ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2015
Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Development of SNP and InDel markers by genome resequencing and transcriptome sequencing in radish (Raphanus sativus L.).BMC genomics · 2023Article
- Genome-wide identification and characterization of the bHLH gene family and analysis of their potential relevance to chlorophyll metabolism in Raphanus sativus L.BMC genomics · 2022Article
- An improved Raphanus sativus cv. WK10039 genome localizes centromeres, uncovers variation of DNA methylation and resolves arrangement of the ancestral Brassica genome blocks in radish chromosomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Construction of ultra-high-density genetic linkage map of a sorghum-sudangrass hybrid using whole genome resequencing.PloS one · 2022Article
- QTL mapping for Fusarium wilt resistance based on the whole-genome resequencing and their association with functional genes in Raphanus sativus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation.Genomics & informatics · 2021Article
- Global gene expression perturbations in rapeseed due to the introduction of alien radish chromosomes.Journal of genetics · 2021Article
- Construction of high-density genetic maps defined sex determination region of the Y chromosome in spinach.Molecular genetics and genomics : MGG · 2021Article
- Gibberellin Promotes Bolting and Flowering via the Floral IntegratorsPlants (Basel, Switzerland) · 2020Article
- Article
- An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.).Plant biotechnology journal · 2020Article
- Fine-mapping of a major QTL (Fwr1) for fusarium wilt resistance in radish.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Genetic Mapping of Prince Rupprecht's Larch (Genes · 2019Article
- Article
- The radish genome database (RadishGD): an integrated information resource for radish genomics.Database : the journal of biological databases and curation · 2019Article
- A re-sequencing-based ultra-dense genetic map reveals a gummy stem blight resistance-associated gene in Cucumis melo.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.).BMC genomics · 2017Article
- Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Identification of Flowering-Related Genes Responsible for Differences in Bolting Time between Two Radish Inbred Lines.Frontiers in plant science · 2016Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageThis manuscript provides a genetic map of Raphanus sativus that has been used as a reference genetic map for an ongoing genome sequencing project. The map was constructed based on genotyping by whole-genome resequencing of mapping parents and F 2 population. Raphanus sativus is an annual vegetable crop species of the Brassicaceae family and is one of the key plants in the seed industry, especially in East Asia. Assessment of the R. sativus genome provides fundamental resources for crop improvement as well as the study of crop genome structure and evolution. With the goal of anchoring genome sequence assemblies of R. sativus cv. WK10039 whose genome has been sequenced onto the chromosomes, we developed a reference genetic map based on genotyping of two parents (maternal WK10039 and paternal WK10024) and 93 individuals of the F2 mapping population by whole-genome resequencing. To develop high-confidence genetic markers, ~83 Gb of parental lines and ~591 Gb of mapping population data were generated as Illumina 100 bp paired-end reads. High stringent sequence analysis of the reads mapped to the 344 Mb of genome sequence scaffolds identified a total of 16,282 SNPs and 150 PCR-based markers. Using a subset of the markers, a high-density genetic map was constructed from the analysis of 2,637 markers spanning 1,538 cM with 1,000 unique framework loci. The genetic markers integrated 295 Mb of genome sequences to the cytogenetically defined chromosome arms. Comparative analysis of the chromosome-anchored sequences with Arabidopsis thaliana and Brassica rapa revealed that the R. sativus genome has evident triplicated sub-genome blocks and the structure of gene space is highly similar to that of B. rapa. The genetic map developed in this study will serve as fundamental genomic resources for the study of R. sativus.
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