Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers

PCR-based Landmark Unique Gene (PLUG) markers are EST-PCR markers developed based on the orthologous gene conservation between rice and wheat, and on the intron polymorphisms among the three orthologous genes derived from the A, B and D genomes of wheat. We designed a total of 960 primer sets from w...

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Bibliographic Details
Published in:Theoretical and applied genetics 2009-02, Vol.118 (3), p.499-514
Main Authors: Ishikawa, Goro, Nakamura, Toshiki, Ashida, Taizo, Saito, Mika, Nasuda, Shuhei, Endo, Takashi R, Wu, Jianzhong, Matsumoto, Takashi
Format: Article
Language:English
Subjects:
Agriculture
bacterial artificial chromosomes
Biochemistry
Biological and medical sciences
Biomedical and Life Sciences
Biotechnology
Chromosomes
Chromosomes, Artificial, Bacterial - genetics
Chromosomes, Plant
Classical genetics, quantitative genetics, hybrids
Cloning
cytogenetic analysis
Design
DNA Primers
DNA, Plant
Expressed Sequence Tags
Fundamental and applied biological sciences. Psychology
Genes
Genetic Markers
genetic polymorphism
Genetics of eukaryotes. Biological and molecular evolution
Genome, Plant
Genomes
introns
Life Sciences
Localization
loci
Original Paper
Oryza - genetics
Oryza sativa
Plant Biochemistry
Plant Breeding/Biotechnology
Plant Genetics and Genomics
Polymerase Chain Reaction
Pteridophyta, spermatophyta
Rice
spring wheat
Synteny
Triticum - genetics
Triticum aestivum
Vegetals
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Summary:PCR-based Landmark Unique Gene (PLUG) markers are EST-PCR markers developed based on the orthologous gene conservation between rice and wheat, and on the intron polymorphisms among the three orthologous genes derived from the A, B and D genomes of wheat. We designed a total of 960 primer sets from wheat ESTs that showed high similarity with 951 single-copy rice genes. When genomic DNA of Chinese Spring wheat was used as a template, 872 primer sets amplified one to five distinct products. Out of these 872 PLUG markers, 531 were assigned to one or more chromosomes by nullisomic-tetrasomic analysis. For each wheat chromosome, the number of loci detected ranged from 32 for chromosome 6A to 73 for chromosome 7D, with an average of 48 loci per chromosome. Several novel synteny perturbations were identified using deletion bin-mapping of markers. Furthermore, we demonstrated that PLUG markers can be used as probes to simultaneously identify BAC clones that contain homoeologous regions from all three genomes.
ISSN:0040-5752
1432-2242
DOI:10.1007/s00122-008-0916-y