation of medulloblastoma which showed a loss of chromosome 17p sequences in 45% of these tu...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(90)90283-z

    authors: Cogen PH,Daneshvar L,Metzger AK,Edwards MS

    更新日期:1990-10-01 00:00:00

  • Nucleotide variation, haplotype structure, and association with end-stage renal disease of the human interleukin-1 gene cluster.

    abstract::A dense gene-based SNP map was constructed across a 360-kb region containing the interleukin-1 gene cluster (IL1A, IL1B, and IL1RN), focusing on IL1RN. In total, 95 polymorphisms were confirmed or identified primarily by direct sequencing. Polymorphisms were precisely mapped to completed BAC and genomic sequences span...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/s0888-7543(03)00123-x

    authors: Bensen JT,Langefeld CD,Hawkins GA,Green LE,Mychaleckyj JC,Brewer CS,Kiger DS,Binford SM,Colicigno CJ,Allred DC,Freedman BI,Bowden DW

    更新日期:2003-08-01 00:00:00

  • Exploring the characteristics of sequence elements in proximal promoters of human genes.

    abstract::Central to reconstruction of cis-regulatory networks is identification and classification of naturally occurring transcription factor-binding sites according to the genes that they control. We have examined salient characteristics of 9-mers that occur in various orders and combinations in the proximal promoters of hum...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2004.08.013

    authors: Bina M,Wyss P,Ren W,Szpankowski W,Thomas E,Randhawa R,Reddy S,John PM,Pares-Matos EI,Stein A,Xu H,Lazarus SA

    更新日期:2004-12-01 00:00:00

  • Discrimination between alpha-satellite DNA sequences from chromosomes 21 and 13 by using polymerase chain reaction.

    abstract::alpha-Satellite subfamilies from chromosomes 21 and 13 are almost identical in sequence and cannot be distinguished from each other by hybridization techniques. A general method based on membrane-bound PCR is described here, allowing the discrimination of alpha-satellite DNA sequences from each of these two chromosome...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/s0888-7543(05)80256-3

    authors: Charlieu JP,Murgue B,Laurent AM,Marçais B,Bellis M,Roizès G

    更新日期:1992-10-01 00:00:00

  • A postimplantation lethal mutation induced by transgene insertion on mouse chromosome 8.

    abstract::We have produced three lines of transgenic mice that contain additional copies of the mouse phosphoglycerate kinase 1 (Pgk1) gene. Two of these lines, 94-A and 94-K, which are descendants of a common founder, did not produce liveborn progeny carrying two copies of these transgenes (i.e., A/A, K/K, or A/K). Genotyping ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.1274

    authors: Pravtcheva DD,Wise TL

    更新日期:1995-12-10 00:00:00

  • A 3-Mb map of a large Segmental duplication overlapping the alpha7-nicotinic acetylcholine receptor gene (CHRNA7) at human 15q13-q14.

    abstract::Several neuropsychiatric disorders map to human 15q13-q14, which contains a strong candidate in the alpha7-nicotinic acetylcholine receptor subunit gene (CHRNA7) and is partly duplicated, complicating further genetic analysis. We have shown that the partial duplication is in a hybrid (CHRFAM7A)between CHRNA7 and one o...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2002.6694

    authors: Riley B,Williamson M,Collier D,Wilkie H,Makoff A

    更新日期:2002-02-01 00:00:00

  • The NACP/synuclein gene: chromosomal assignment and screening for alterations in Alzheimer disease.

    abstract::The major component of the vascular and plaque amyloid deposits in Alzheimer disease is the amyloid beta peptide (A beta). A second intrinsic component of amyloid, the NAC (non-A beta component of amyloid) peptide, has recently been identified, and its precursor protein was named NACP. A computer homology search allow...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(95)80208-4

    authors: Campion D,Martin C,Heilig R,Charbonnier F,Moreau V,Flaman JM,Petit JL,Hannequin D,Brice A,Frebourg T

    更新日期:1995-03-20 00:00:00

  • A human mitochondrial DNA standard reference material for quality control in forensic identification, medical diagnosis, and mutation detection.

    abstract::A human mitochondrial DNA (mtDNA) standard reference material (SRM 2392) will provide quality control when mtDNA is sequenced for forensic identifications, medical diagnosis, or mutation detection. SRM 2392 includes DNA from two lymphoblast cell cultures (CHR and 9947A) and cloned DNA from the CHR HV1 region, which co...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1998.5513

    authors: Levin BC,Cheng H,Reeder DJ

    更新日期:1999-01-15 00:00:00

  • Molecular cloning and characterization of a novel human CC chemokine, SCYA26.

    abstract::By searching the Expressed Sequence Tag database, a full-length cDNA for a novel human CC chemokine was cloned. This cDNA encoded a 94-amino-acid protein with a putative signal peptide of 26 amino acids. The deduced mature protein had the four conserved cysteine residues characteristic of CC chemokines and showed 44% ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.5837

    authors: Guo RF,Ward PA,Hu SM,McDuffie JE,Huber-Lang M,Shi MM

    更新日期:1999-06-15 00:00:00

  • Expression profiling following local muscle inactivity in humans provides new perspective on diabetes-related genes.

