Molecular Genetics and Genomics

, Volume 290, Issue 1, pp 225–237 | Cite as

Prediction of retrotransposons and assessment of genetic variability based on developed retrotransposon-based insertion polymorphism (RBIP) markers in Pyrus L

  • Shuang Jiang
  • Yu Zong
  • Xiaoyan Yue
  • Joseph Postman
  • Yuanwen Teng
  • Danying Cai
Original Paper

Abstract

Interspecific hybridization has been considered the major mode of evolution in Pyrus (pear), and thus, the genetic relationships within this genus have not been well documented. Retrotransposons are ubiquitous components of plant genomes and 42.4 % of the pear genome was reported to be long terminal repeat (LTR) retrotransposons, implying that retrotransposons might be significant in the evolution of Pyrus. In this study, 1,836 putative full-length LTR retrotransposons were isolated and 196 retrotransposon-based insertion polymorphism (RBIP) primers were developed, of which 24 pairs to the Ppcr1 subfamily of copia retrotransposons were used to analyze genetic diversity among 110 Pyrus accessions from Eurasia. Our results showed that Ppcr1 replicated many times in the development of cultivated Asian pears. The genetic structure analysis and the unweighted pair group method with arithmetic mean (UPGMA) dendrogram indicated that all accessions could be divided into Oriental and Occidental groups. In Oriental pears, wild pea pears clustered separately into independent groups in accordance with their morphological classifications. Cultivars of P. ussuriensis Maxim, P. pyrifolia Nakai, and P. pyrifolia Chinese white pear were mingled together, which inferred that hybridization events occurred during the development of the cultivated Asian pears. In Occidental pears, two clades were obtained in the UPGMA dendrogram in accordance with their geographical distribution; one contained the European species and the other included species from North Africa and West Asia. New findings in this study will be important to further understand the phylogeny of Pyrus and origins of cultivated pears.

Keywords

Retrotransposon Pyrus RBIP marker Insertion polymorphism Genetic relationship 

Notes

Acknowledgments

This work was financed by a Grant from the National Natural Science Foundation of China (No. 31201592), a Specialized Research Fund for the Doctoral Program of Higher Education (20110101110091), and a Grant for Innovative Research Team of Zhejiang Province of China (2013TD05).

Supplementary material

438_2014_914_MOESM1_ESM.xlsx (20 kb)
Supplementary material 1 (XLSX 20 kb)
438_2014_914_MOESM2_ESM.xlsx (23 kb)
Supplementary material 2 (XLSX 23 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Shuang Jiang
    • 1
  • Yu Zong
    • 1
  • Xiaoyan Yue
    • 1
  • Joseph Postman
    • 2
  • Yuanwen Teng
    • 1
  • Danying Cai
    • 1
  1. 1.Department of Horticulture, The State Agricultural Ministry Key Laboratory of Horticultural Plant Growth, Development of Quality ImprovementZhejiang UniversityHangzhouChina
  2. 2.National Clonal Germplasm Repository, USDA-ARSCorvallisUSA

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