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Identification of SNPs and development of allele-specific PCR markers for gamma-gliadin alleles in Triticum aestivum.
Theor Appl Genet. 2003 Jun; 107(1):130-8.TA

Abstract

The coding regions of 28 entries of hexaploid wheat gamma-gliadin genes, gene fragments or pseudogenes in GenBank were used for nucleotide alignment. These sequences could be divided into nine subgroups based on nucleotide variation. The chromosomal locations of five of the seven unassigned subgroups were identified through subgroup-specific polymerase chain reactions (PCR) using Chinese Spring group-1 nulli-tetrasomic lines. Multiple single nucleotide polymorphisms (SNPs) and small insertions/deletions were identified in each subgroup. With further mining from wheat expressed sequence tag databases and targeted DNA sequencing, two SNPs were confirmed and one SNP was discovered for genes at the Gli-A1, Gli-B1 and Gli-D1 loci. A modified allele-specific PCR procedure for assaying SNPs was used to generate dominant DNA markers based on these three SNPs. For each of these three SNPs, two allele-specific primer sets were used to test Chinese Spring and 52 commercial Australian wheat varieties representing a range of low-molecular-weight (LMW) alleles. PCR results indicated that all were positive with one of the primer sets and negative with the other, with the exception of three varieties containing the 1BL/1RS chromosomal translocation that were negative for both. Furthermore, markers GliA1.1, GliB1.1 and GliD1.1 were found to be correlated with Glu-A3 a, b or c, Glu-B3 b, c, d or e and Glu-D3 a, b or e LMW glutenin alleles, respectively. Markers GliA1.2, GliB1.2 and GliD1.2 were found to be correlated with the Glu-A3 d or e, Glu-B3 a, g or h and Glu-D3 c alleles, respectively. These results indicated that the gamma-gliadin SNP markers could be used for detecting linked LMW glutenin subunit alleles that are important in determining the quality attributes of wheat products.

Authors+Show Affiliations

Commonwealth Scientific and Industrial Research Organisation, Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

12712246

Citation

Zhang, W, et al. "Identification of SNPs and Development of Allele-specific PCR Markers for Gamma-gliadin Alleles in Triticum Aestivum." TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, vol. 107, no. 1, 2003, pp. 130-8.
Zhang W, Gianibelli MC, Ma W, et al. Identification of SNPs and development of allele-specific PCR markers for gamma-gliadin alleles in Triticum aestivum. Theor Appl Genet. 2003;107(1):130-8.
Zhang, W., Gianibelli, M. C., Ma, W., Rampling, L., & Gale, K. R. (2003). Identification of SNPs and development of allele-specific PCR markers for gamma-gliadin alleles in Triticum aestivum. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 107(1), 130-8.
Zhang W, et al. Identification of SNPs and Development of Allele-specific PCR Markers for Gamma-gliadin Alleles in Triticum Aestivum. Theor Appl Genet. 2003;107(1):130-8. PubMed PMID: 12712246.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of SNPs and development of allele-specific PCR markers for gamma-gliadin alleles in Triticum aestivum. AU - Zhang,W, AU - Gianibelli,M C, AU - Ma,W, AU - Rampling,L, AU - Gale,K R, Y1 - 2003/04/24/ PY - 2002/08/12/received PY - 2002/12/12/accepted PY - 2003/4/25/pubmed PY - 2004/2/20/medline PY - 2003/4/25/entrez SP - 130 EP - 8 JF - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JO - Theor Appl Genet VL - 107 IS - 1 N2 - The coding regions of 28 entries of hexaploid wheat gamma-gliadin genes, gene fragments or pseudogenes in GenBank were used for nucleotide alignment. These sequences could be divided into nine subgroups based on nucleotide variation. The chromosomal locations of five of the seven unassigned subgroups were identified through subgroup-specific polymerase chain reactions (PCR) using Chinese Spring group-1 nulli-tetrasomic lines. Multiple single nucleotide polymorphisms (SNPs) and small insertions/deletions were identified in each subgroup. With further mining from wheat expressed sequence tag databases and targeted DNA sequencing, two SNPs were confirmed and one SNP was discovered for genes at the Gli-A1, Gli-B1 and Gli-D1 loci. A modified allele-specific PCR procedure for assaying SNPs was used to generate dominant DNA markers based on these three SNPs. For each of these three SNPs, two allele-specific primer sets were used to test Chinese Spring and 52 commercial Australian wheat varieties representing a range of low-molecular-weight (LMW) alleles. PCR results indicated that all were positive with one of the primer sets and negative with the other, with the exception of three varieties containing the 1BL/1RS chromosomal translocation that were negative for both. Furthermore, markers GliA1.1, GliB1.1 and GliD1.1 were found to be correlated with Glu-A3 a, b or c, Glu-B3 b, c, d or e and Glu-D3 a, b or e LMW glutenin alleles, respectively. Markers GliA1.2, GliB1.2 and GliD1.2 were found to be correlated with the Glu-A3 d or e, Glu-B3 a, g or h and Glu-D3 c alleles, respectively. These results indicated that the gamma-gliadin SNP markers could be used for detecting linked LMW glutenin subunit alleles that are important in determining the quality attributes of wheat products. SN - 0040-5752 UR - https://www.unboundmedicine.com/medline/citation/12712246/Identification_of_SNPs_and_development_of_allele_specific_PCR_markers_for_gamma_gliadin_alleles_in_Triticum_aestivum_ L2 - https://dx.doi.org/10.1007/s00122-003-1223-2 DB - PRIME DP - Unbound Medicine ER -