    abstract::Physical activity enhances muscle mitochondrial gene expression, while inactivity and mitochondrial dysfunction are both risk factors for developing diabetes. Defective activation of the transcriptional coactivator PGC-1alpha may contribute to the gene expression pattern observed in diabetic and insulin-resistant skel...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2005.09.007

    authors: Timmons JA,Norrbom J,Schéele C,Thonberg H,Wahlestedt C,Tesch P

    更新日期:2006-01-01 00:00:00

  • Molecular genetic mapping of the mouse male sterility and histoincompatibility (mshi) mutation on proximal chromosome 10.

    abstract::The recessive male sterility and histoincompatibility (mshi) mutation in the mouse generates pleiotropic effects on histocompatibility and male reproduction, while female mutants appear to be reproductively normal. We have mapped the mshi mutation to mouse Chromosome (Chr) 10 by analysis of 126 progeny from an intrasp...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.4475

    authors: Turner JP,Carpentino JE,Cantwell AM,Hildebrandt AL,Myrie KA,King TR

    更新日期:1997-01-01 00:00:00

  • Point mutation in the human dystrophin gene: identification through western blot analysis.

    abstract::Using antibodies directed against the amino-terminus of dystrophin, we identified a truncated protein in a Duchenne muscular dystrophy patient. Antibodies directed against the carboxy-terminus failed to identify any cross-reactive material, a result consistent with premature termination of dystrophin translation. The ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90332-9

    authors: Bulman DE,Gangopadhyay SB,Bebchuck KG,Worton RG,Ray PN

    更新日期:1991-06-01 00:00:00

  • Precise mapping of the brain alpha 2-adrenergic receptor gene within chromosome 4p16.

    abstract::The gene encoding the brain alpha 2-adrenergic receptor (ADRA2C) is located on human chromosome 4. It has been circumstantially associated with a number of human disorders, including Parkinson disease, panic disorders, and Huntington disease (HD). Using somatic cell hybrids, we localized the gene to chromosome 4p16 di...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1061

    authors: Riess O,Thies U,Siedlaczck I,Potisek S,Graham R,Theilmann J,Grimm T,Epplen JT,Hayden MR

    更新日期:1994-01-15 00:00:00

  • Polycystin-1L2 is a novel G-protein-binding protein.

    abstract::Mutations in genes encoding polycystin-1 (PC1) and polycystin-2 cause autosomal dominant polycystic kidney disease. The polycystin protein family is composed of Ca2+-permeable pore-forming subunits and receptor-like integral membrane proteins. Here we describe a novel member of the polycystin-1-like subfamily, polycys...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2004.02.008

    authors: Yuasa T,Takakura A,Denker BM,Venugopal B,Zhou J

    更新日期:2004-07-01 00:00:00

  • DNA-methylation dependent regulation of embryo-specific 5S ribosomal DNA cluster transcription in adult tissues of sea urchin Paracentrotus lividus.

    abstract::We have previously reported a molecular and cytogenetic characterization of three different 5S rDNA clusters in the sea urchin Paracentrotus lividus and recently, demonstrated the presence of high heterogeneity in functional 5S rRNA. In this paper, we show some important distinctive data on 5S rRNA transcription for t...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2013.08.001

    authors: Bellavia D,Dimarco E,Naselli F,Caradonna F

    更新日期:2013-10-01 00:00:00

  • Solh, the mouse homologue of the Drosophila melanogaster small optic lobes gene: organization, chromosomal mapping, and localization of gene product to the olfactory bulb.

    abstract::The Drosophila melanogaster small optic lobes gene (sol) is required for normal development of the neuropiles of the medulla and lobula complexes of the adult optic lobes. The predicted protein products of sol and its human homologue SOLH contain zinc-finger-like repeats, a calpain-like protease domain, and a C-termin...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.6098

    authors: Kamei M,Webb GC,Heydon K,Hendry IA,Young IG,Campbell HD

    更新日期:2000-02-15 00:00:00

  • Physical mapping within the tuberous sclerosis linkage group in region 9q32-q34.

    abstract::Pulsed-field gel electrophoresis and flow dot-blot analysis have been used to construct a physical map of the q32-q34 region of chromosome 9, where one of the loci responsible for tuberous sclerosis (TSC1) has been mapped by genetic linkage. Five linked groups of markers have been defined by pulsed-field gel electroph...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1993.1056

    authors: Harris RM,Carter NP,Griffiths B,Goudie D,Hampson RM,Yates JR,Affara NA,Ferguson-Smith MA

    更新日期:1993-02-01 00:00:00

  • Assignment of a novel protein tyrosine phosphatase gene (Hcph) to mouse chromosome 6.

