Open Access Highly Accessed Research article

Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

Alfonso Cuesta-Marcos1*, Péter Szűcs1, Timothy J Close2, Tanya Filichkin1, Gary J Muehlbauer3, Kevin P Smith3 and Patrick M Hayes1

Author Affiliations

1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA

2 Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA

3 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA

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BMC Genomics 2010, 11:707  doi:10.1186/1471-2164-11-707

Published: 15 December 2010

Additional files

Additional file 1:

Table S1. Passport information and phenotypic characterization of the CAP Core for flowering time and inflorescence type and genotypic characterization for the main loci controlling these traits.

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Additional file 2:

Table S2. Accession numbers of the sequences deposited with GenBank.

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Additional file 3:

Table S3. Primers used for genotyping and/or re-sequencing VRN-H, PPD-H, FR-H, and VRS1 specific genes in the CAP Core.

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Additional file 4:

Figure S1. Neighbor-Joining phylogenetic cluster analyses of several re-sequenced genes of the barley CAP Core set. Confidence values on the branches are based on 1000 bootstraps. For each gene, sequence length and number of lines used is indicated in the heading of each cluster. Number of genotypes per haplotype is indicated in brackets.

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Additional file 5:

Text S1. Detailed results of re-sequencing.

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Additional file 6:

Figure S2. Schematic representation of VRN-H1 intron 1 found in the barley CAP Core set (102 genotypes). Deletion types are named based on the first cultivar whose sequence was deposited in GenBank. Edges of exons 1 and 2 are indicated by flanking black boxes. Gaps represent deletions (>50 bp) relative to the full-length Strider allele. The 2.8 kb barley-wheat conserved region (dashed line) and the 436 bp vernalization critical region (dotted box) are indicated. Number of genotypes per deletion type is denoted.

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Additional file 7:

Figure S3. Sequence alignment of HvHOX1 from seven accessions with different VRS1 haplotypes. Similarity is shown to four levels.

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Additional file 8:

Table S4. Detailed information about SNP markers highly significant in the analysis of interactions in the CAP Core.

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Additional file 9:

Table S5. POPA SNP markers developed from re-sequencing of loci related to vernalization sensitivity and inflorescence type.

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