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Development of retrotransposon-based molecular markers and their application in genetic mapping in chokecherry (Prunus virginiana L.)

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Abstract

Retrotransposons are the largest group of transposable elements (TEs) that are ubiquitous and well dispersed in plant genomes. Transposition/insertion of TEs on chromosomes often generates unique repeat junctions (RJs) between TEs and their flanking sequences. Long terminal repeats (LTR) are well conserved and abundant in plant genomes, making LTR retrotransposons valuable for development of TE junction-based markers. In this study, LTR retrotransposons and their RJs were detected from chokecherry genome sequences generated by Roche 454 sequencing. A total of 1246 LTR retrotransposons were identified, and 338 polymerase chain reaction primer pairs were designed. Of those, 336 were used to amplify DNA from chokecherry and other rosaceous species. An average of 283 of 336 (84.2 %) LTR primer pairs effectively amplified DNA from chokecherries. One hundred and seventeen chokecherry LTR primers also produced amplification in other Prunus (99) or rosaceous species (19). A total of 59 of 78 polymorphic LTR markers were qualified for linkage map construction according to the segregation distortion Chi-square (χ 2) test. Forty-eight LTR markers were successfully located on a previously constructed chokecherry map. The majority of the LTR markers were mapped on LG XI of the chokecherry map. Our results suggest that LTR marker development using random genome sequences is rapid and cost-efficient. Confirmed applicability of LTR markers in map construction and genetic mapping will facilitate genetic research in chokecherry and other rosaceous species.

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Acknowledgements

We thank Drs. D. Huang and H. Wang for valuable suggestions and comments when we were conducting the research. This research was supported in part by McIntire-Stennis Project ND06212, USDA-CSREES-2005-35300-15457, and the Talent Foundation of Jilin Academy of Agricultural Sciences and Department of Foreign Experts Affairs Project (SH132200038), Jilin Province, P. R. China.

Author’s contribution

YL and WD conceived and designed the study. YL and RL conducted the experiments and contributed equally to the work. WD supervised the research and guided data interpretation. YL, RL, and WD wrote the paper. All authors read and approved the final manuscript.

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Authors and Affiliations

  1. Department of Plant Sciences, North Dakota State University, Fargo, ND, USA

    Yinghai Liang, Ryan R. Lenz & Wenhao Dai

  2. Institute of Pomology, Jilin Academy of Agricultural Sciences, Jilin, China

    Yinghai Liang

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  1. Yinghai Liang
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  2. Ryan R. Lenz
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  3. Wenhao Dai
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Correspondence to Wenhao Dai.

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Liang, Y., Lenz, R.R. & Dai, W. Development of retrotransposon-based molecular markers and their application in genetic mapping in chokecherry (Prunus virginiana L.). Mol Breeding 36, 109 (2016). https://doi.org/10.1007/s11032-016-0535-2

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