Open Access Highly Accessed Research article

Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa

María Pazos-Navarro1, Mercedes Dabauza1, Enrique Correal2, Kelly Hanson3, Natasha Teakle45, Daniel Real567 and Matthew N Nelson5*

Author Affiliations

1 Departamento de Biotecnología y Protección de cultivos, Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), C/Mayor s/n, 30150-La Alberca, Murcia, Spain

2 Departamento de Recursos Naturales, IMIDA. C/Mayor s/n, 30150-La Alberca, Murcia, Spain

3 Australian Genome Research Facility, Level 5 Gehrmann Laboratories, Research Road, University of Queensland, St Lucia, QLD 4072, Australia

4 Centre for Ecohydrology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia

5 School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia

6 Department of Agriculture and Food, Western Australia, South Perth, WA 6151, Australia

7 Future Farm Industries Cooperative Research Centre, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia

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BMC Genetics 2011, 12:104  doi:10.1186/1471-2156-12-104

Published: 15 December 2011

Additional files

Additional file 1:

Gene ontology (GO) terms for 3,419 Bituminaria bituminosa mRNA sequences. GO terms with associated descriptions generated using Blast2GO software.

Format: XLSX Size: 297KB Download file

Open Data

Additional file 2:

240 primer pairs targeting simple sequence repeat motifs. Primer pairs designed using Primer3 based on Roche 454 sequences identified as containing simple sequence repeats using QDD software.

Format: XLSX Size: 94KB Download file

Open Data

Additional file 3:

Primer pairs selected for testing. Details of 94 primer pairs targeting simple sequence repeat (SSR) motifs in transcribed genes of Bituminaria bituminosa leaves sampled by Roche 454 transcriptome sequencing.

Format: XLSX Size: 19KB Download file

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Additional file 4:

Allele frequencies in Bituminaria bituminosa plants. A total of 118 simple sequence repeat (SSR) marker alleles were detected using 19 single-locus markers. Marker Bbit-SSR079 detected two loci and so was not included here. Polymorphic information content (PIC) and allele frequencies were calculated based on the whole population of 79 B. bituminosa plants. Allele frequencies are also presented for four original populations of botanical varieties albomarginata, bituminosa (from the Canary Islands and Mediterranean region) and crassiuscula that together comprised 27 plants.

Format: XLSX Size: 14KB Download file

Open Data

Additional file 5:

Euclidean distance matrix. 79 Bituminaria bituminosa plants were genotyped at 21 simple sequence repeat loci. The resulting 130 alleles were used to calculate pairwise Euclidean distances.

Format: XLSX Size: 38KB Download file

Open Data

Additional file 6:

Cluster tree of 79 Bituminaria bituminosa plants. Based on Euclidean distances estimated using 130 simple sequence repeat marker alleles. Symbols indicate botanical variety and type of line (original collection or breeding line).

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Open Data