ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2016
A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 1 of them a synthesis that pooled it.
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Who cites it
124 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Pooled it
- Review
- Mapping QTLs with main, epistatic, and QTL × environment effects for secondary seed dormancy using backcross recombinant inbred lines in Brassica napus L.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Segregating BCMolecular breeding : new strategies in plant improvement · 2026Article
- The Bra1K array: an efficient and versatile 1K liquid-phase SNP chip for genetics and breeding in Chinese cabbage.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Machine learning and multi-omic analysis reveal contrasting recombination landscape of A and C subgenomes of winter oilseed rape.The plant genome · 2026Article
- Hybridization between different Brassica allohexaploid lineages produces viable, fertile progeny but does not improve genome stability or fertility in F1 hybrids.Annals of botany · 2026Article
- Genetic diversity study and molecular marker development for economic traits in Korean pine based on RAD-Seq.Frontiers in plant science · 2026Article
- Harnessing genomic prediction in Brassica napus through a nested association mapping population.The plant genome · 2025Article
- Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Genome-wide association mapping reveals genetic loci underlying phenotypic variation in early root vigour improvement induced by osmopriming in Brassica napus L.BMC plant biology · 2025Article
- Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).BMC plant biology · 2025Article
- Genetic dissection of plant architecture reveals haplotypes controlling sink-related traits in oilseed rape under limited nitrogen fertilization.BMC plant biology · 2025Article
- Multifactor Analysis of a Genome-Wide Selection System inPlants (Basel, Switzerland) · 2025Article
- Cytological and genetic analyses of the seed number per silique locus BnSNSC09 in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- TEA5K: a high-resolution and liquid-phase multiple-SNP array for molecular breeding in tea plant.Journal of nanobiotechnology · 2025Article
- Advances in genomic tools for plant breeding: harnessing DNA molecular markers, genomic selection, and genome editing.Biological research · 2024Review
- Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres.The Plant cell · 2024Article
- An NGS approach for the identification of precise homoeologous recombination sites between A and C genomes inBreeding science · 2024Article
64 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors.
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No grant is acknowledged in the PubMed record.
Abstract
key messageThe Brassica napus Illumina array provides genome-wide markers linked to the available genome sequence, a significant tool for genetic analyses of the allotetraploid B. napus and its progenitor diploid genomes. A high-density single nucleotide polymorphism (SNP) Illumina Infinium array, containing 52,157 markers, was developed for the allotetraploid Brassica napus. A stringent selection process employing the short probe sequence for each SNP assay was used to limit the majority of the selected markers to those represented a minimum number of times across the highly replicated genome. As a result approximately 60 % of the SNP assays display genome-specificity, resolving as three clearly separated clusters (AA, AB, and BB) when tested with a diverse range of B. napus material. This genome specificity was supported by the analysis of the diploid ancestors of B. napus, whereby 26,504 and 29,720 markers were scorable in B. oleracea and B. rapa, respectively. Forty-four percent of the assayed loci on the array were genetically mapped in a single doubled-haploid B. napus population allowing alignment of their physical and genetic coordinates. Although strong conservation of the two positions was shown, at least 3 % of the loci were genetically mapped to a homoeologous position compared to their presumed physical position in the respective genome, underlying the importance of genetic corroboration of locus identity. In addition, the alignments identified multiple rearrangements between the diploid and tetraploid Brassica genomes. Although mostly attributed to genome assembly errors, some are likely evidence of rearrangements that occurred since the hybridisation of the progenitor genomes in the B. napus nucleus. Based on estimates for linkage disequilibrium decay, the array is a valuable tool for genetic fine mapping and genome-wide association studies in B. napus and its progenitor genomes.
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