Large-scale development of functional markers in Brassica species.

Abstract:

:Numerous quantitative trait loci (QTL) have been detected in Brassica species, but fine-mapping of major QTL has advanced slowly. The development of functional markers can overcome this barrier. We used publicly available PlantGDB-assembled unique transcripts (PUTs) from Brassica species to design 7836 functional simple sequence repeat (SSR) primer pairs. Functional annotation of the PUTs containing SSRs was done by Blast2GO. The PUTs harbouring SSRs were mainly involved with nucleotide or protein binding and enzyme activity, and preferentially functioned in membranes and cytoplasm. Totally, 210 PUT primer pairs were selected to test their polymorphism, stability, and PCR quality. Approximately 70% (147) of the primer pairs resulted in successful amplification with an average polymorphic information content (PIC) value of 0.49. The highest level of polymorphism was dinucleotide repeat SSRs, followed by tri- and mononucleotide repeats. Approximately 60% of the primer pairs showed good transferability among Brassica species. These results show that the development of markers from PUTs is a feasible and simple approach to develop functional SSR markers on a large scale across Brassica species. In addition, these markers can provide a novel alternative that is a putative approach for rapid determination of candidate genes, genetic mapping, genetic diversity analysis, and comparative mapping in Brassica species.

journal_name

Genome

journal_title

Genome

authors

An Z,Gao C,Li J,Fu D,Tang Z,Ortegón O

doi

10.1139/g11-042

subject

Has Abstract

pub_date

2011-09-01 00:00:00

pages

763-70

issue

9

eissn

0831-2796

issn

1480-3321

journal_volume

54

pub_type

杂志文章

相关文献

GENOME文献大全
  • Computers: the best friends a human genome ever had.

    abstract::Mapping and sequencing the human genome will generate large amounts of data, which must be sorted, analyzed, and stored for rapid retrieval to complete this enormous task. Computers and their software programs provide the most important tool to the molecular biologist today. A discussion of current capabilities and fu...

    journal_title:Genome

    pub_type: 杂志文章,评审

    doi:10.1139/g89-177

    authors: Kelly MJ

    更新日期:1989-01-01 00:00:00

  • Isolation and characterization of polymorphic microsatellites in Cocos nucifera L.

    abstract::Microsatellites or simple sequence repeats (SSRs) were isolated from coconut (Cocos nucifera) and tested for polymorphism on restricted germplasm. Sequencing of 197 clones from a cv. Tagnanan Tall-enriched genomic library showed that 75% contained a microsatellite, of which 64% were dinucleotide (GA/CT, CA/GT and GC/C...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g98-170

    authors: Rivera R,Edwards KJ,Barker JH,Arnold GM,Ayad G,Hodgkin T,Karp A

    更新日期:1999-08-01 00:00:00

  • Mapping of genes expressed in Fusarium graminearum-infected heads of wheat cultivar 'Frontana'.

    abstract::The isolation, physical, and genetic mapping of a group of wheat genes expressed in infected heads of Triticum aestivum 'Frontana' resistant to Fusarium head blight is reported. A cDNA library was built from heads of 'Frontana' through suppressive subtractive hybridization, to enrich for sequences induced by the patho...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g04-098

    authors: Han FP,Fedak G,Ouellet T,Dan H,Somers DJ

    更新日期:2005-02-01 00:00:00

  • Analysis of Brachypodium genomes with genome-wide optical maps.

    abstract::Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hy...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2018-0013

    authors: Zhu T,Hu Z,Rodriguez JC,Deal KR,Dvorak J,Vogel JP,Liu Z,Luo MC

    更新日期:2018-08-01 00:00:00

  • Amphipod genome sizes: first estimates for Arctic species reveal genomic giants.

    abstract::The genome sizes of 8 species of amphipods collected from the Canadian Arctic were estimated by flow cytometry. Haploid genome sizes ranged from 2.94 +/- 0.04 pg DNA in Acanthostepheia malmgreni (Oedicerotidae) to 64.62 +/- 2.85 pg in Ampelisca macrocephala (Ampeliscidae). The value for Ampelisca macrocephala represen...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g06-155

    authors: Rees DJ,Dufresne F,Glémet H,Belzile C

    更新日期:2007-02-01 00:00:00

  • Genetic control and identification of QTLs associated with visual quality traits of field pea (Pisum sativum L.).

