Open Access Highly Accessed Research article

Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus

Xun Chen12, Xuemin Li12, Bing Zhang3, Jinsong Xu12, Zhikun Wu12, Bo Wang12, Haitao Li12, Muhammad Younas12, Lei Huang12, Yingfeng Luo3, Jiangsheng Wu12, Songnian Hu3 and Kede Liu12*

Author Affiliations

1 National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

2 Key Laboratory of Rapeseed Genetic Improvement, The Ministry of Agriculture, Wuhan, China

3 Beijing Institute of Genomics, Chinese Academy of Science, Beijing, China

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BMC Genomics 2013, 14:346  doi:10.1186/1471-2164-14-346

Published: 24 May 2013



The 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.


To 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.


These 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.

Polyploid crops; Brassica napus; Pseudo-reference sequence; Single nucleotide polymorphism; Presence/absence variation