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Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji

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Abstract

Retrotransposon-based molecular markers are a powerful tool for mapping and diversity studies. The scarcity of retrotransposon long terminal repeat (LTR) sequences limits the application of retrotransposon-based molecular marker systems. Here, we isolated two novel complete Ty1-copia retrotransposons (CTcrm1 and CTcrm2) in apple using a genome walking strategy. The CTcrm retrotransposons are nearly 5 kb long, and they have all the features of Ty1-copia retrotransposons. The differences in gene organization and nucleotide sequence length between the CTcrm retrotransposons and other reported complete retrotransposons in apple showed that CTcrm1 and CTcrm2 are the first two distinct complete Ty1-copia retrotransposons in the apple genome. To investigate the potential utility of the two retrotransposons as molecular markers, primers complementary to the CTcrm LTRs were designed to develop sequence-specific amplification polymorphism markers for discriminating bud sports of Fuji apple. Multiple polymorphisms corresponding to CTcrm1 and CTcrm2 were detected and could easily be used to discriminate bud sports from their Fuji progenitor, as well as from each other.

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Acknowledgments

This work was supported by National Natural Science Foundation of China (No. 30500348) and Science Foundation of Department of Education from Liaoning Province (No. 2008T177).

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Authors and Affiliations

  1. Team of Biotechnology and Genetic Improvement of Fruit Trees, Shenyang Agricultural University, Shenyang, 110161, People’s Republic of China

    Guiling Zhao, Hongyan Dai & Zhihong Zhang

  2. College of Horticulture, Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning, 110161, People’s Republic of China

    Hongyan Dai, Linlin Chang, Yue Ma, Haiyue Sun, Ping He & Zhihong Zhang

  3. College of Forestry, Shenyang Agricultural University, Dongling Road 120, Shenyang, Liaoning, 110161, People’s Republic of China

    Guiling Zhao

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  1. Guiling Zhao
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  2. Hongyan Dai
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  3. Linlin Chang
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  5. Haiyue Sun
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Correspondence to Zhihong Zhang.

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Communicated by A. Abbott

Guiling Zhao and Hongyan Dai contributed equally to this work.

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Supplemental Fig. 1

S-SAP spectrograms obtained with the primer combination LTRP1 and MseI(ggt) in selective amplification. The horizontal scale indicates fragment size (in base pairs), and the vertical scale indicates relative fluorescence intensity (in RFU). The number in the pane specifies the fragment size (in base pairs) of the corresponding S-SAP peak. Spectrograms of each sample from ZGL-01 to ZGL-20 are as follows: FJ, NFN2, NFN3, NFN6, NFN7, AF, AF1, YF, IL1, L1, MHF1, HMS, SF, ES, MS, K, IF10, G, CH, 2001. (PDF 407 kb)

Supplemental Fig. 2

S-SAP spectrograms obtained with the primer combination LTRP2 and PstI(aat) in selective amplification. The horizontal scale indicates fragment size (in base pairs), and the vertical scale indicates relative fluorescence intensity (in RFU). The number in the pane specifies the fragment size (in base pairs) of the corresponding S-SAP peak. Spectrograms of each sample from ZGL-01 to ZGL-20 are as follows: FJ, NFN2, NFN3, NFN6, NFN7, AF, AF1, YF, IL1, L1, MHF1, HMS, SF, ES, MS, K, IF10, G, CH, 2001. (PDF 371 kb)

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Zhao, G., Dai, H., Chang, L. et al. Isolation of two novel complete Ty1-copia retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of Malus domestica cv. Fuji. Tree Genetics & Genomes 6, 149–159 (2010). https://doi.org/10.1007/s11295-009-0236-7

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