ArticleBMC genomics2017
Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Chrysanthemum genomics reveals the origin and domestication of modern cultivated chrysanthemums.Nature plants · 2026Article
- Augmenting plant-pollinator interactions to promote biodiversity and global food security.Frontiers in plant science · 2026Review
- Defining autopolyploidy: Cytology, genetics, and taxonomy.American journal of botany · 2024Review
- Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit.Plant biotechnology journal · 2023Article
- Diversity analyses in two ornamental and large-genomeFrontiers in plant science · 2023Article
- PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.BMC bioinformatics · 2022Article
- Genomic prediction with allele dosage information in highly polyploid species.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- De novo whole-genome assembly of Chrysanthemum makinoi, a key wild chrysanthemum.G3 (Bethesda, Md.) · 2022Article
- A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome.Horticulture research · 2022Article
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
- A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum.Communications biology · 2021Article
- DNA marker for resistance toBreeding science · 2021Article
- Linkage Map Development by EST-SSR Markers and QTL Analysis for Inflorescence and Leaf Traits in Chrysanthemum (Plants (Basel, Switzerland) · 2020Article
- High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Horticulture research · 2020Article
- Genome-wide association study overcomes the genome complexity in autohexaploid chrysanthemum and tags SNP markers onto the flower color genes.Scientific reports · 2019Article
- De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Identification of favorable SNP alleles and candidate genes responsible for inflorescence-related traits via GWAS in chrysanthemum.Plant molecular biology · 2019Article
- Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums.Horticulture research · 2019Article
- Current achievements and future prospects in the genetic breeding of chrysanthemum: a review.Horticulture research · 2019Review
- polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCultivated 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).
resultsWith 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.
conclusionsThe 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.