title: High resolution melting analysis of almond SNPs derived from ESTs.
abstract: High resolution melting curve (HRM) is a recent advance for the detection of SNPs. The technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between samples. It has been applied to the analysis and scan of mutations in the genes causing human diseases. In plant species, the use of this approach is limited. We applied HRM analysis to almond SNP discovery and genotyping based on the predicted SNP information derived from the almond and peach EST database. Putative SNPs were screened from almond and peach EST contigs by HRM analysis against 25 almond cultivars. All 4 classes of SNPs, INDELs and microsatellites were discriminated, and the HRM profiles of 17 amplicons were established. The PCR amplicons containing single, double and multiple SNPs produced distinctive HRM profiles. Additionally, different genotypes of INDEL and microsatellite variations were also characterised by HRM analysis. By sequencing the PCR products, 100 SNPs were validated/revealed in the HRM amplicons and their flanking regions. The results showed that the average frequency of SNPs was 1:114 bp in the genic regions, and transition to transversion ratio was 1.16:1. Rare allele frequencies of the SNPs varied from 0.02 to 0.5, and the polymorphic information contents of the SNPs were from 0.04 to 0.53 at an average of 0.31. HRM has been demonstrated to be a fast, low cost, and efficient approach for SNP discovery and genotyping, in particular, for species without much genomic information such as almond.
authors.affiliation: School of Environmental and Rural Science and The Institute of Genetics and Bioinformatics, The University of New England, Armidale, NSW, 2351, Australia. shubiao.wu@une.edu.au
authors.forename: Shu-Biao
authors.initials: SB
authors.lastname: Wu
authors.forename: Michelle G
authors.initials: MG
authors.lastname: Wirthensohn
authors.forename: Peter
authors.initials: P
authors.lastname: Hunt
authors.forename: John P
authors.initials: JP
authors.lastname: Gibson
authors.forename: Margaret
authors.initials: M
authors.lastname: Sedgley
mesh_terms: D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D005838:Genotype; D054643:INDEL Mutation; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D027861:Prunus / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant
references.citation: Nucleic Acids Res. 2007;35(6):e41
references.pmid: 17289753
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Mol Biol Evol. 2003 Jun;20(6):988-93
references.pmid: 12716982
references.citation: Clin Chem. 2007 Nov;53(11):1960-2
references.pmid: 17890436
references.citation: Mol Biol Evol. 1994 May;11(3):436-42
references.pmid: 8015437
references.citation: Pharmacogenomics. 2007 Jun;8(6):597-608
references.pmid: 17559349
references.citation: Hum Pathol. 2005 May;36(5):486-93
references.pmid: 15948115
references.citation: Nucleic Acids Res. 1994 Mar 25;22(6):972-6
references.pmid: 8152929
references.citation: J Mol Biol. 1974 May 25;85(3):411-31
references.pmid: 22003574
references.citation: BMC Bioinformatics. 2005 Dec 01;6 Suppl 4:S16
references.pmid: 16351742
references.citation: Clin Chem. 2005 Oct;51(10):1770-7
references.pmid: 16189378
references.citation: Comput Appl Biosci. 1996 Aug;12(4):357-8
references.pmid: 8902363
references.citation: FEMS Microbiol Lett. 1999 May 15;174(2):247-50
references.pmid: 10339815
references.citation: Clin Chem. 2003 Jun;49(6 Pt 1):853-60
references.pmid: 12765979
references.citation: PLoS Genet. 2007 Feb 2;3(2):e22
references.pmid: 17274688
references.citation: Am J Hum Genet. 1980 May;32(3):314-31
references.pmid: 6247908
references.citation: Mutat Res. 2003 May 15;526(1-2):53-61
references.pmid: 12714183
references.citation: Clin Chem. 2007 Aug;53(8):1544-8
references.pmid: 17556647
references.citation: Science. 2001 Aug 10;293(5532):1070-4
references.pmid: 11498574
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W577-81
references.pmid: 15980540
references.citation: Biochem Biophys Res Commun. 1974 Dec 23;61(4):1249-55
references.pmid: 4455258
references.citation: Theor Appl Genet. 2005 Mar;110(5):959-68
references.pmid: 15700145
references.citation: Theor Appl Genet. 2006 Jan;112(2):366-72
references.pmid: 16307227
references.citation: Clin Chem. 2007 Feb;53(2):349-52
references.pmid: 17200131
references.citation: Biotechniques. 2003 Jun;34(6):1288-92, 1294-5
references.pmid: 12813898
references.citation: BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S9
references.pmid: 18387211
references.citation: Clin Biochem. 2002 Feb;35(1):35-40
references.pmid: 11937076
references.citation: Theor Appl Genet. 2008 Sep;117(5):721-8
references.pmid: 18553067
references.citation: Clin Chem. 2006 Mar;52(3):494-503
references.pmid: 16423901
references.citation: BMC Genet. 2002 Oct 7;3:19
references.pmid: 12366868
references.citation: Clin Chem. 2004 Jul;50(7):1156-64
references.pmid: 15229148
references.citation: Mol Cell Probes. 2007 Feb;21(1):8-11
references.pmid: 16879946
references.citation: Clin Chem. 2001 Apr;47(4):635-44
references.pmid: 11274012
references.citation: Theor Appl Genet. 2005 May;110(8):1467-72
references.pmid: 15809850
references.citation: Mol Psychiatry. 2000 Sep;5(5):489-494
references.pmid: 11035444
references.citation: J Hum Genet. 2001;46(8):471-7
references.pmid: 11501945
references.citation: Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460-5
references.pmid: 9465037
references.citation: Nature. 1994 Mar 31;368(6470):455-7
references.pmid: 7510853
references.citation: BMC Cancer. 2007 Aug 31;7:168
references.pmid: 17764544
references.citation: Genome Res. 2003 Jun;13(6A):1250-7
references.pmid: 12799357
references.citation: Anal Biochem. 1997 Feb 15;245(2):154-60
references.pmid: 9056205
references.citation: Clin Biochem. 2008 Feb;41(3):162-6
references.pmid: 18199430
references.citation: Nature. 2007 Oct 18;449(7164):851-61
references.pmid: 17943122
references.citation: Plant Physiol. 2003 May;132(1):84-91
references.pmid: 12746514
references.citation: Clin Chem. 2008 Feb;54(2):432-6
references.pmid: 18223135
references.citation: Plant Methods. 2008 May 19;4:8
references.pmid: 18489740
references.citation: Pharmacogenomics J. 2002;2(2):103-10
references.pmid: 12049172
references.citation: Tissue Antigens. 2004 Aug;64(2):156-64
references.pmid: 15245370
references.citation: Theor Appl Genet. 2004 May;108(7):1212-20
references.pmid: 14740086