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PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes.
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- المؤلفون: Ishikawa G;Ishikawa G; Yonemaru J; Saito M; Nakamura T
- المصدر:
BMC genomics [BMC Genomics] 2007 May 30; Vol. 8, pp. 135. Date of Electronic Publication: 2007 May 30.
- نوع النشر :
Comparative Study; Journal Article; Research Support, Non-U.S. Gov't
- اللغة:
English
- معلومة اضافية
- المصدر:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
- بيانات النشر:
Original Publication: London : BioMed Central, [2000-
- الموضوع:
- نبذة مختصرة :
Background: EST-PCR markers normally represent specific products from target genes, and are therefore effective tools for genetic analysis. However, because wheat is an allohexaploid plant, PCR products derived from homoeologous genes are often simultaneously amplified. Such products may be easier to differentiate if they include intron sequences, which are more polymorphic than exon sequences. However, genomic sequence data for wheat are limited; therefore it is difficult to predict the location of introns. By using the similarities in gene structures between rice and wheat, we developed a system called PLUG (PCR-based Landmark Unique Gene) to design primers so that PCR products include intron sequences. We then investigated whether products amplified using such primers could serve as markers able to distinguish multiple products derived from homoeologous genes.
Results: The PLUG system consists of the following steps: (1) Single-copy rice genes (Landmark Unique Gene loci; LUGs) exhibiting high degrees of homology to wheat UniGene sequences are extracted; (2) Alignment analysis is carried out using the LUGs and wheat UniGene sequences to predict exon-exon junctions, and LUGs which can be used to design wheat primers flanking introns (TaEST-LUGs) are extracted; and (3) Primers are designed in an interactive manner. From a total of 4,312 TaEST-LUGs, 24 loci were randomly selected and used to design primers. With all of these primer sets, we obtained specific, intron-containing products from the target genes. These markers were assigned to chromosomes using wheat nullisomic-tetrasomic lines. By PCR-RFLP analysis using agarose gel electrophoresis, 19 of the 24 markers were located on at least one chromosome.
Conclusion: In the development of wheat EST-PCR markers capable of efficiently sorting products derived from homoeologous genes, it is important to design primers able to amplify products that include intron sequences with insertion/deletion polymorphisms. Using the PLUG system, wheat EST sequences that can be used for marker development are selected based on comparative genomics with rice, and then primer sets flanking intron sequences are prepared in an interactive, semi-automatic manner. Hence, the PLUG system is an effective tool for large-scale marker development.
- References:
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- الرقم المعرف:
0 (DNA Primers)
0 (Genetic Markers)
- الموضوع:
Date Created: 20070531 Date Completed: 20080124 Latest Revision: 20181113
- الموضوع:
20231215
- الرقم المعرف:
PMC1904201
- الرقم المعرف:
10.1186/1471-2164-8-135
- الرقم المعرف:
17535443
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