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

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.

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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

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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.

Author information

Correspondence to Simen R. Sandve.

Additional information

Communicated by Hong-Qing Ling.

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Belova, T., Grønvold, L., Kumar, A. et al. Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome. Theor Appl Genet 127, 2029–2040 (2014). https://doi.org/10.1007/s00122-014-2358-z

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Keywords

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