Open Access Highly Accessed Research article

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

Yada Chutimanitsakun1, Rick W Nipper2, Alfonso Cuesta-Marcos1, Luis Cistué3, Ann Corey1, Tanya Filichkina1, Eric A Johnson2 and Patrick M Hayes1*

Author Affiliations

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

2 Floragenex, Inc., Eugene, Oregon, USA

3 Departamento de Genética y Producción Vegetal. Estación Experimental de Aula Dei. Consejo Superior de Investigaciones Científicas. Zaragoza, Spain

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BMC Genomics 2011, 12:4  doi:10.1186/1471-2164-12-4

Published: 4 January 2011

Additional files

Additional file 1:

Table S1: Oregon Wolf Barley DH Sequencing Summary. The aggregate sequence reads obtained for both parents and each member of the OWB mapping population are provided. Sequencing coverage for each sample is also calculated based on the formula (Number of SbfI genome sequences from Barley genome/raw sequences obtained). Clustering of RAD data from multiple individuals indicates there are approximately 10,000 SbfI sequences in the typical Hordeum genome.

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Additional file 2:

Table S2: Oregon Wolf Barley DH RAD Marker Sequences. The sequence data for each RAD marker positioned on the genetic map is provided in this spreadsheet.

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Additional file 3:

Figure S1: Linkage map of Oregon Wolfe Barley population based on RAD markers.

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Additional file 4:

Table S4: Oregon Wolf Barley RAD EST/Genome Alignments. Bowtie alignments of OWB RAD markers to three sequence databases are provided: The Hordeum gene index (HvGI v10.2) from the Dana-Farber Cancer Institute, the MSU Rice Genome Annotation Project Release 6.0 (January 30, 2009) and the 8× Brachypodium Genome Assembly from brachypodium.org. The table columns detail, from left to right: the OWB marker name, sequence alignment orientation, the name (either EST/contig/chromosome identifier) and position (in bp) of the sequence alignment within the reference assembly, the sequence of the RAD marker and any variations observed between query (RAD marker) and reference. Variations are reported as: position in read, reference allele and query allele.

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Additional file 5:

Table S5: Syntenic Oregon Wolf Barley/Brachypodium RAD Marker Sequences. Bowtie alignments of OWB RAD markers to the 8× Brachypodium Genome Assembly from brachypodium.org are shown. OWB RAD markers have been ordered by linkage group and map position. The corresponding alignment positions for each marker on the Bd21 assembly are shown in columns at right, with chromosome, alignment position, sequence and observed sequence variation between Brachypodium and OWB RAD markers.

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