title: 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.
abstract: BACKGROUND
  Single 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.
  
  
  RESULTS
  Based 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. gqcai@mail.hzau.edu.cn.|Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, 430070, China. gqcai@mail.hzau.edu.cn.
authors.forename: Guangqin
authors.initials: G
authors.lastname: Cai
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. yqy@mail.hzau.edu.cn.|Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, 430070, China. yqy@mail.hzau.edu.cn.
authors.forename: Qingyong
authors.initials: Q
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. yibin@mail.hzau.edu.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Yi
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. fanchuchuan@mail.hzau.edu.cn.
authors.forename: Chuchuan
authors.initials: C
authors.lastname: Fan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. zhchy@mail.hzau.edu.cn.
authors.forename: Chunyu
authors.initials: C
authors.lastname: Zhang
authors.affiliation: School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia. dave.edwards@uq.edu.au.
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.affiliation: School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia. j.batley@uq.edu.au.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. ymzhou@mail.hzau.edu.cn.|Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, Huazhong Agricultural University, Wuhan, 430070, China. ymzhou@mail.hzau.edu.cn.
authors.forename: Yongming
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D029688:Brassica napus / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant; D005838:Genotype; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA / Q000379:methods