Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat.

Abstract:

:Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Avena genes, and surveyed 22 hexaploid oat cultivars and 2 diploid Avena species for amplification-product polymorphism. In maize, 67% of promoter markers, 58% of intron markers, and 13% of exon markers exhibited amplification-product polymorphisms. Among polymorphic primer pairs in maize, genotype diversity was highest for SSR markers (0.60) followed by intron markers (0.46), exon markers (0.42), and promoter markers (0.28). Among all Avena genotypes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, but among the cultivars only, 21% of SSR markers and 50% of intron markers were polymorphic. Polymorphic-sequence-tagged sites for plant-breeding applications can be created easily by targeting noncoding gene regions.

journal_name

Genome

journal_title

Genome

authors

Holland JB,Helland SJ,Sharopova N,Rhyne DC

subject

Has Abstract

pub_date

2001-12-01 00:00:00

pages

1065-76

issue

6

eissn

0831-2796

issn

1480-3321

journal_volume

44

pub_type

杂志文章

相关文献

GENOME文献大全
  • Genetic control of chromosome synapsis in yeast meiosis.

    abstract::Both meiosis-specific and general recombination functions, recruited from the mitotic cell cycle, are required for elevated levels of recombination and for chromosome synapsis (assembly of the synaptonemal complex) during yeast meiosis. The meiosis-specific SPO11 gene (previously shown to be required for meiotic recom...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g89-017

    authors: Giroux CN,Dresser ME,Tiano HF

    更新日期:1989-01-01 00:00:00

  • Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti.

    abstract::Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFG...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g09-060

    authors: Guo H,Sun S,Eardly B,Finan T,Xu J

    更新日期:2009-10-01 00:00:00

  • Colocalization of antisense RNAs and ribozymes with their target mRNAs.

    abstract::The use of complementary RNA sequences such as antisense RNAs and ribozymes to regulate the expression of specific genes in eukaryotic cells has been well-documented, particularly with their application to both human gene therapy and plant biotechnology. Despite the simplicity of this approach, this technique usually ...

    journal_title:Genome

    pub_type: 杂志文章,评审

    doi:10.1139/g97-802

    authors: Arndt GM,Rank GH

    更新日期:1997-12-01 00:00:00

  • A genome-wide identification and classification of basic helix-loop-helix genes in the jewel wasp, Nasonia vitripennis (Hymenoptera: Pteromalidae).

    abstract::Basic helix-loop-helix (bHLH) proteins are highly conserved DNA-binding transcription factors of a large superfamily. Animal bHLH proteins play important regulatory roles in various developmental processes such as neurogenesis, myogenesis, heart development, and hematopoiesis. The jewel wasp (Nasonia vitripennis) is a...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2014-0171

    authors: Liu XT,Wang Y,Wang XH,Tao XF,Yao Q,Chen KP

    更新日期:2014-10-01 00:00:00

  • Visualizing DNA domains and sequences by microscopy: a fifty-year history of molecular cytogenetics.

    abstract::This short review presents a historical perspective of chromosome research during the last 50 years. It shows how molecular knowledge and technology of DNA entered cytogenetics step by step making it now daily practice in almost every modern chromosome lab. A crucial milestone in these decades has been the development...

    journal_title:Genome

    pub_type: 杂志文章,评审

    doi:10.1139/g03-107

    authors: de Jong H

    更新日期:2003-12-01 00:00:00

  • A single molecular marker to distinguish between species of Dioscorea.

    abstract::Yams are species of the genus Dioscorea (family Dioscoreaceae), which consists of approximately 630 species. The majority of the world production of yams occurs in Africa with 58.8 million t annually, but they are also produced in the Americas and Asia. The saponins in yams have been reported to possess various proper...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2015-0105

    authors: Techen N,Parveen I,Khan IA

    更新日期:2017-03-01 00:00:00

  • Distribution of highly repeated DNA sequences in species of the genus Lens Miller.