    abstract::Hematopoietic cell phosphatase (Hcph) was identified by amplification of conserved protein tyrosine phosphatase sequences from a myeloid cell line and is predominantly expressed in hematopoietic cells. Hcph is unique in containing two, tandemly repeated, src-homology 2 domains in the amino terminal region of the phosp...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/s0888-7543(05)80189-2

    authors: Yi T,Gilbert DJ,Jenkins NA,Copeland NG,Ihle JN

    更新日期:1992-11-01 00:00:00

  • A physical and transcriptional map of the preaxial polydactyly locus on chromosome 7q36.

    abstract::Preaxial polydactyly is a congenital hand malformation that includes duplicated thumbs, various forms of triphalangeal thumbs, and duplications of the index finger. A locus for preaxial polydactyly has been mapped to a region of 1.9 cM on chromosome 7q36 between polymorphic markers D7S550 and D7S2423. We constructed a...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.5796

    authors: Heus HC,Hing A,van Baren MJ,Joosse M,Breedveld GJ,Wang JC,Burgess A,Donnis-Keller H,Berglund C,Zguricas J,Scherer SW,Rommens JM,Oostra BA,Heutink P

    更新日期:1999-05-01 00:00:00

  • Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers.

    abstract::The use of short tandem repeat polymorphisms (STRPs) as marker loci for linkage analysis is becoming increasingly important due to their large numbers in the human genome and their high degree of polymorphism. Fluorescence-based detection of the STRP pattern with an automated DNA sequencer has improved the efficiency ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.1264

    authors: Oetting WS,Lee HK,Flanders DJ,Wiesner GL,Sellers TA,King RA

    更新日期:1995-12-10 00:00:00

  • A map of the distal region of the long arm of human chromosome 21 constructed by radiation hybrid mapping and pulsed-field gel electrophoresis.

    abstract::We have used radiation hybrid (RH) mapping and pulsed-field gel electrophoresis (PFGE) to determine the order and positions of 28 DNA markers from the distal region of the long arm of human chromosome 21. The maps generated by these two methods are in good agreement. This study, combined with that of D. R. Cox et al. ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90216-2

    authors: Burmeister M,Kim S,Price ER,de Lange T,Tantravahi U,Myers RM,Cox DR

    更新日期:1991-01-01 00:00:00

  • Stage-specific transcriptomic analysis of the model cestode Hymenolepis microstoma.

    abstract::Most parasitic flatworms go through different life stages with important physiological and morphological changes. In this work, we used a transcriptomic approach to analyze the main life-stages of the model tapeworm Hymenolepis microstoma (eggs, cysticercoids, and adults). Our results showed massive transcriptomic cha...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2021.01.005

    authors: Preza M,Calvelo J,Langleib M,Hoffmann F,Castillo E,Koziol U,Iriarte A

    更新日期:2021-01-21 00:00:00

  • Molecular cloning and characterization of the mouse carboxyl ester lipase gene and evidence for expression in the lactating mammary gland.

    abstract::DNA hybridization was used to isolate a 2.04-kb cDNA encoding carboxyl ester lipase (CEL) from a mouse lactating mammary gland, lambda gt10 cDNA library. The cDNA sequence translated into a protein of 599 amino acids, including 20 amino acids of a putative signal peptide. Comparison of the deduced amino acid sequence ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.1221

    authors: Lidmer AS,Kannius M,Lundberg L,Bjursell G,Nilsson J

    更新日期:1995-09-01 00:00:00

  • The mitochondrial genomes of three skippers: Insights into the evolution of the family Hesperiidae (Lepidoptera).

    abstract::We sequenced the mitogenomes of Astictopterus jama, Isoteinon lamprospilus and Notocrypta curvifascia to obtain further insight into the mitogenomic architecture evolution and performed phylogenetic reconstruction using 29 Hesperiidae mitogenome sequences. The complete mitogenome sequences of A. jama, I. lamprospilus ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2019.03.006

    authors: Ma L,Liu F,Chiba H,Yuan X

    更新日期:2020-01-01 00:00:00

  • Application of an allele-specific polymerase chain reaction to the direct determination of ABO blood group genotypes.

    abstract::The allele-specific polymerase chain reaction (ASPCR) procedure has proven a powerful tool for the detection and analysis of known genetic polymorphisms. Here, we present a novel application of the ASPCR technique to determine the ABO genotypes of individuals without the need of family analysis. The method introduces ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(92)90292-z

    authors: Ugozzoli L,Wallace RB

    更新日期:1992-04-01 00:00:00

  • New variants of the human and rat nuclear hormone receptor, TR4: expression and chromosomal localization of the human gene.

    abstract::TR4 is a new member of the nuclear hormone receptor family. This receptor is highly conserved in rat and human, but an in-frame insertion of 19 amino acid residues in the amino-terminal (A/B) region was found in the human homolog, which we refer to as hTR4alpha1. By reverse transcription-PCR (RT-PCR) we have identifie...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.0368

    authors: Yoshikawa T,DuPont BR,Leach RJ,Detera-Wadleigh SD

    更新日期:1996-07-15 00:00:00