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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1559-4) contains supplementary material, which is available to authorized users.
Highlights
Single nucleotide polymorphism (SNP) markers have a wide range of applications in crop genetics and genomics
Majority of polymorphic SNP loci exhibited heterozygous signals in B. napus Previously, the HJ-doubled haploid (DH) population and its parental lines were genotyped with simple sequence repeat (SSR) markers and the 6K SNP arrays for B. napus [29,30] and the call rate of all 5,306 SNP loci on the array for all 192 samples was >0.7 [30]
Other types of genotyping data were observed after clustering, including SNPs with cluster separation score (CSS)
Summary
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 interhomoeologue polymorphisms (mHemi-SNPs and Pseudo-simple SNPs) between closely related sub-genomes. Most orthologous gene pairs in B. rapa and B. oleracea remain as homoeologous pairs in B. napus An and Cn subgenomes (An ortholog gene in the An genome in most cases has a highly homologous copy of the sequence in the Cn genome) [2,5]
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