Highly parallel gene-to-BAC addressing using microarrays

Hui Liu, Jim McNicol, Micha Bayer, Jenny A Morris, Linda Cardle, David F Marshall, Daniela Schulte, Nils Stein, Bu-Jun Shi, Stefan Taudien, Robbie Waugh, Peter E Hedley

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Abstract

Second-generation sequencing now provides the potential for low-cost generation of whole-genome sequences. However, for large-genome organisms with high repetitive DNA content, genome-wide short read sequence assembly is currently impossible, with accurate ordering and localization of genes still relying heavily on integration with physical and genetic maps. To facilitate this process, we have used Agilent microarrays to simultaneously address thousands of gene sequences to individual BAC clones and contiguous sequences that form part of an emerging physical map of the large and currently unsequenced 5.3-Gb barley genome. The approach represents a cost-effective, highly parallel alternative to traditional addressing methods. By coupling the gene-to-BAC address data with gene-based molecular markers, thousands of BACs can be anchored directly to the genetic map, thereby generating a framework for orientating and ordering genes, and providing direct links to phenotypic traits.

Original languageEnglish
Pages (from-to)165-74
Number of pages10
JournalBioTechniques
Volume50
Issue number3
DOIs
Publication statusPrint publication - Mar 2011
Externally publishedYes

Fingerprint

Microarrays
Genes
Genome
Costs and Cost Analysis
Hordeum
Clone Cells
DNA
Costs

Keywords

  • Chromosomes, Artificial, Bacterial
  • DNA, Plant/genetics
  • Genome, Plant
  • High-Throughput Nucleotide Sequencing/methods
  • Hordeum/genetics
  • Oligonucleotide Array Sequence Analysis/methods
  • Sequence Analysis, DNA/methods

Cite this

Liu, H., McNicol, J., Bayer, M., Morris, J. A., Cardle, L., Marshall, D. F., ... Hedley, P. E. (2011). Highly parallel gene-to-BAC addressing using microarrays. BioTechniques, 50(3), 165-74. https://doi.org/10.2144/000113627
Liu, Hui ; McNicol, Jim ; Bayer, Micha ; Morris, Jenny A ; Cardle, Linda ; Marshall, David F ; Schulte, Daniela ; Stein, Nils ; Shi, Bu-Jun ; Taudien, Stefan ; Waugh, Robbie ; Hedley, Peter E. / Highly parallel gene-to-BAC addressing using microarrays. In: BioTechniques. 2011 ; Vol. 50, No. 3. pp. 165-74.
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Liu, H, McNicol, J, Bayer, M, Morris, JA, Cardle, L, Marshall, DF, Schulte, D, Stein, N, Shi, B-J, Taudien, S, Waugh, R & Hedley, PE 2011, 'Highly parallel gene-to-BAC addressing using microarrays', BioTechniques, vol. 50, no. 3, pp. 165-74. https://doi.org/10.2144/000113627

Highly parallel gene-to-BAC addressing using microarrays. / Liu, Hui; McNicol, Jim; Bayer, Micha; Morris, Jenny A; Cardle, Linda; Marshall, David F; Schulte, Daniela; Stein, Nils; Shi, Bu-Jun; Taudien, Stefan; Waugh, Robbie; Hedley, Peter E.

In: BioTechniques, Vol. 50, No. 3, 03.2011, p. 165-74.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Liu, Hui

AU - McNicol, Jim

AU - Bayer, Micha

AU - Morris, Jenny A

AU - Cardle, Linda

AU - Marshall, David F

AU - Schulte, Daniela

AU - Stein, Nils

AU - Shi, Bu-Jun

AU - Taudien, Stefan

AU - Waugh, Robbie

AU - Hedley, Peter E

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Liu H, McNicol J, Bayer M, Morris JA, Cardle L, Marshall DF et al. Highly parallel gene-to-BAC addressing using microarrays. BioTechniques. 2011 Mar;50(3):165-74. https://doi.org/10.2144/000113627