Theoretical and Applied Genetics

, Volume 123, Issue 3, pp 455–464 | Cite as

Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon

  • Naxin Huo
  • David F. Garvin
  • Frank M. You
  • Stephanie McMahon
  • Ming-Cheng Luo
  • Yong Q. Gu
  • Gerard R. Lazo
  • John Philip Vogel
Original Paper


The small annual grass Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to study questions unique to the grasses. Many Brachypodium resources have been developed including a whole genome sequence, highly efficient transformation and a large germplasm collection. We developed a genetic linkage map of Brachypodium using single nucleotide polymorphism (SNP) markers and an F2 mapping population of 476 individuals. SNPs were identified by targeted resequencing of single copy genomic sequences. Using the Illumina GoldenGate Genotyping platform we placed 558 markers into five linkage groups corresponding to the five chromosomes of Brachypodium. The unusually long total genetic map length, 1,598 centiMorgans (cM), indicates that the Brachypodium mapping population has a high recombination rate. By comparing the genetic map to genome features we found that the recombination rate was positively correlated with gene density and negatively correlated with repetitive regions and sites of ancestral chromosome fusions that retained centromeric repeat sequences. A comparison of adjacent genome regions with high versus low recombination rates revealed a positive correlation between interspecific synteny and recombination rate.


Recombination Rate Long Terminal Repeat Single Nucleotide Polymorphism Marker Gene Density Brachypodium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Bacterial artificial chromosome


BAC end sequence


Base pair






Long terminal repeat


Single nucleotide polymorphism


Oligo pool array


Untranslated region



We would like to thank Haiming Xu (Zhejiang University) for QGA station analysis, Alan Schulman for LTR locations, and Edward Buckler for suggestions on presenting cumulative features (Fig. 4). This work was funded by an NSF 06-555 Plant Genome Research program grant and by USDA CRIS projects 5325-21000-013-00 and 3640-21000-021-00D.

Supplementary material

122_2011_1598_MOESM1_ESM.xls (748 kb)
Online Resource 1: This file contains an excel spreadsheet with all the SNPs identified, their flanking sequence and their designability rank score used to predict their performance in the Illumina GoldeGate genotyping system. (XLS 748 kb)
122_2011_1598_MOESM2_ESM.pdf (1.6 mb)
Online Resource 2: A PDF file containing linkage maps where all the markers and distances can be read. (PDF 1621 kb)
122_2011_1598_MOESM3_ESM.xls (178 kb)
Online Resource 3: This file contains an excel spreadsheet with all the mapped SNP markers, genomic coordinates, genetic distance, SNP score and marker sequence. (XLS 178 kb)
122_2011_1598_MOESM4_ESM.xls (38 kb)
Online Resource 4: This file contains an excel spreadsheet with all the genomic features for the paired low and high recombination intervals. (XLS 38 kb)


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Copyright information

© Springer-Verlag (outside the USA) 2011

Authors and Affiliations

  • Naxin Huo
    • 1
    • 2
  • David F. Garvin
    • 3
  • Frank M. You
    • 1
    • 2
  • Stephanie McMahon
    • 1
  • Ming-Cheng Luo
    • 2
  • Yong Q. Gu
    • 1
  • Gerard R. Lazo
    • 1
  • John Philip Vogel
    • 1
  1. 1.USDA-ARS Western Regional Research CenterAlbanyUSA
  2. 2.Department of Plant SciencesUniversity of CaliforniaDavisUSA
  3. 3.USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA

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