OpenSSL SSL_connect: Connection reset by peer in connection to v2.sherpa.ac.uk:443 PuSH - Publication Server of Helmholtz Zentrum München: A powerful tool for genome analysis in maize: Development and evaluation of the high density 600k SNP genotyping array.

PuSH - Publication Server of Helmholtz Zentrum München

Unterseer, S.* ; Bauer, E.* ; Haberer, G. ; Seidel, M. ; Knaak, C.* ; Ouzunova, M.* ; Meitinger, T. ; Strom, T.M. ; Fries, R.* ; Pausch, H.* ; Bertani, C.* ; Davassi, A.* ; Mayer, K.F.X. ; Schön, C.C.*

A powerful tool for genome analysis in maize: Development and evaluation of the high density 600k SNP genotyping array.

BMC Genomics 15:823 (2014)
Publ. Version/Full Text DOI
Open Access Gold
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Background High density genotyping data are indispensable for genomic analyses of complex traits in animal and crop species. Maize is one of the most important crop plants worldwide, however a high density SNP genotyping array for analysis of its large and highly dynamic genome was not available so far. Results We developed a high density maize SNP array composed of 616,201 variants (SNPs and small indels). Initially, 57 M variants were discovered by sequencing 30 representative temperate maize lines and then stringently filtered for sequence quality scores and predicted conversion performance on the array resulting in the selection of 1.2 M polymorphic variants assayed on two screening arrays. To identify high-confidence variants, 285 DNA samples from a broad genetic diversity panel of worldwide maize lines including the samples used for sequencing, important founder lines for European maize breeding, hybrids, and proprietary samples with European, US, semi-tropical, and tropical origin were used for experimental validation. We selected 616 k variants according to their performance during validation, support of genotype calls through sequencing data, and physical distribution for further analysis and for the design of the commercially available Affymetrix(R) Axiom(R) Maize Genotyping Array. This array is composed of 609,442 SNPs and 6,759 indels. Among these are 116,224 variants in coding regions and 45,655 SNPs of the Illumina(R) MaizeSNP50 BeadChip for study comparison. In a subset of 45,974 variants, apart from the target SNP additional off-target variants are detected, which show only a minor bias towards intermediate allele frequencies. We performed principal coordinate and admixture analyses to determine the ability of the array to detect and resolve population structure and investigated the extent of LD within a worldwide validation panel. Conclusions The high density Affymetrix(R) Axiom(R) Maize Genotyping Array is optimized for European and American temperate maize and was developed based on a diverse sample panel by applying stringent quality filter criteria to ensure its suitability for a broad range of applications. With 600 k variants it is the largest currently publically available genotyping array in crop species.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords High Density Genotyping Array ; Maize ; Snp; Single Nucleotide Polymorphisms; Plant Variety Protection; Zea-mays L.; Wide Association; Inbred Lines; Linkage Disequilibrium; Unrelated Individuals; Ascertainment Bias; Genetic Diversity; Sequencing Data
ISSN (print) / ISBN 1471-2164
e-ISSN 1471-2164
Journal BMC Genomics
Quellenangaben Volume: 15, Issue: 1, Pages: , Article Number: 823 Supplement: ,
Publisher BioMed Central
Publishing Place London
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)
Institute of Human Genetics (IHG)