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Development of a core set of single-locus SSR markers for allotetraploid rapeseed (Brassica napus L.)

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Abstract

Brassica napus (AACC) is a recent allotetraploid species evolved through hybridization between two diploids, B. rapa (AA) and B. oleracea (CC). Due to extensive genome duplication and homoeology within and between the A and C genomes of B. napus, most SSR markers display multiple fragments or loci, which limit their application in genetics and breeding studies of this economically important crop. In this study, we collected 3,890 SSR markers from previous studies and also developed 5,968 SSR markers from genomic sequences of B. rapa, B. oleracea and B. napus. Of these, 2,701 markers that produced single amplicons were putative single-locus markers in the B. napus genome. Finally, a set of 230 high-quality single-locus SSR markers were established and assigned to the 19 linkage groups of B. napus using a segregating population with 154 DH individuals. A subset of 78 selected single-locus SSR markers was proved to be highly stable and could successfully discriminate each of the 45 inbred lines and hybrids. In addition, most of the 230 SSR markers showed the single-locus nature in at least one of the Brassica species of the U’s triangle besides B. napus. These results indicated that this set of single-locus SSR markers has a wide range of coverage with excellent stability and would be useful for gene tagging, sequence scaffold assignment, comparative mapping, diversity analysis, variety identification and association mapping in Brassica species.

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Acknowledgments

The research was supported by the National Natural Science Foundation of China (No. 31071452), the Doctoral Fund of Ministry of Education of China (No. 20100146110019) and the Huazhong Agricultural University Scientific & Technological Self-innovation Foundation (No. 2011SC04). The authors are grateful to Drs. Chaozhi Ma, Jun Zou and Cheng Cui for providing cultivar information and DNA samples.

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Authors and Affiliations

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

    Haitao Li, Muhammad Younas, Xiaofeng Wang, Xuemin Li, Lin Chen, Bo Zhao, Xun Chen, Jinsong Xu, Fan Hou, Baohua Hong, Gang Liu, Hongyang Zhao, Xueli Wu, Hongzhi Du, Jiangsheng Wu & Kede Liu

  2. Key Laboratory of Rapeseed Genetic Improvement, Ministry of Agriculture, Wuhan, 430070, China

    Haitao Li, Muhammad Younas, Xiaofeng Wang, Xuemin Li, Lin Chen, Bo Zhao, Xun Chen, Jinsong Xu, Fan Hou, Baohua Hong, Gang Liu, Hongyang Zhao, Xueli Wu, Hongzhi Du, Jiangsheng Wu & Kede Liu

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  1. Haitao Li
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  2. Muhammad Younas
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  3. Xiaofeng Wang
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  4. Xuemin Li
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  5. Lin Chen
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  7. Xun Chen
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  11. Gang Liu
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  12. Hongyang Zhao
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  14. Hongzhi Du
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  15. Jiangsheng Wu
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  16. Kede Liu
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Corresponding author

Correspondence to Kede Liu.

Additional information

Communicated by C. Quiros.

Electronic supplementary material

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122_2012_2027_MOESM1_ESM.xls

Supplemental Table S1 Sequence information of the 230 validated single-locus SSR markers assigned to linkage groups of B. napus

Supplemental Table S2 List of detail information of 90 accessions of rapeseed inbred lines and hybrids

122_2012_2027_MOESM3_ESM.xls

Supplemental Table S3 Summary of the allele distribution for 78 single-locus SSR markers in the inbred lines and hybrids population

122_2012_2027_MOESM4_ESM.xls

Supplemental Table S4 Amplification of the 230 single-locus SSR markers in other five species of the U’s triangle except for B. napus

122_2012_2027_MOESM5_ESM.ppt

Supplemental Fig. 1 Neighbor-joining (N-J) tree constructed using 45 inbreeds and 45 hybrids. The inbred lines and hybrids were prefixed by letter G and K, respectively

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Li, H., Younas, M., Wang, X. et al. Development of a core set of single-locus SSR markers for allotetraploid rapeseed (Brassica napus L.). Theor Appl Genet 126, 937–947 (2013). https://doi.org/10.1007/s00122-012-2027-z

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