    abstract::Visual quality of field pea (Pisum sativum L.) is one of the most important determinants of the market value of the harvested crop. Seed coat color, seed shape, and seed dimpling are the major components of visual seed quality of field pea and are considered as important breeding objectives. The objectives of this res...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g10-117

    authors: Ubayasena L,Bett K,Tar'an B,Warkentin T

    更新日期:2011-04-01 00:00:00

  • Genetic and cytogenetic analyses of the A genome of Triticum monococcum. IX. Cytological behaviour, phenotypic characteristics, breeding behaviour, and fertility of primary, double, and triple trisomics.

    abstract::Cytogenetic studies in Triticum monococcum (2n = 2x = 14, AA) were initiated by generating a series of primary as well as double and triple trisomics from autotriploids derived from crosses between induced autotetraploids and a diploid progenitor. Analysis of meiotic chromosome behaviour revealed that, with the except...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g93-077

    authors: Kim NS,Kuspira J

    更新日期:1993-06-01 00:00:00

  • Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids.

    abstract::Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand owing to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2016-0215

    authors: Parveen I,Singh HK,Malik S,Raghuvanshi S,Babbar SB

    更新日期:2017-08-01 00:00:00

  • Identification and mapping of a third blackleg resistance locus in Brassica napus derived from B. rapa subsp. sylvestris.

    abstract::The spectrum of resistance to isolates of Leptosphaeria maculans and the map location of a new blackleg resistance gene found in the canola cultivar Brassica napus 'Surpass 400' are described. Two blackleg resistance genes, LepR1 and LepR2, from B. rapa subsp. sylvestris and introgressed in B. napus were identified pr...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g07-103

    authors: Yu F,Lydiate DJ,Rimmer SR

    更新日期:2008-01-01 00:00:00

  • Recombination nodule mapping and chiasma distribution in spermatocytes of the pigeon, Columba livia.

    abstract::Pigeon spermatocytes were processed with a drying-down technique and their synaptonemal complex (SC) complements were analyzed by electron microscopy. The synaptonemal complex karyotype of the macrobivalents shows an excellent correspondence with the mitotic karyotype. The number and distribution of recombination nodu...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g98-138

    authors: Pigozzi MI,Solari AJ

    更新日期:1999-04-01 00:00:00

  • Genetic analysis and historical perspective of cashew (Anacardium occidentale L.) introduction into India.

    abstract::Cashew (Anacardium occidentale L.), introduced into India about 400 years ago, is distributed widely in the coastal regions as spontaneous populations as well as in cultivation. Despite the plant's commercial exploitation, little is known about its actual introduction and diversification. We attempted to construct the...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G08-119

    authors: Archak S,Gaikwad AB,Swamy KR,Karihaloo JL

    更新日期:2009-03-01 00:00:00

  • User Centric Genomics Infrastructure: trends and technologies.

    abstract::Genomics is both data and compute intensive discipline. The success of genomics depends on adequate informatics infrastructure that can address growing data demands and enable a diverse range of resource-intensive computational activities. Designing a suitable Infrastructure is a challenging task, and its success larg...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2020-0096

    authors: Krishna R,Elisseev V

    更新日期:2020-11-20 00:00:00

  • Localization of the 68,000-Da human neurofilament gene (NF68) using a murine cDNA probe.

    abstract::A recent investigation, using a human genomic probe, has indicated that the 68,000 dalton neurofilament gene (NF68) is on the short arm of chromosome 8. We have used a murine cDNA probe on 65 metaphase spreads in situ to localize the human NF68 gene to 8p21 (20/370 grains; p less than 0.0001). In addition, we have fou...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g88-083

    authors: Somerville MJ,McLachlan DR,Percy ME

    更新日期:1988-08-01 00:00:00

  • Quantitative trait loci on barley (Hordeum vulgare L.) chromosome 7 associated with components of winterhardiness.

