ArticleBMC genomics2015
A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 16 citations in OpenAlex.
- Review
- Discovery of Genomic Regions and Candidate Genes Controlling Root Development Using a Recombinant Inbred Line Population in Rapeseed (International journal of molecular sciences · 2022Article
- Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed (Frontiers in plant science · 2022Article
- QTL Mapping and Diurnal Transcriptome Analysis Identify Candidate Genes RegulatingInternational journal of molecular sciences · 2021Article
- Genetic dissection of thousand-seed weight and fine mapping of cqSW.A03-2 via linkage and association analysis in rapeseed (Brassica napus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Identification of QTLs Containing Resistance Genes for Sclerotinia Stem Rot inFrontiers in plant science · 2020Article
- QTL mapping and genetic effect of chromosome segment substitution lines with excellent fiber quality from Gossypium hirsutum × Gossypium barbadense.Molecular genetics and genomics : MGG · 2019Article
- Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.).Scientific reports · 2019Article
- The initial deficiency of protein processing and flavonoids biosynthesis were the main mechanisms for the male sterility induced by SX-1 in Brassica napus.BMC genomics · 2018Article
- Diversity and Genome Analysis of Australian and Global OilseedFrontiers in plant science · 2018Article
- Novel and major QTL for branch angle detected by using DH population from an exotic introgression in rapeseed (Brassica napus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Genetic dissection of plant architecture and yield-related traits in Brassica napus.Scientific reports · 2016Article
- Co-linearity and divergence of the A subgenome of Brassica juncea compared with other Brassica species carrying different A subgenomes.BMC genomics · 2016Article
- Transcriptome Analysis of Stem and Globally Comparison with Other Tissues inFrontiers in plant science · 2016Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSingle nucleotide polymorphism (SNP) markers have a wide range of applications in crop genetics and genomics. Due to their polyploidy nature, many important crops, such as wheat, cotton and rapeseed contain a large amount of repeat and homoeologous sequences in their genomes, which imposes a huge challenge in high-throughput genotyping with sequencing and/or array technologies. Allotetraploid Brassica napus (AACC, 2n = 4x = 38) comprises of two highly homoeologous sub-genomes derived from its progenitor species B. rapa (AA, 2n = 2x = 20) and B. oleracea (CC, 2n = 2x = 18), and is an ideal species to exploit methods for reducing the interference of extensive inter-homoeologue polymorphisms (mHemi-SNPs and Pseudo-simple SNPs) between closely related sub-genomes.
resultsBased on a recent B. napus 6K SNP array, we developed a bi-filtering procedure to identify unauthentic lines in a DH population, and mHemi-SNPs and Pseudo-simple SNPs in an array data matrix. The procedure utilized both monomorphic and polymorphic SNPs in the DH population and could effectively distinguish the mHemi-SNPs and Pseudo-simple SNPs that resulted from superposition of the signals from multiple SNPs. Compared with conventional procedure for array data processing, the bi-filtering method could minimize the pseudo linkage relationship caused by the mHemi-SNPs and Pseudo-simple SNPs, thus improving the quality of SNP genetic map. Furthermore, the improved genetic map could increase the accuracies of mapping of QTLs as demonstrated by the ability to eliminate non-real QTLs in the mapping population.
conclusionsThe bi-filtering analysis of the SNP array data represents a novel approach to effectively assigning the multi-loci SNP genotypes in polyploid B. napus and may find wide applications to SNP analyses in polyploid crops.
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