Development and Evaluation of a Barley 50k iSelect SNP Array

Frontiers in Plant Science
Micha M BayerRobbie Waugh

Abstract

High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segre...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Nov 15, 2001·Mammalian Genome : Official Journal of the International Mammalian Genome Society·K F ManlyJ M Meer
Sep 2, 2004·Cold Spring Harbor Symposia on Quantitative Biology·J B FanM S Chee
Oct 26, 2005·Molecular Genetics and Genomics : MGG·Nils RostoksRobbie Waugh
Dec 8, 2009·BMC Genomics·Timothy J CloseRobbie Waugh
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Feb 17, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·M MoraguesJoanne R Russell
Oct 20, 2010·Bioinformatics·Iain MilneDavid Marshall
Dec 1, 2010·Proceedings of the National Academy of Sciences of the United States of America·James CockramDonal M O'Sullivan
Oct 31, 2012·Journal of Biosciences·Martin W GanalGregor Durstewitz
Dec 12, 2012·International Journal of Plant Genomics·Santosh KumarSylvie Cloutier
Jul 31, 2013·The Plant Journal : for Cell and Molecular Biology·Martin MascherNils Stein
Oct 15, 2013·Molecular Plant·Haodong ChenQifa Zhang
Nov 29, 2014·Current Protocols in Bioinformatics·Geraldine A Van der AuweraMark A DePristo
Jul 30, 2015·BMC Bioinformatics·Howard W HuangNancy F Hansen
Aug 13, 2015·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Peter G VosHerman J van Eck
Oct 16, 2015·Plant Biotechnology Journal·Mark O WinfieldKeith J Edwards
Feb 27, 2016·The Plant Journal : for Cell and Molecular Biology·Luca BiancoMichela Troggio
Jul 2, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Wayne E ClarkeIsobel A P Parkin
Feb 22, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Annaliese S MasonIsobel A P Parkin
Apr 28, 2017·Scientific Data·Sebastian BeierMartin Mascher

❮ Previous
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Citations

Nov 23, 2018·The Plant Journal : for Cell and Molecular Biology·Kathleen BeilsmithJoy Bergelson
Nov 11, 2018·Journal of Integrative Plant Biology·Matthew HaasMartin Mascher
Jan 23, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Mark E LooseleyAnna Avrova
Jan 31, 2020·G3 : Genes - Genomes - Genetics·Allison M HaaningGary J Muehlbauer
Jun 6, 2020·PloS One·Mathias Ruben GemmerAndreas Maurer
Jun 9, 2020·Critical Reviews in Biotechnology·Ramaswamy ManimekalaiMallikarjuna Kandalam
May 28, 2020·Journal of Experimental Botany·Leonard GolMaria von Korff
Sep 5, 2020·Molecular Biology Reports·Smitha Kunhiraman VasumathyManickavelu Alagu
Sep 27, 2020·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Kazuhiro Sato
Dec 14, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Max CoulterAnna Avrova
Dec 15, 2018·Journal of Integrative Plant Biology·Salar ShaafLaura Rossini
May 28, 2019·Frontiers in Plant Science·Tsuyoshi TanakaKazuhiro Sato
May 7, 2020·Frontiers in Plant Science·Beata Orman-LigezaKay Trafford
May 24, 2020·Communications Biology·Kelly HoustonRobbie Waugh
Jun 9, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Mark E LooseleyWilliam T B Thomas
Sep 23, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Rui WangShaobin Zhong
Jan 20, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Timm BernhardBenjamin Wittkop
Nov 18, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Cécile MonatMartin Mascher
Jun 19, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Fluturë NovakaziFrank Ordon
Jul 20, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Qian YouJianping Wang
Jul 1, 2020·Frontiers in Plant Science·Javier HernandezPatrick Hayes
Apr 30, 2019·Frontiers in Plant Science·Arantxa MonteagudoErnesto Igartua
Feb 14, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Javier Sánchez-Martín, Beat Keller
Jan 11, 2019·Frontiers in Plant Science·Tanja OsthushenrichEva Herzog
Feb 4, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Inger Åhman, Therése Bengtsson
Dec 21, 2018·Frontiers in Plant Science·Roshan Sharma PoudelRobert Brueggeman
Nov 18, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Sandra RollarFrank Ordon
Jan 8, 2021·Journal of Plant Physiology·Mahendar ThudiRajeev K Varshney

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Methods Mentioned

BETA
genotyping
RNAseq
chip
Assay
Genome Sequencing

Software Mentioned

BLAST
Illumina
Genome Analysis Toolkit ( GATK )
BLASTN
GenomeStudio Genotyping
JoinMap
Illumina GenomeStudio
Germinate
Map Manager QTXb20
Flapjack

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