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Construction of a High-Density Simple Sequence Repeat Consensus Genetic Map for Pear (Pyrus spp.)

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Abstract

As an important fruit crop that is widely grown commercially in temperate regions of the world, pear (Pyrus) is a target for pursuing efficient breeding strategies. Construction of a reliable and dense genetic linkage map is critical for undertaking marker-assisted breeding. In this study, a population of 56 F1 seedlings of ‘Bayuehong’ × ‘Dangshansuli’ was used to construct a high-density simple sequence repeat (SSR)-based genetic linkage map. A total of 1,756 SSR markers, including 1,341 newly designed SSRs based on whole-genome sequencing of an Asiatic pear along with 415 previously reported SSRs, were first evaluated for polymorphism. Based on 894 SSRs demonstrating polymorphism, a consensus genetic map consisting of 734 loci distributed along all 17 linkage groups (LG) was constructed, with a total length of 1,661.4 cM and with an average marker interval of 2.26 cM. Comparisons among different maps of pear and apple were then made based on positions of previously mapped SSR markers on the consensus map. As a result, homologous linkage groups LG3 and LG11, LG5 and LG10, LG9 and LG17, LG13 and LG16, LG8 and LG15 have been identified. This high-density SSR map along with a set of SSR markers covering the whole genome of pear will greatly facilitate integration of independent maps, aid in pursuing comparative genome studies, and in evaluation of different germplasm in future genetic and breeding studies.

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Acknowledgments

This work was supported by the earmarked fund for China Agriculture Research System (CARS-29), National Natural Science Foundation of China (31230063 and 31171928), the Fundamental Research Funds for the Central Universities (KYZ201146), and the National Science and Technology Ministry (2013AA102606-02).

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Author notes

  1. M. Awais Khan

    Present address: International Potato Center (CIP), Apartado 1558, Lima, 12, Peru

Authors and Affiliations

  1. College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Hui Chen, Yue Song, Lei-Ting Li, Jun Wu & Shao-Ling Zhang

  2. Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, 61801, USA

    M. Awais Khan & Schuyler S. Korban

  3. Zhengzhou Fruit Research institute, CAAS, Zhengzhou, Henan, 450009, China

    Xiu-Gen Li

  4. Department of Biology, University of Massachusetts-Boston, Boston, MA, 02125, USA

    Schuyler S. Korban

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  1. Hui Chen
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  2. Yue Song
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  3. Lei-Ting Li
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Correspondence to Jun Wu or Shao-Ling Zhang.

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Hui Chen, Yue Song and Lei-Ting Li contributed equally to this work

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Figure S1

Alignment of our consensus map with other published pear maps using common SSRs. LG1 to17 are from the pear consensus map constructed in this study (Fig. 1), in the center; Ba1 to 17 are from the map of European pear ‘Bartlett’ (Ba) map (Yamamoto et al. 2007), on the left; Ho1 to 17 are from Asian pear ‘Hosui’ (Ho) map linkage groups (Terakami et al. 2009), on the right. The linkage groups show common markers among the three maps, and the interval distances between two adjacent markers. Markers in red are those located in different groups in our consensus map compared with those of other pear maps. (DOC 76 kb)

Figure S2

Comparison of the pear consensus map with ‘Fiesta’ (F) and ‘Co-op 17’ × ‘Co-op 16’ (Co) apple maps with common SSR markers. Apple ‘Fiesta’ (F) (Silfverberg-Dilworth et al. 2006) and ‘Co-op 17’ × ‘Co-op 16’ (Co) maps (Han et al. 2011) are shown on the left and right respectively, the pear consensus map (LG) (Fig. 1) is shown in the center. The linkage groups show common markers among the three maps and the interval distances between two adjacent markers. Markers in red are those that were located in different groups in our consensus map compared with those of other pear maps. (DOC 107 kb)

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Chen, H., Song, Y., Li, LT. et al. Construction of a High-Density Simple Sequence Repeat Consensus Genetic Map for Pear (Pyrus spp.). Plant Mol Biol Rep 33, 316–325 (2015). https://doi.org/10.1007/s11105-014-0745-x

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