    abstract::Quantitative trait loci (QTL) controlling traits associated with winterhardiness in barley (field survival, LT50, growth habit, and crown fructan content) were mapped to chromosome 7 in a population of 100 F1-derived doubled haploid lines. The largest QTL effects for all traits were detected in a 21% recombination int...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g93-009

    authors: Hayes PM,Blake T,Chen TH,Tragoonrung S,Chen F,Pan A,Liu B

    更新日期:1993-02-01 00:00:00

  • Spontaneous structural rearrangements in Solanum phureja Juz. et Buk. 2. Meiotic behaviour and identification of interchange chromosomes using primary trisomics.

    abstract::Meiosis was studied in two diploid (2n = 2x = 24) siblings of Solanum phureja Juz. et Buk. and in 11 disomic and 2 trisomic descendants. The diploid siblings carry the same heterozygous interchange and either one or two inversions. The frequency of quadrivalents at diakinesis/metaphase I in these clones was 0.56 and 0...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g95-017

    authors: Wagenvoort M

    更新日期:1995-02-01 00:00:00

  • Genetic diversity of different apricot geographical groups determined by SSR markers.

    abstract::Forty apricot cultivars with different geographic origins belonging to the germplasm collections of St. Istvan University (Budapest, Hungary) and the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were studied by means of SSR markers. The aim of the study was to determine the genetic relatio...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g02-128

    authors: Romero C,Pedryc A,Muñoz V,Llácer G,Badenes ML

    更新日期:2003-04-01 00:00:00

  • DNA barcodes and new primers for nature's pest controllers: the social wasps.

    abstract::Globally, biodiversity is declining as a result of anthropogenic pressures, and this could lead to extinction of some species before they are discovered. The loss of insect taxa is of prime concern, given recent reports of significant declines in the populations of many taxa across the globe. Efforts to document biodi...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2019-0193

    authors: Onah IE,Sumner S

    更新日期:2020-11-10 00:00:00

  • Tubulin-based polymorphism (TBP): a new tool, based on functionally relevant sequences, to assess genetic diversity in plant species.

    abstract::TBP (tubulin-based polymorphism) is a new molecular marker based tool that relies on the presence of intron-specific DNA polymorphisms of the plant beta-tubulin gene family. The multifunctional and essential role of the tubulin proteins is reflected in the conservation of regions within their primary amino acid sequen...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g03-132

    authors: Bardini M,Lee D,Donini P,Mariani A,Gianì S,Toschi M,Lowe C,Breviario D

    更新日期:2004-04-01 00:00:00

  • Chromosomal location of three wheat sequences with homology to pollen allergen encoding, DNA replication regulating, and DNA (cytosine-5)-methyltransferase genes in wheat and rye.

    abstract::Three wheat sequences, shown to be homologous to pollen allergen encoding, DNA replication regulating, and DNA (cytosine-5)-methyltransferase genes were localized on chromosomes using nullisomic-tetrasomic wheat ('Chinese Spring') and wheat-rye ('Chinese Spring'/'Imperial') addition lines. Whereas the loci for the pol...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g96-154

    authors: Korzun V,Balzer HJ,Balzer A,Bäumlein H,Börner A

    更新日期:1996-12-01 00:00:00

  • Development of RNA-seq-based molecular markers for characterizing Thinopyrum bessarabicum and Secale introgressions in wheat.

    abstract::Sequence-based markers have added a new dimension in the efficiency of identifying alien introgressions in wheat. Expressed sequence tag-sequence tagged sites (EST-STS) markers have proved useful in tracing alien chromatin. In this study, we report the development of Thinopyrum bessarabicum- and Secale anatolicum-spec...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2020-0057

    authors: Singh AK,Lo K,Dong C,Zhang P,Trethowan RM,Sharp PJ

    更新日期:2020-11-01 00:00:00

  • Development of a set of near isogenic and backcross recombinant inbred lines containing most of the Lycopersicon hirsutum genome in a L. esculentum genetic background: a tool for gene mapping and gene discovery.

    abstract::A novel population consisted of a set of 99 near isogenic lines (NILs) and backcross recombinant inbred lines (BCRILs) derived from a cross between the cultivated tomato Lycopersicon esculentum cv. E6206 and L. hirsutum accession LA1777 is presented. Most of the lines contain a single defined introgression from L. hir...