    abstract::Multiple-target fluorescence in situ hybridization (FISH) was applied on mitotic chromosomes of seven Lens taxa using two highly repetitive sequences (pLc30 and pLc7) isolated from the cultivated lentil and the multigene families for the 18S-5.8S-25S (pTa71) and 5S rRNA (pTa794) from wheat simultaneously as probes. Th...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g03-077

    authors: Galasso I

    更新日期:2003-12-01 00:00:00

  • A major suppressor of cell death, slm1, modifies the expression of the maize (Zea mays L.) lesion mimic mutation les23.

    abstract::Disease lesion mimics provide an excellent biological system to study the genetic basis of cell death in plants. Many lesion mimics show variation in phenotype expression in different genetic backgrounds. Our goal was to identify quantitative trait loci (QTL) modifying lesion mimic expression thereby identifying genet...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-046

    authors: Penning BW,Johal GS,McMullen MD

    更新日期:2004-10-01 00:00:00

  • Chromosome segregation from cell hybrids. III. Segregation is independent of spindle constitution.

    abstract::Hamster beta-tubulin (detected as a mutant subunit that confers Colcemid resistance) is either not expressed or is underexpressed in Chinese hamster-mouse somatic cell hybrids. This selectivity of tubulin expression suggests that a uniparental mouse spindle might preferentially engage mouse chromosomes and lead to los...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g87-090

    authors: Zelesco PA,Graves JA

    更新日期:1987-08-01 00:00:00

  • Genetic and cytological mapping of a "Y-2" translocation in the Mediterranean fruit fly Ceratitis capitata.

    abstract::In this paper we analyze genetically and cytologically a Y-chromosome 2 translocation with several markers, some of which are potentially useful for large scale sex separation. The breakpoint of this Y-2 translocation is located at region 6B on the trichogene polytene chromosome map. It is found that, in strains carry...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g95-145

    authors: Cladera JL,Delprat MA

    更新日期:1995-12-01 00:00:00

  • Genetic map of the powdery mildew resistance gene in soybean PI 243540.

    abstract::Powdery mildew (caused by Microsphaera diffusa Cooke & Peck) is a common disease of soybean in many soybean-growing regions of the world and under greenhouse conditions. The previously reported Rmd locus of soybean for resistance to powdery mildew was mapped on soybean molecular linkage group J (chromosome 16). We hav...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g10-015

    authors: Kang ST,Mian MA

    更新日期:2010-05-01 00:00:00

  • Families of repeated DNA in the oomycete Phytophthora infestans and their distribution within the genus.

    abstract::The abundance, genomic organization, species distribution, and structure of 33 distinct families of repetitive DNA in Phytophthora are described. The families were identified by screening a library of Phytophthora infestans DNA for repetitive sequences. These was subsequently characterized within 26 species distribute...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g98-060

    authors: Judelson HS,Randall TA

    更新日期:1998-08-01 00:00:00

  • Characterization of a microsatellite in the promoter region of the IGF1 gene in domestic horses and other equids.

    abstract::Insulin-like growth factor 1 (IGF1) regulates growth and metabolic functions in vertebrates. A dinucleotide repeat sequence located at the promoter region of the IGF1 gene has been reported in several vertebrate species and may affect the control of the transcriptional activity of this gene. The genotypes of animals f...

    journal_title:Genome

    pub_type: 杂志文章

    doi:

    authors: Caetano AR,Bowling AT

    更新日期:1998-02-01 00:00:00

  • Genetic diversity in Elymus caninus as revealed by isozyme, RAPD, and microsatellite markers.

    abstract::Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), w...

    journal_title:Genome

    pub_type: 杂志文章

    doi:

    authors: Sun GL,Díaz O,Salomon B,von Bothmer R

    更新日期:1999-06-01 00:00:00

  • QTL mapping of BNYVV resistance from the WB41 source in sugar beet.

