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A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

Ervin D Nagy1, Yufang Guo1, Shunxue Tang1, John E Bowers1, Rebecca A Okashah1, Christopher A Taylor1, Dong Zhang1, Sameer Khanal1, Adam F Heesacker1, Nelly Khalilian1, Andrew D Farmer2, Noelia Carrasquilla-Garcia3, R Varma Penmetsa3, Douglas Cook3, H Thomas Stalker4, Niels Nielsen4, Peggy Ozias-Akins5* and Steven J Knapp1

Author Affiliations

1 Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Rd, Athens, GA, 30605, USA

2 National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA

3 Department of Plant Pathology, University of California, Davis, CA, 95616, USA

4 Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA

5 Department of Horticulture, University of Georgia, Tifton, GA, 31793, USA

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BMC Genomics 2012, 13:469  doi:10.1186/1471-2164-13-469

Published: 11 September 2012

Additional files

Additional file 1:

SNP markers on Illumina GoldenGate array. Marker ID along with sequence information for OPAs and target ESTs are provided.

Format: XLSX Size: 271KB Download file

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Additional file 2:

Comparative genetic mapping ofArachis duranensisusing two different software programs on the same dataset. Genetic maps were constructed by MSTMap (left) using 1673 co-dominant markers and Joinmap 3.0 (right) using 1724 markers. Linkage group assignments, marker orders and genetic distances were highly consistent, except for the order among a few closely linked loci. Marker positions determined by Joinmap 3.0 are provided in Additional file 6.

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Additional file 3:

Mapped markers with segregation distortion (p = 0.05) and their position on the map. Column A lists the marker positions on each chromosome, column B indicates marker name, column C is the chromosome number, columns D to H list the number of individuals in each genotype class, and columns J and K provide χ2 and P values, respectively.

Format: XLSX Size: 42KB Download file

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Additional file 4:

Annotated loci mapped inArachis duranensis. Columns B to J include homologs identified in the Medicago (B-D), GenBank-NR (E-G) and Uniprot-Sprot (H- J) databases. Columns L to S include gene ontology (GO) terms identified in the three major GO categories: molecular function (N, O), biological process (P,Q) and cellular component (R,S).

Format: XLSX Size: 362KB Download file

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Additional file 5:

Sequences associated with SSR and SSCP markers for synteny analysis. Column A is the marker name and column B is the Genebank ID or sequence used as query for synteny analysis.

Format: XLSX Size: 31KB Download file

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Additional file 6:

Marker positions for the linkage map.

Format: XLSX Size: 53KB Download file

Open Data