Open Access Highly Accessed Research article

Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

Rebekah E Oliver1, Gerard R Lazo2, Joseph D Lutz3, Marc J Rubenfield134, Nicholas A Tinker5, Joseph M Anderson6, Nicole H Wisniewski Morehead1, Dinesh Adhikary7, Eric N Jellen7, P Jeffrey Maughan7, Gina L Brown Guedira8, Shiaoman Chao9, Aaron D Beattie10, Martin L Carson11, Howard W Rines12, Donald E Obert1, J Michael Bonman1 and Eric W Jackson1*

Author Affiliations

1 USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA

2 USDA-ARS, Western Regional Research Center, Albany, CA, USA

3 General Mills Agriculture Research, LeSueur, MN, USA

4 Beckman Coulter Genomics, Beverly, MA, USA

5 Agriculture and Agri-Food Canada, Ottawa, ON, Canada

6 USDA-ARS, Dept. Agronomy, Purdue University, West Lafayette, IN, USA

7 Dept. Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA

8 USDA-ARS, Plant Science Research, Raleigh, NC, USA

9 USDA-ARS, Cereal Crops Research, Fargo, ND, USA

10 Crop Development Centre, University of Saskatchewan, Saskatoon, SK Canada

11 USDA-ARS, Cereal Disease Laboratory, St. Paul, MN, USA

12 Dept. Agronomy and Plant Genetics, University of MN, St. Paul, MN, USA

13 Current Address: Knome, Inc., Cambridge, MA, USA

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BMC Genomics 2011, 12:77  doi:10.1186/1471-2164-12-77

Published: 27 January 2011

Additional files

Additional file 1:

Diversity panel allele designations. Allele calls were based on high-resolution melting analysis of PCR amplicons generated with 36 EST-SNP markers in a panel of 34 diverse oat genotypes. Supplementary alleles were designated as insertion (In), deletion (Del), or null (no amplification). When SNP sequences were not available, alternate alleles were designated X and Y.

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Additional file 2:

Origin and pedigree links of oat genotypes used in SNP development, validation, and diversity analysis. The first four genotypes were used in cDNA library construction and sequencing and SNP marker discovery. All genotypes in this table, together with the additional genotypes listed in Table 4, were used for SNP genotyping and diversity analysis.

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Additional file 3:

Tissue types. RNA was extracted from etiolated shoots (A) and roots (B), pistillate structures (C), and mature embryos (D) from four different oat varieties. Tissues were grown at standardized conditions, and RNA for each tissue type was extracted at the same stage of development.

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Additional file 4:

Header report files generated by Roche gsMapper. Powerpoint file displaying header report files generated by Roche gsMapper.

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Additional file 5:

Command line processing of header files and sequences for SNP candidate design. Powerpoint file displaying command line processing of header files and sequences for SNP candidate design.

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Additional file 6:

Primer and allele sequences of SNP markers mapped in the Ogle1040/TAM O-301 RIL population. Word DOC file displaying primer and allele sequences of SNP markers mapped in the Ogle1040/TAM O-301 RIL population.

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