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Theoretical and Applied Genetics

, Volume 127, Issue 9, pp 2029–2040 | Cite as

Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome

  • Tatiana Belova
  • Lars Grønvold
  • Ajay Kumar
  • Shahryar Kianian
  • Xinyao He
  • Morten Lillemo
  • Nathan M. Springer
  • Sigbjørn Lien
  • Odd-Arne Olsen
  • Simen R. Sandve
Original Paper

Abstract

Key message

A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome.

Abstract

Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.

Keywords

Comparative Genome Hybridization Sequence Contigs Deletion Line Ditelosomic Line Comparative Genome Hybridization Microarray 
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.

Abbreviations

CGH

Comparative genomic hybridization

IWGSC

International wheat genome sequencing consortium

CSS

Chromosome survey sequencing

cv CS

Cultivar chinese spring

LDN

Langdon

LDN-DS 7D(7B)

Langdon 7B substitution line

ISBP

Insertion site-based polymorphism

RG

Random genomic probes

FL

Fraction length

RIL

Recombinant inbred lines

Notes

Acknowledgments

The project was funded by grants from the Norwegian Research Council (project no. 199387/I99) and Graminor A/S to Odd-Arne Olsen.

Conflict of interest

The authors declare they have no conflict interests.

Supplementary material

122_2014_2358_MOESM1_ESM.pdf (929 kb)
Supplementary material 1 (PDF 928 kb)
122_2014_2358_MOESM2_ESM.pdf (59 kb)
Supplementary material 2 (PDF 58 kb)
122_2014_2358_MOESM3_ESM.xlsx (10 kb)
Supplementary material 3 (XLSX 10 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Tatiana Belova
    • 1
  • Lars Grønvold
    • 1
  • Ajay Kumar
    • 2
  • Shahryar Kianian
    • 2
  • Xinyao He
    • 3
  • Morten Lillemo
    • 1
  • Nathan M. Springer
    • 4
  • Sigbjørn Lien
    • 5
  • Odd-Arne Olsen
    • 1
  • Simen R. Sandve
    • 1
  1. 1.Department of Plant SciencesNorwegian University of Life SciencesÅsNorway
  2. 2.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  3. 3.International Maize and Wheat Improvement Center (CIMMYT)Mexico, DFMexico
  4. 4.Department of Plant Biology, Microbial and Plant Genomics InstituteUniversity of MinnesotaSaint PaulUSA
  5. 5.Centre for Integrative Genetics (CIGENE)Norwegian University of Life SciencesÅsNorway

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