ArticleBMC genomics2014
Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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70 citing papers in PubMed, 139 citations in OpenAlex.
- Larval antibiosis to cabbage stem flea beetle (Psylliodes chrysocephala) is absent within oilseed rape (Brassica napus).Pest management science · 2026Article
- Harnessing polyploidy for climate-resilient crops: Lessons from the evolutionary model, allotetraploid cotton.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- Machine learning and multi-omic analysis reveal contrasting recombination landscape of A and C subgenomes of winter oilseed rape.The plant genome · 2026Article
- Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressedFrontiers in plant science · 2026Article
- Pangenomic structural variant patterns reflect evolutionary diversification in Brassica napus.Genome biology · 2025Article
- Whole-genome sequencing of 1,060 Brettanomyces bruxellensis isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids.Nature communications · 2025Article
- Genetic Diversity and Population Structure of a Large USDA Sesame Collection.Plants (Basel, Switzerland) · 2024Article
- Genome-wide association studies of root system architecture traits in a broad collection ofFrontiers in plant science · 2024Article
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- Rapeseed Domestication Affects the Diversity of Rhizosphere Microbiota.Microorganisms · 2023Article
- Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits inInternational journal of molecular sciences · 2022Article
- Regional association and transcriptome analysis revealed candidate genes controlling plant height inMolecular breeding : new strategies in plant improvement · 2022Article
- The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome.The Plant cell · 2022Article
- Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (International journal of molecular sciences · 2022Article
- Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding.Nature genetics · 2022Article
- Linkage disequilibrium and population structure in a core collection of Brassica napus (L.).PloS one · 2022Article
- Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits inFrontiers in plant science · 2022Article
- Breeding Canola (Plants (Basel, Switzerland) · 2021Review
- Gradual evolution of allopolyploidy in Arabidopsis suecica.Nature ecology & evolution · 2021Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns of population structure and linkage disequilibrium (LD). In this study we used the Brassica 60kSNP Illumina consortium genotyping array to assess the influence of selection and breeding for important agronomic traits on LD and haplotype structure in a diverse panel of 203 Chinese semi-winter rapeseed (Brassica napus) breeding lines.
resultsPopulation structure and principal coordinate analysis, using a subset of the SNPs, revealed diversification into three subpopulations and one mixed population, reflecting targeted introgressions from external gene pools during breeding. Pairwise LD analysis within the A- and C-subgenomes of allopolyploid B. napus revealed that mean LD, at a threshold of r2=0.1, decayed on average around ten times more rapidly in the A-subgenome (0.25-0.30 Mb) than in the C-subgenome (2.00-2.50 Mb). A total of 3,097 conserved haplotype blocks were detected over a total length of 182.49 Mb (15.17% of the genome). The mean size of haplotype blocks was considerably longer in the C-subgenome (102.85 Kb) than in the A-subgenome (33.51 Kb), and extremely large conserved haplotype blocks were found on a number of C-genome chromosomes. Comparative sequence analysis revealed conserved blocks containing homoloeogous quantitative trait loci (QTL) for seed erucic acid and glucosinolate content, two key seed quality traits under strong agronomic selection. Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues.
conclusionsThe data we present in this paper provide evidence for strong selection of large chromosome regions associated with important rapeseed seed quality traits conferred by C-subgenome QTL. This implies that an increase in genetic diversity and recombination within the C-genome is particularly important for breeding. The resolution of genome-wide association studies is also expected to vary greatly across different genome regions.
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