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

Scientific Reports
Ewa BorzęckaHanna Bolibok-Brągoszewska

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.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Oct 1, 1974·Biochemical Genetics·R B FlavellD B Smith
Oct 4, 2008·Science·Etienne PauxCatherine Feuillet
Dec 5, 2009·BMC Genomics·Hanna Bolibok-BragoszewskaMonika Rakoczy-Trojanowska
Apr 14, 2011·BioTechniques·Hui LiuPeter E Hedley
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Dec 14, 2011·PloS One·Paweł MilczarskiMonika Rakoczy-Trojanowska
Jan 10, 2013·FEMS Microbiology Reviews·Paul C Blainey
Mar 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Lyza G MaronLeon V Kochian
Oct 10, 2013·The Plant Cell·Mihaela M MartisNils Stein
Feb 4, 2014·The Plant Cell·Candice N HirschC Robin Buell
Feb 18, 2014·Bioinformatics·Jeffrey B Endelman, Christophe Plomion
Jun 12, 2014·Nature·Alexander A MyburgJeremy Schmutz
Nov 25, 2014·Nature Genetics·Jing CaiZhong-Jian Liu
Feb 11, 2015·Journal of Applied Genetics·Beata BakeraMonika Rakoczy-Trojanowska
Apr 19, 2015·BMC Plant Biology·Kateřina CvikováJan Bartoš
Aug 2, 2015·Cell·Mohammad PourkheirandishTakao Komatsuda
Jan 23, 2016·Plant Methods·Paul VisendiDavid Edwards
Aug 19, 2016·Proceedings of the National Academy of Sciences of the United States of America·Jianwei ZhangQifa Zhang
Nov 12, 2016·Frontiers in Plant Science·Piotr GawrońskiHanna Bolibok-Brągoszewska
Nov 12, 2016·Nature Communications·Agnieszka A GoliczDavid Edwards

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Citations

Oct 16, 2020·International Journal of Molecular Sciences·Magdalena GóralskaBeata Myśków

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Datasets Mentioned

BETA
MG669358

Methods Mentioned

BETA
whole genome shotgun sequencing
PCR
genotyping
electrophoresis

Software Mentioned

GenomeZipper
Excel
Silico
LPMerge
DArT
BLAST
DArTseq
Biomercator
BLASTN
DArTSoft14

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