Open Access Highly Accessed Research article

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

Kankshita Swaminathan1, Won Byoung Chae128, Therese Mitros34, Kranthi Varala29, Liang Xie12, Adam Barling12, Katarzyna Glowacka15, Megan Hall3, Stanislaw Jezowski5, Ray Ming16, Matthew Hudson12, John A Juvik12, Daniel S Rokhsar347* and Stephen P Moose12*

Author Affiliations

1 Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois Urbana, 1206 West Gregory Drive, Urbana, IL 61801, USA

2 Crop Sciences, Edward R. Madigan Laboratory, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA

3 Energy Biosciences Institute, University of California, 130 Calvin Laboratory, Berkeley, CA 94720, USA

4 Department of Molecular and Cell Biology, Life Sciences Annex, University of California, Berkeley, CA 94720, USA

5 Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland

6 Department of Plant Biology, Edward R. Madigan Laboratory, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA

7 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

8 National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea

9 Present address: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA

For all author emails, please log on.

BMC Genomics 2012, 13:142  doi:10.1186/1471-2164-13-142

Published: 24 April 2012

Additional files

Additional file 1:

Table S1. Phenotypes of the M.sinensis 'Grosse Fontaine' and M.sinensis 'Undine' parents, as measured in mature plants grown in the greenhouse (Figure 1 panels C).

Format: DOCX Size: 18KB Download file

Open Data

Additional file 2:

Fasta file of the M.sinensis RNAseq assembly.

Format: ZIP Size: 6.3MB Download file

Open Data

Additional file 3:

Table S3. GoldenGate OPA containing the probe details for every marker, as provided by Illumina.

Format: XLSX Size: 346KB Download file

Open Data

Additional file 4:

Table S4. File containing the primer details for all the SSRs.

Format: XLSX Size: 48KB Download file

Open Data

Additional file 5:

Figure S2. Different amplicon profiles seen in the fragment analysis of SSR markers. The length of the amplicon, in bp, is shown on the horizontal axis and the fluorescence intensity on the vertical axis. Several profiles show "stutter peaks" that are associated with a main peak. These are not counted as distinct marker states.

Format: JPEG Size: 1.4MB Download file

Open Data

Additional file 6:

Figure S6. Sequence alignment of two independent regions of Miscanthus PPDK paralogs 1 and 2 illustrating indels and SNV used as molecular markers to place C4-PPDK on the linkage map. A) 129 base pairs of sequence from PPDK paralog 1. The G/A single nucleotide polymorphism was converted into the CAPS marker, EBI 847. B) 129 base pairs of PPDK paralog 2 containing indels that were converted into a sequence length polymorphism marker, EBI 848. The oligonucleotide primers, UD3F and UD3R, used to amplify this region are shown.

Format: PDF Size: 7.7MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Table S2. RNA sequencing and assembly data table.

Format: DOCX Size: 54KB Download file

Open Data

Additional file 8:

Figure S1. Distribution of sorghum gene models (top stripe, green), Grosse Fontaine and Undine RNAseq reads (middle stripe, depth in log scale Blue-Orange-Green), and genotyped SNVs (bottom stripe, red) along the ten Sorghum bicolor chromosomes. Each chromosome shown to scale (length in Mb shown to left).

Format: JPEG Size: 735KB Download file

Open Data

Additional file 9:

Table S5. Markers listed in the order of occurrence on the combined maximum likelihood linkage map, with linkage group and map position in cM.

Format: XLSX Size: 158KB Download file

Open Data

Additional file 10:

Figure S3. Colinearity dot plots of the two mapping methods, maximum likelihood and regression (Kosambi).

Format: PDF Size: 258KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 11:

Figure S4. Colinearity dot plots of the Grosse Fontaine maps versus the Undine maps made using the maximum likelihood (top) and regression algorithms (bottom).

Format: PDF Size: 278KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 12:

Table S6. Genotype scores and marker statistics including segregation distortion for markers and mapping statistics for the integrated map shown in Figure 3.

Format: XLSX Size: 124KB Download file

Open Data

Additional file 13:

Table S7. Details of revised linkage groups 16 and 17 including two C4-PPDK markers.

Format: XLSX Size: 38KB Download file

Open Data

Additional file 14:

Figure S5. Linearity of genetic maps for Sorghum bicolor and Miscanthus sinensis. Markers with unique placement in sorghum were assigned map positions by interpolation relative to the map of Mace et al. 2009 [30].

Format: PDF Size: 168KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data