    abstract::The most important rhizomania-resistance gene in sugar beet is the Rz1 gene from the Holly Sugar Company in California, the source widely used to breed partially resistant varieties. Other important gene sources are WB41 and WB42, which both originate from Beta vulgaris subsp. maritima collected in Denmark, and which ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-108

    authors: Gidner S,Lennefors BL,Nilsson NO,Bensefelt J,Johansson E,Gyllenspetz U,Kraft T

    更新日期:2005-04-01 00:00:00

  • Genomic in situ hybridization analysis of Thinopyrum chromatin in a wheat-Th. intermedium partial amphiploid and six derived chromosome addition lines

    abstract::The genomic origin of alien chromosomes present in a wheat-Thinopyrum intermedium partial amphiploid TAF46 (2n = 8x = 56) and six derived chromosome addition lines were analyzed by genomic in situ hybridization (GISH) using S genomic DNA from Pseudoroegneria strigosa (2n = 2x = 14, SS) as a probe. The GISH analysis cl...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g99-090

    authors: Chen Q,Conner RL,Laroche A,Ji WQ,Armstrong KC,Fedak G

    更新日期:1999-12-01 00:00:00

  • RAPD analysis of seed purity in a commercial hybrid cabbage (Brassica oleracea var. capitata) cultivar.

    abstract::The use of random amplified polymorphic DNA (RAPD) markers for evaluating seed purity in a commercial F1-hybrid cabbage (Brassica oleracea var. capitata) cultivar is demonstrated. Genomic DNA isolated from single ungerminated seed was found to be suitable for RAPD analysis. DNA from F1-hybrid and its parental lines wa...

    journal_title:Genome

    pub_type: 杂志文章

    doi:

    authors: Crockett PA,Bhalla PL,Lee CK,Singh MB

    更新日期:2000-04-01 00:00:00

  • SSR-based genetic linkage map of Cucurbita moschata and its synteny with Cucurbita pepo.

    abstract::The first SSR-based genetic linkage map of Cucurbita moschata was created by integrating the maps of two F2 populations with one common parent developed from the crosses Waltham Butternut (WB) x Nigerian Local (NL) and ZHOU (a hull-less type) x WB. The integrated C. moschata map comprises 205 SSR markers and two morph...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G08-072

    authors: Gong L,Pachner M,Kalai K,Lelley T

    更新日期:2008-11-01 00:00:00

  • Repair of base-base mismatches in simian and human cells.

    abstract::Mismatched heteroduplexes arise as intermediates of several dissimilar genetic processes. The outcome of these genetic events will therefore be influenced by the efficiency and specificity of mismatch repair. We have studied the correction of base-base mispairs in simian and human fibroblasts by transfecting the cells...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g89-107

    authors: Brown TC,Jiricny J

    更新日期:1989-01-01 00:00:00

  • Analysis of codon usage patterns in Morus notabilis based on genome and transcriptome data.

    abstract::Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tr...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2016-0129

    authors: Wen Y,Zou Z,Li H,Xiang Z,He N

    更新日期:2017-06-01 00:00:00

  • Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species.

    abstract::The genus Alstroemeria contains species with large genomes (2C = 36.5-78.9 pg (17,600-38,000 Mb) in those species with 2n = 2x = 16). We investigated the diversity and genomic and chromosomal organisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Analysis of 33 PCR-amplified sequences correspond...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g98-048

    authors: Kuipers AG,Heslop-Harrison JS,Jacobsen E

    更新日期:1998-06-01 00:00:00

  • A method for assaying the sensitivity of Drosophila replication checkpoint mutants to anti-cancer and DNA-damaging drugs.

    abstract::In multi-cellular organisms, failure to properly regulate cell-cycle progression can result in inappropriate cell death or uncontrolled cell division leading to tumor formation. To guard against such events, conserved regulatory mechanisms called "checkpoints" block progression into mitosis in response to DNA damage a...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g02-051

    authors: Radcliffe CM,Silva EA,Campbell SD

    更新日期:2002-10-01 00:00:00

  • Conversion of AFLP markers associated with FHB resistance in wheat into STS markers with an extension-AFLP method.