    journal_title:Genome

    pub_type: 杂志文章

    doi:

    authors: Monforte AJ,Tanksley SD

    更新日期:2000-10-01 00:00:00

  • Segmental chromosomal duplications harbouring group IV CONSTANS-like genes in cereals.

    abstract::Comparative mapping is an important component of map-based cloning in large-genome cereal species. We describe evidence of a segmental chromosomal duplication harbouring CONSTANS-like genes in barley that predates the divergence of the Oryzoideae (rice) and Pooideae (brachypodium, barley, wheat) clades, and discuss th...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g09-101

    authors: Cockram J,Howells RM,O'Sullivan DM

    更新日期:2010-03-01 00:00:00

  • S1 satellite DNA as a taxonomic marker in brown frogs: molecular evidence that Rana graeca graeca and Rana graeca italica are different species.

    abstract::The brown frog Rana graeca was believed to be present in two areas, the Balkan Peninsula and the Italian Apennines. We have characterised the S1 satellite DNA family from Rana graeca graeca and compared it with that of Rana graeca italica. On Southern blots, the patterns of S1 satellite DNA bands are very different be...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g01-125

    authors: Picariello O,Feliciello I,Bellinello R,Chinali G

    更新日期:2002-02-01 00:00:00

  • Karyotype variation in the albino rainbow trout (Oncorhynchus mykiss (Walbaum)).

    abstract::A Robertsonian polymorphism resulting in diploid chromosome number ranging from 59 to 61 and constant chromosome arm number (fundamental number = 104) was observed in the albino rainbow trout (Oncorhynchus mykiss (Walbaum)) from the yellow color strain. In one individual, 90 mitotic chromosomes and 156 chromosome arms...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g09-009

    authors: Ocalewicz K,Dobosz S

    更新日期:2009-04-01 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

  • Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density and a complex arrangement of genes related to disease resistance.

    abstract::Vast differences exist in genome sizes of higher plants; however, gene count remains relatively constant among species. Differences observed in DNA content can be attributed to retroelement amplification leading to genome expansion. Cytological and genetic studies have demonstrated that genes are clustered in islands ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g02-049

    authors: Brooks SA,Huang L,Gill BS,Fellers JP

    更新日期:2002-10-01 00:00:00

  • QTL mapping of seed-quality traits in sunflower recombinant inbred lines under different water regimes.

    abstract::The objectives of the present research were to determine the effects of water stress on seed-quality traits and to map QTLs controlling the studied traits under two different water treatments in a population of sunflower recombinant inbred lines (RILs). Two experiments were conducted in greenhouse and field conditions...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/G08-038

    authors: Ebrahimi A,Maury P,Berger M,Kiani SP,Nabipour A,Shariati F,Grieu P,Sarrafi A

    更新日期:2008-08-01 00:00:00

  • Likelihood estimation of quantitative genetic parameters when selection occurs: models and problems.

    abstract::Conceptual aspects of estimation of genetic components of variance and covariance under selection are discussed, with special attention to likelihood methods. Certain selection processes are described and alternative likelihoods that can be used for analysis are specified. There is a mathematical relationship between ...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g89-136

    authors: Gianola D,Fernando RL,Im S,Foulley JL

    更新日期:1989-01-01 00:00:00

  • Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.

    abstract::High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/gen-2015-0208

    authors: Al-Rshaidat MM,Snider A,Rosebraugh S,Devine AM,Devine TD,Plaisance L,Knowlton N,Leray M

    更新日期:2016-09-01 00:00:00

  • Genetic segregation of random amplified polymorphic DNA in diploid cultivated alfalfa.

    abstract::Polymerase chain reaction was used, with single 10-mer primers of arbitrary sequence, to amplify random regions of genomic DNA from a diploid cultivated alfalfa backcross population. Segregation of the random amplified polymorphic DNA (RAPD) fragments was analysed to determine if RAPD markers are suitable for use as g...

    journal_title:Genome

    pub_type: 杂志文章

    doi:10.1139/g92-014

    authors: Echt CS,Erdahl LA,McCoy TJ

    更新日期:1992-02-01 00:00:00