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Evaluation of new IRAP markers of pear and their potential application in differentiating bud sports and other Rosaceae species

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Abstract

Inter-retrotransposon amplified polymorphisms (IRAP) are one of the main components of the retrotransposon-based molecular marker system, but currently have no applications in pear. In this context, new IRAP markers were developed and used to study the genetic polymorphism of pear cultivars and bud mutants. In total, eight polymorphic IRAP markers were selected in ten genotypes of pear with a wide variation in genetic backgrounds and for further genotypic identification of cultivars and bud sports. A total of 76 alleles with an average of 9.5 per locus were amplified and 96.05 % showed polymorphism. Through genetic structure analysis, 62 pear cultivars were divided into two groups, i.e., Oriental and Occidental pears, with a few samples showing a distinct admixed genetic background. When polymorphic IRAP markers were tested on a total of 33 bud sports and their corresponding parent cultivars, the genetic similarity coefficient ranged from 0.54 to 0.96. Each bud mutation was separated from its original variety, and 92.3 % of bud sports clustered perfectly with their original varieties. Furthermore, the transferability of pear IRAP to apples and other Rosaceae species was very high, ranging from 87.5 to 100 %. Our results demonstrate that IRAP markers are an excellent tool for the study of genetic relationships and comparative genomics analysis in pear and Rosaceae species.

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Acknowledgments

The work was financially supported by the Jiangsu Agriculture Science and Technology Innovation Fund (JASTIF) (CX (14) 2020), National Science Foundation of China (31372045), Ministry of Education Program for New Century Excellent Talents in University (NCET-13-0864).

Conflict of interests

The authors declare that they have no conflict of interests.

Data archiving statement

We followed standard Tree Genetics and Genomes policy. We archived the contigs in the FASTA format from the sequences which are available at our genome website http://peargenome.njau.edu.cn.

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    1. Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nan**g Agricultural University, Nan**g, Jiangsu, 210095, China

      Jiangmei Sun, Hao Yin, Leiting Li, Yue Song, Lian Fan, Shaoling Zhang & Jun Wu

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    1. Jiangmei Sun
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    2. Hao Yin
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    Correspondence to Jun Wu.

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    Communicated by D. Chagné

    Jiangmei Sun and Hao Yin contributed equally to this work.

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    Sun, J., Yin, H., Li, L. et al. Evaluation of new IRAP markers of pear and their potential application in differentiating bud sports and other Rosaceae species. Tree Genetics & Genomes 11, 25 (2015). https://doi.org/10.1007/s11295-015-0849-y

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