ArticleBMC genomics2012
High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 136 citations in OpenAlex.
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- Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers.PloS one · 2024Article
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- Genome-wide association analysis identified molecular markers and candidate genes for flower traits in Chinese orchid (Horticulture research · 2023Article
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- Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus.G3 (Bethesda, Md.) · 2023Article
- Genetic diversity and structure of the 4Frontiers in plant science · 2023Article
- QTL associated with Gummy Stem Blight (GSB) resistance in watermelon.BMC genomics · 2022Article
- Genome-wide identification and development of InDel markers in tobacco (Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Linkage disequilibrium and population structure in a core collection of Brassica napus (L.).PloS one · 2022Article
- Omics: The way forward to enhance abiotic stress tolerance inGM crops & food · 2021Review
- High accuracy of pooled DNA genotyping by 2b-RAD sequencing in the Pacific white shrimp, Litopenaeus vannamei.PloS one · 2020Article
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- Genotyping-by-sequencing based QTL mapping for rice grain yield under reproductive stage drought stress tolerance.Scientific reports · 2019Article
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- Development of High-Density SNP Markers and Their Application in Evaluating Genetic Diversity and Population Structure inFrontiers in plant science · 2019Article
- QTL delineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population.Molecular genetics and genomics : MGG · 2018Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD) fragments for polymorphism detection and genotyping.
resultsMore than 113,000 RAD clusters with more than 20,000 single nucleotide polymorphisms (SNPs) and 125 insertions/deletions were detected and characterized. About one third of the RAD clusters and polymorphisms mapped to the Brassica rapa reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the B. rapa chromosomes, which suggests that there might be an equal distribution over the Brassica oleracea chromosomes, too. The representation of Gene Ontology (GO) terms for unigenes with RAD clusters and polymorphisms revealed no signature of selection with respect to the distribution of polymorphisms within genes belonging to a specific GO category.
conclusionsConsidering the decreasing costs for next-generation sequencing, the results of our study suggest that RAD sequencing is not only a simple and cost-effective method for high-density polymorphism detection but also an alternative to SNP genotyping from transcriptome sequencing or SNP arrays, even for species with complex genomes such as B. napus.
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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.