    abstract::Amplified fragment length polymorphism (AFLP) has proven a powerful tool for tagging genes or quantitative trait loci (QTLs) of interest in plants. However, conversion of AFLP markers into sequence-tagged site (STS) markers is technically challenging in wheat owing to the complicated nature of its genome. In this stud...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-022

    authors: Xu DH,Ban T

    更新日期:2004-08-01 00:00:00

  • Identification and analysis of copine/BONZAI proteins among evolutionarily diverse plant species.

    abstract::Copines are evolutionarily conserved calcium-dependent membrane-binding proteins with potentially critical biological functions. In plants, the function of these proteins has not been analyzed except for in Arabidopsis thaliana where they play critical roles in development and disease resistance. To facilitate functio...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2016-0015

    authors: Zou B,Hong X,Ding Y,Wang X,Liu H,Hua J

    更新日期:2016-08-01 00:00:00

  • Moth sex chromatin probed by comparative genomic hybridization (CGH).

    abstract::Abstract: Comparative genomic hybridization (CGH) with a probe mixture of differently labeled genomic DNA from females and males highlighted the W chromosomes in mitotic plates and the W chromatin in polyploid interphase nuclei of the silkworm Bombyx mori, the flour moth Ephestia kuehniella, and the wax moth Galleria ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g03-003

    authors: Sahara K,Marec F,Eickhoff U,Traut W

    更新日期:2003-04-01 00:00:00

  • Detection of rRNA and phaseolin genes on polytene chromosomes of Phaseolus coccineus by fluorescence in situ hybridization after pepsin pretreatment.

    abstract::This is the first report of fluorescence in situ hybridization (FISH) on plant polytene chromosomes. Different protease pretreatments have been tested to improve fluorescence in situ hybridization FISH on polytene chromosomes of a plant, Phaseolus coccineus, with the aim to enable the detection of low-copy genes. The ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g94-144

    authors: Nenno M,Schumann K,Nagl W

    更新日期:1994-12-01 00:00:00

  • Cerastoderma glaucum 5S ribosomal DNA: characterization of the repeat unit, divergence with respect to Cerastoderma edule, and PCR-RFLPs for the identification of both cockles.

    abstract::The 5S rDNA repeat unit of the cockle Cerastoderma glaucum from the Mediterranean and Baltic coasts was PCR amplified and sequenced. The length of the units was 539-568 bp, of which 120 bp were assigned to the 5S rRNA gene and 419-448 bp to the spacer region, and the G/C content was 46%-49%, 54%, and 44%-47%, respecti...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-123

    authors: Freire R,Insua A,Méndez J

    更新日期:2005-06-01 00:00:00

  • A family study to examine clonal diversity in unisexual salamanders (genus Ambystoma).

    abstract::Unisexual Ambystoma are the oldest known unisexual vertebrates and comprise a lineage of eastern North American all female salamanders that reproduce by stealing sperm from as many as five normally bisexual congeneric species. The sperm may be used to only stimulate egg development by gynogenesis but can be incorporat...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2019-0034

    authors: Bogart JP

    更新日期:2019-08-01 00:00:00

  • Construction of a genetic linkage map in celery using DNA-based markers.

    abstract::A F2 population of two celery cultivated types (Apium graveolens L. var. rapaceum and A. graveolens L. var. secalinum) was used to construct a linkage map consisting of 29 RFLP (restriction fragment length polymorphism), 100 RAPD (random amplified polymorphic DNA), four isozyme, one disease resistance, and one growth ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g95-005

    authors: Yang X,Quiros CF

    更新日期:1995-02-01 00:00:00

  • Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types.

    abstract::Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2020-0001

    authors: Salek Ardestani S,Aminafshar M,Zandi Baghche Maryam MB,Banabazi MH,Sargolzaei M,Miar Y

    更新日期:2020-08-01 00:00:00