Functional & Integrative Genomics

, Volume 12, Issue 1, pp 173–182

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

  • Stuart J. Lucas
  • Hana Šimková
  • Jan Šafář
  • Irena Jurman
  • Federica Cattonaro
  • Sonia Vautrin
  • Arnaud Bellec
  • Hélène Berges
  • Jaroslav Doležel
  • Hikmet Budak
Original Paper

DOI: 10.1007/s10142-011-0250-3

Cite this article as:
Lucas, S.J., Šimková, H., Šafář, J. et al. Funct Integr Genomics (2012) 12: 173. doi:10.1007/s10142-011-0250-3

Abstract

Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so far there is no such survey of sequences from the A genome of wheat. Greater understanding of an A chromosome could facilitate wheat improvement and future sequencing of the entire genome. We have constructed BAC library from the long arm of T. aestivum chromosome 1A (1AL) and obtained BAC end sequences from 7,470 clones encompassing the arm. We obtained 13,445 (89.99%) useful sequences with a cumulative length of 7.57 Mb, representing 1.43% of 1AL and about 0.14% of the entire A genome. The GC content of the sequences was 44.7%, and 90% of the chromosome was estimated to comprise repeat sequences, while just over 1% encoded expressed genes. From the sequence data, we identified a large number of sites suitable for development of molecular markers (362 SSR and 6,948 ISBP) which will have utility for mapping this chromosome and for marker assisted breeding. From 44 putative ISBP markers tested 23 (52.3%) were found to be useful. The BAC end sequence data also enabled the identification of genes and syntenic blocks specific to chromosome 1AL, suggesting regions of particular functional interest and targets for future research.

Keywords

WheatA genomeBAC end sequencingComparative genomicsMarker design

Supplementary material

10142_2011_250_MOESM1_ESM.xlsx (42 kb)
Online resource 1Excel spreadsheet of 362 putative SSR markers identified in chromosome 1AL BES sequences. (XLSX 42.3 kb)
10142_2011_250_MOESM2_ESM.xlsx (1.7 mb)
Online resource 2Excel spreadsheet of 9,338 putative ISBP markers identified in chromosome 1AL BES sequences, including details of repetitive element junctions. (XLSX 1.71 mb)
10142_2011_250_MOESM3_ESM.xlsx (43 kb)
Online resource 3Excel spreadsheet of 147 putative ISBP markers that incorporate an SSR from 1AL BES sequences, including details of repetitive element junctions and microsatellite sequences. (XLSX 42.7 kb)
10142_2011_250_MOESM4_ESM.xlsx (14 kb)
Online resource 4Excel spreadsheet of primer pairs used to test 26 ISBP, eight SSR, and ten combined ISBP/SSR markers in PCR screens, along with summary of results from amplification of both pooled BAC clones and gDNA from wheat cultivars and nullitetrasomic lines. (XLSX 14.1 kb)
10142_2011_250_MOESM5_ESM.docx (21 kb)
Online resource 5Table of syntenic relationships of masked 1AL BES sequences. All BES that had significant homology to coding regions in at least two sequenced grass species are shown. CDS that are out of syntenic sequence in one species are highlighted. (DOCX 21.1 kb)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Stuart J. Lucas
    • 1
  • Hana Šimková
    • 2
  • Jan Šafář
    • 2
  • Irena Jurman
    • 3
  • Federica Cattonaro
    • 3
  • Sonia Vautrin
    • 4
  • Arnaud Bellec
    • 4
  • Hélène Berges
    • 4
  • Jaroslav Doležel
    • 2
  • Hikmet Budak
    • 1
  1. 1.Sabanci University, Biological Sciences and Bioengineering ProgramIstanbulTurkey
  2. 2.Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental BotanyOlomoucCzech Republic
  3. 3.IGA Institute of Applied GenomicsUdineItaly
  4. 4.INRA-CNRGV French Plant Genomic Resources CentreCastanet TolosanFrance