PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes.

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

Original Publication: London : BioMed Central, [2000-

Expressed Sequence Tags* ; Genome, Plant*; Genetic Markers/*genetics ; Introns/*genetics ; Polymerase Chain Reaction/*methods ; Triticum/*genetics; Base Sequence ; DNA Primers/genetics ; Molecular Sequence Data ; Oryza/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology ; Species Specificity

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.

Plant Mol Biol. 2002 Mar-Apr;48(5-6):767-90. (PMID: 11999849)
J AOAC Int. 2005 Jan-Feb;88(1):128-35. (PMID: 15759735)
Theor Appl Genet. 2005 Nov;111(7):1347-56. (PMID: 16167139)
Plant J. 2003 Oct;36(1):82-93. (PMID: 12974813)
BMC Genomics. 2006;7:207. (PMID: 16907970)
Genetics. 2004 Oct;168(2):585-93. (PMID: 15514037)
Genome Res. 2007 Feb;17(2):175-83. (PMID: 17210932)
Mol Genet Genomics. 2003 Dec;270(4):315-23. (PMID: 14508680)
Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1971-4. (PMID: 9482816)
Plant Mol Biol. 2005 Apr;57(6):907-24. (PMID: 15952073)
Theor Appl Genet. 2005 May;110(8):1467-72. (PMID: 15809850)
Gene. 1999 Jun 24;234(1):71-9. (PMID: 10393240)
Funct Integr Genomics. 2004 Jul;4(3):139-62. (PMID: 15095058)
Plant Physiol. 2006 Apr;140(4):1183-91. (PMID: 16607031)
J Exp Bot. 2004 Feb;55(396):365-75. (PMID: 14718498)
Genetics. 2006 Nov;174(3):1407-20. (PMID: 16951058)
Nature. 2005 Aug 11;436(7052):793-800. (PMID: 16100779)
Genome Res. 2003 Aug;13(8):1818-27. (PMID: 12902377)
Funct Integr Genomics. 2003 Mar;3(1-2):39-55. (PMID: 12590342)
Theor Appl Genet. 2005 Oct;111(6):1072-9. (PMID: 16172895)
Theor Appl Genet. 2006 Mar;112(5):808-17. (PMID: 16429310)
Bioinformatics. 2000 Nov;16(11):1046-7. (PMID: 11159318)
Cytogenet Genome Res. 2005;109(1-3):250-8. (PMID: 15753584)
Methods Mol Biol. 2000;132:365-86. (PMID: 10547847)
Genome. 2004 Oct;47(5):805-18. (PMID: 15499395)
Plant Physiol. 2005 Oct;139(2):643-51. (PMID: 16219925)
Plant Physiol. 2005 May;138(1):18-26. (PMID: 15888674)
Ann Bot. 2002 Jan;89(1):3-10. (PMID: 12096816)
Funct Integr Genomics. 2005 Apr;5(2):80-96. (PMID: 15650880)
Mol Genet Genomics. 2005 Mar;273(1):54-65. (PMID: 15690172)
Genetics. 1995 Oct;141(2):721-31. (PMID: 8647405)
Theor Appl Genet. 2003 Dec;108(1):154-9. (PMID: 12955208)
Chromosome Res. 2004;12(7):703-14. (PMID: 15505405)
Nucleic Acids Res. 2003 Jan 1;31(1):183-6. (PMID: 12519977)
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D39-45. (PMID: 15608222)
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80. (PMID: 7984417)
BMC Genomics. 2005;6:23. (PMID: 15720707)
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9. (PMID: 15215394)
Electrophoresis. 2003 Jan;24(1-2):93-5. (PMID: 12652577)
Trends Plant Sci. 2003 Nov;8(11):554-60. (PMID: 14607101)

0 (DNA Primers)
0 (Genetic Markers)

Date Created: 20070531 Date Completed: 20080124 Latest Revision: 20181113

20231215

PMC1904201

10.1186/1471-2164-8-135

17535443