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Construction of a high-density SNP genetic map in flue-cured tobacco based on SLAF-seq

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Abstract

Tobacco (Nicotiana tabacum L., 2n = 48) is an important agronomic crop and model plant. Flue-cured tobacco is the most important type and accounts for approximately 80 % of tobacco production worldwide. The low genetic diversity of flue-cured tobacco impedes the construction of a high-density genetic linkage map using simple sequence repeat (SSR) markers and warrants the exploitation of single nucleotide polymorphic (SNP) markers from genomic regions. In this article, initially using specific locus-amplified fragment sequencing, we discovered 10,891 SNPs that were subsequently used as molecular markers for genetic map construction. Combined with SSR markers, a final high-density genetic map was generated containing 4215 SNPs and 194 SSRs distributed on 24 linkage groups (LGs). The genetic map was 2662.43 cM in length, with an average distance of 0.60 cM between adjacent markers. Furthermore, by mapping the SNP markers to the ancestral genomes of Nicotiana tomentosiformis and Nicotiana sylvestris, a large number of genome rearrangements were identified as occurring after the polyploidization event. Finally, using this novel integrated map and mapping population, two major quantitative trait loci (QTLs) were identified for flue-curing and mapped to the LG6 of tobacco. This is the first report of SNP markers and a SNP-based linkage map being developed in tobacco. The high-density genetic map and QTLs related to tobacco curing will support gene/QTL fine mapping, genome sequence assembly and molecular breeding in tobacco.

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Acknowledgments

This work was supported by China National Public Industrial (Agriculture) Specific Project (no. 201203091).

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    Authors and Affiliations

    1. Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China

      Daping Gong, Xiuhong Xu, Chuanyi Wang, Min Ren, Chunkai Wang & Mingli Chen

    2. Biomarker Technologies Corporation, Beijing, 101300, China

      Long Huang

    3. Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture, Qingdao, 266101, China

      Xiuhong Xu & Chuanyi Wang

    4. Graduate School of the Chinese Academy of Agricultural Sciences, Beijing, 100081, China

      Chunkai Wang

    Authors
    1. Daping Gong
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    2. Long Huang
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    3. Xiuhong Xu
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    4. Chuanyi Wang
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    5. Min Ren
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    6. Chunkai Wang
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    7. Mingli Chen
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    Correspondence to Xiuhong Xu.

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    Daping Gong and Long Huang contributed equally to this article.

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    Gong, D., Huang, L., Xu, X. et al. Construction of a high-density SNP genetic map in flue-cured tobacco based on SLAF-seq. Mol Breeding 36, 100 (2016). https://doi.org/10.1007/s11032-016-0514-7

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