ArticleBMC genomics2013
Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 51 citations in OpenAlex.
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- Parallel ddRAD and Genome Skimming Analyses Reveal a Radiative and Reticulate Evolutionary History of the Temperate Bamboos.Systematic biology · 2021Article
- Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus.BMC plant biology · 2020Article
- High-throughput phenotyping accelerates the dissection of the dynamic genetic architecture of plant growth and yield improvement in rapeseed.Plant biotechnology journal · 2020Article
- Genome-wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut.Plant biotechnology journal · 2020Article
- Fine mapping and candidate gene analysis of a seed glucosinolate content QTL, qGSL-C2, in rapeseed (Brassica napus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data.Frontiers in plant science · 2020Article
- ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea.BMC plant biology · 2019Article
- Frog Virus 3 Genomes Reveal Prevalent Recombination between Ranavirus Lineages and Their Origins in Canada.Journal of virology · 2019Article
- Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.).Scientific reports · 2019Article
- Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species.Plant biotechnology journal · 2019Article
- A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (Brassica napus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.).BMC plant biology · 2018Article
- Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics.Scientific reports · 2018Article
- A Major and Stable QTL for Bacterial Wilt Resistance on Chromosome B02 Identified Using a High-Density SNP-Based Genetic Linkage Map in Cultivated Peanut Yuanza 9102 Derived Population.Frontiers in genetics · 2018Article
- Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola.Frontiers in plant science · 2018Article
- Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA.PloS one · 2018Article
- Genetic Properties of a Nested Association Mapping Population Constructed With Semi-Winter and Spring Oilseed Rapes.Frontiers in plant science · 2018Article
- Genetic mapping of anthocyanin accumulation-related genes in pepper fruits using a combination of SLAF-seq and BSA.PloS one · 2018Article
- High-density ddRAD linkage and yield-related QTL mapping delimits a chromosomal region responsible for oil content in rapeseed (Breeding science · 2017Article
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe presence of homoeologous sequences and absence of a reference genome sequence make discovery and genotyping of single nucleotide polymorphisms (SNPs) more challenging in polyploid crops.
resultsTo address this challenge, we constructed reduced representation libraries (RRLs) for two Brassica napus inbred lines and their 91 doubled haploid (DH) progenies using a modified ddRADseq technique. A bioinformatics pipeline termed RFAPtools was developed to discover and genotype SNPs and presence/absence variations (PAVs). Using this pipeline, a pseudo-reference sequence (PRF) containing 180,991 sequence tags was constructed. By aligning sequence reads to the pseudo-reference sequence, allelic SNPs as well as PAVs were identified and genotyped with RFAPtools. Two parallel linkage maps, one SNP bin map containing 8,780 SNP loci and one PAV linkage map containing 12,423 dominant loci, were constructed. By aligning marker sequences to B. rapa sequence scaffolds, whose genome is available, we assigned 44 unassembled sequence scaffolds comprising 8.15 Mb onto the B. rapa chromosomes, and also identified 14 instances of misassembly and eight instances of mis-ordering sequence scaffolds.
conclusionsThese results indicate that the modified ddRADseq approach is a cost-effective and simple method to genotype tens of thousands SNPs and PAV markers in a polyploidy plant species. The results also demonstrated that RFAPtools developed in this study are powerful to mine allelic SNPs from homoeologous sequences in polyploids, therefore they are generally applicable in either diploid or polyploid species with or without a reference genome sequence.
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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.