Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 525245
Title Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array
Author(s) Geest, Geert van; Voorrips, Roeland E.; Esselink, Danny; Post, Aike; Visser, Richard G.F.; Arens, Paul
Source BMC Genomics 18 (2017). - ISSN 1471-2164
DOI https://doi.org/10.1186/s12864-017-4003-0
Department(s) Horticulture & Product Physiology
PBR Quantitative aspects of Plant Breeding
PE&RC
PBR Biodiversity and genetic variation
Plant Breeding
EPS
PBR Ornamentals, tissue culture and gene transfer
Publication type Refereed Article in a scientific journal
Publication year 2017
Keyword(s) Allelic expression bias - Disomic - Hexaploid - Polyploid - Polysomic - RNA-seq - SNP array - SNP retrieval
Abstract Background: Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5). Results: With use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage. Conclusions: The large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.
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