Abstract
Insertions/deletions (INDELs), a type of abundant length polymorphisms in the plant genomes, combine the characteristics of both simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNP), and thus can be developed as desired molecular markers for genetic studies and crop breeding. There has been no large-scale characterization of INDELs variations in Brassica napus yet. In this study, we identified a total of 538,691 INDELs in size range of 1–10 bp by aligning whole-genome re-sequencing data of 23 B. napus inbred lines (ILs) to the B. napus genome sequence of ‘Darmor-bzh.’ Of these, 104,190 INDELs were uniquely mapped on the pseudochromosomes of the reference genome. A set of 595 unique INDELs of 2–5 bp in length was selected for experimental validation in the 23 ILs. Of these INDELs, 530 (89.01 %) produced a single PCR product and were single locus. A total of 523 (87.9 %) INDELs were found polymorphic among the 23 ILs. A genetic linkage map containing 108 single-locus INDELs and 89 anchor SSR markers was constructed using 188 recombinant ILs. The majority of INDELs markers on the linkage map showed consistency with the pseudochromosomes of the B. napus cultivar ‘Darmor-bzh.’ The INDELs variations and markers reported here will be valuable resources in future for genetic studies and molecular breeding in oilseed rape.
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Acknowledgments
This work was supported by the National Hi-Tech R&D Program (2013AA102602) and the National Natural Science Foundation of China (31071452).
Authors’ contribution statement
SM, XY and JC performed the experiments. JC developed the RILs. ZL and BW performed the bioinformatics analyses. KL, SM and ZL wrote the paper. KL conceived and supervised this study. The manuscript was read and approved by all authors.
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Sammina Mahmood and Zhaohong Li have contributed equally to this work.
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11032_2016_501_MOESM1_ESM.xlsx
Supplementary Table 1 Detail information of the 595 INDELs markers including their physical positions along the pseudochromosomes of B. rapa and B. oleracea, primers, predicted size of PCR products, primers and their annealing temperatures. (XLSX 97 kb)
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Mahmood, S., Li, Z., Yue, X. et al. Development of INDELs markers in oilseed rape (Brassica napus L.) using re-sequencing data. Mol Breeding 36, 79 (2016). https://doi.org/10.1007/s11032-016-0501-z
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DOI: https://doi.org/10.1007/s11032-016-0501-z