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. 2018 May 30;8(1):8428.
doi: 10.1038/s41598-018-26541-y.

Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye

Ewa Borzęcka  1 , Anna Hawliczek-Strulak  1 , Leszek Bolibok  2 , Piotr Gawroński  1 , Katarzyna Tofil  1 , Paweł Milczarski  3 , Stefan Stojałowski  3 , Beata Myśków  3 , Małgorzata Targońska-Karasek  1 , Agnieszka Grądzielewska  4 , Miłosz Smolik  3 , Andrzej Kilian  5 , Hanna Bolibok-Brągoszewska  6
Affiliations

Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye

Ewa Borzęcka et al. Sci Rep. .

Abstract

Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.

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Conflict of interest statement

A.K. is director of Diversity Arrays Technology Pty Ltd, which offers DArT and DArTseq genome profiling services. This fact has not interfered whatsoever with the full, objective, transparent, and unbiased presentation of the research results described in the manuscript nor alters the authors’ adherence to all the journal’s policies on sharing data and materials. All the other authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Percentages of DArT and DArTSeq markers with a given number of occurrences in the library screening data at different settings.
Figure 2
Figure 2
Numbers of BAC clones anchored per method and setting. Top of the blue bar indicates the number of BACs with at least two anchor markers, top of the orange bar indicates the number of BACs with conflicting anchoring.
See this image and copyright information in PMC

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