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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

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

Published: 24 April 2012

Abstract

Background

Miscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, attractive as a biofuel feedstock. The base chromosome number of Miscanthus (x = 19) is different from that of other Saccharinae and approximately twice that of the related Sorghum bicolor (x = 10), suggesting large-scale duplications may have occurred in recent ancestors of Miscanthus. Owing to the complexity of the Miscanthus genome and the complications of self-incompatibility, a complete genetic map with a high density of markers has not yet been developed.

Results

We used deep transcriptome sequencing (RNAseq) from two M. sinensis accessions to define 1536 single nucleotide variants (SNVs) for a GoldenGateā„¢ genotyping array, and found that simple sequence repeat (SSR) markers defined in sugarcane are often informative in M. sinensis. A total of 658 SNP and 210 SSR markers were validated via segregation in a full sibling F1 mapping population. Using 221 progeny from this mapping population, we constructed a genetic map for M. sinensis that resolves into 19 linkage groups, the haploid chromosome number expected from cytological evidence. Comparative genomic analysis documents a genome-wide duplication in Miscanthus relative to Sorghum bicolor, with subsequent insertional fusion of a pair of chromosomes. The utility of the map is confirmed by the identification of two paralogous C4-pyruvate, phosphate dikinase (C4-PPDK) loci in Miscanthus, at positions syntenic to the single orthologous gene in Sorghum.

Conclusions

The genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade. The recent timing of this tetraploidy complicates discovery and mapping of genetic markers for Miscanthus species, since alleles and fixed differences between paralogs are comparable. These difficulties can be overcome by careful analysis of segregation patterns in a mapping population and genotyping of doubled haploids. The genetic map for Miscanthus will be useful in biological discovery and breeding efforts to improve this emerging biofuel crop, and also provide a valuable resource for understanding genomic responses to tetraploidy and chromosome fusion.