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Open Access Research article

Development of SNP markers for genes of the phenylpropanoid pathway and their association to kernel and malting traits in barley

Manuela Peukert, Stephan Weise, Marion S Röder* and Inge E Matthies

Author Affiliations

Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany

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BMC Genetics 2013, 14:97  doi:10.1186/1471-2156-14-97

Published: 2 October 2013

Additional files

Additional file 1:

SNPs detected within 16 reference genotypes for the phenylalanine ammonia-lyase (PAL) gene fragment PAL_1.

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Additional file 2:

SNPs detected within 16 reference genotypes for the phenylalanine ammonia-lyase (PAL) gene fragment PAL_2.

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Additional file 3:

Genetic structure of the resequenced fragments C4H_1 and C4H_4 from the cinnamate 4-hydroxylase (C4H) encoding gene. Double lines indicate UTR regions, single lines indicate no sequenced regions. Violet – CAPS marker and high-throughput SNP marker, green – high-throughput SNP marker.

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Additional file 4:

Positioning of the chalcone synthase (CHS) resequenced gene fragments GM_293 and GM_290, CHS_1, CHS_2 and CHS_3 in relation to cDNA Y09233. Polymorphisms were only detected in the large fragments GM_290 and GM_293. Green – high-throughput SNP marker.

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Open Data

Additional file 5:

Detected SNPs and their resulting haplotypes within 16 reference genotypes for the chalcone synthase (CHS) gene fragment GM_293.

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Additional file 6:

Detected SNPs within 16 reference genotypes for the chalcone synthase (CHS) gene fragment GM_287. Four different haplotypes were identified.

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Additional file 7:

Genetic structure of dihydoflavonol reductase (DFR) according to Kristiansen and Rohde [30]. Primer development for resequencing was performed using sequence information of EST contig Hv.23226. Light grey boxes represent exons and double lines between exons indicate the introns. UTRs are also marked by doubled lines. Green – high-throughput SNP marker, violet – CAPS marker and high-throughput SNP marker.

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Open Data

Additional file 8:

Marker-trait-associations of SNP polymorphisms and haplotypes found in 190 European barley cultivars and selected kernel and malting quality parameters for cinnamate 4-hydroxylase (C4H), flavanone 3-hydroxylase (F3H), dihydoflavonol reductase (DFR), chalcon synthase (CHS) and phenylalanine ammonia-lyase (PAL). Considered statistical models: 1. Mixed linear model (MLM) with principal component analysis (PCA), 2. MLM with kinship, 3. General linear model (GLM) with population structure. Significant at * p < 0.05, ** p < 0.01,*** p < 0.001, n.s. not significant.

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Additional file 9:

List of investigated 190 barley varieties.

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Additional file 10:

List of primers used for PCR amplification and sequencing.

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Additional file 11:

Used restriction enzymes for CAPS marker development and reaction conditions.

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Additional file 12:

Trait statistics of single phenotypic values across 185 varieties (before elimination of outliers) for 22 traits.

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Additional file 13:

Phenotypic data used for association analysis (mean values for each trait/variety combination after elimination of outliers).

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