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The southwestern origin and eastward dispersal of pear (Pyrus pyrifolia) in East Asia revealed by comprehensive genetic structure analysis with SSR markers

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Abstract

Pyrus pyrifolia is considered one of the most important cultivated Pyrus species. Hundreds of landraces and bred cultivars have been developed through the natural and artificial hybridizations necessary due to self-incompatibility. In this study, the genetic diversity of 478 Pyrus accessions, including Chinese landraces, bred cultivars, and wild samples, as well as introduced pear cultivars from Japan and Korea, was investigated with a set of 17 simple sequence repeat (SSR) markers distributed across all 17 linkage groups of the pear genome. A total of 121 alleles were detected, including 4 rare alleles with a frequency lower than 5%. Diversity statistics indicated a high level of genetic variation as quantified by the average values of the observed heterozygosity, the expected heterozygosity, and Wright’s fixation index, at 0.76, 0.78, and 0.02, respectively. Population structure and discriminant analysis of principal component analysis implied extensive genetic communication between sand pears in China and revealed four contiguous geographical clusters with overlapping geographical regions. The diversity of the four clusters and approximate Bayesian computation (ABC) indicated that sand pear spread from west to east along the Pearl River and Yangtze River valleys. High diversity and polyphyletic genetic components of cultivars in southwestern China further support southwestern China as the probable center of divergence for Pyrus species. A core collection of 80 out of 470 cultivars was selected, accounting for about 17% of accessions, and capturing 91% of all alleles, including all rare alleles. Our research provides a comprehensive understanding of sand pear germplasm in East Asia and constructs a preliminary core collection, which will be useful for association genetics studies, germplasm conservation, and breeding programs.

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Funding

This work was financially supported by the National Science Foundation of China (31672111), the Earmarked Fund for China Agriculture Research System (CARS-29), the Science Foundation for Distinguished Young Scientists in Jiangsu Province (BK20150025), and The Six Talent Peaks Project in Jiangsu Province (2014-NY-025).

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Author notes

  1. Lei Xue and Qingwen Liu contributed equally to this work.

Authors and Affiliations

  1. Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Lei Xue, Qingwen Liu, Yue Song, Bing Bai, Mingyue Zhang, Runze Wang, Mengfan Qin, Xiaolong Li & Jun Wu

  2. Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, 430064, Hubei, China

    Hongju Hu & Jing Fan

Authors
  1. Lei Xue
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  2. Qingwen Liu
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  3. Hongju Hu
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  4. Yue Song
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  5. Jing Fan
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  6. Bing Bai
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  10. Xiaolong Li
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  11. Jun Wu
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Corresponding author

Correspondence to Jun Wu.

Additional information

Communicated by D. Chagné

Data archiving statement

The authors declare that all the work described in this manuscript followed standard Tree Genetics and Genomes policy. All primers used were according to the article of Song et al. (2014) and Liu et al. 2015

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Fig. S1

Distribution of pairwise relatedness coefficients among the P. pyrifolia individuals. rxy values among cultivars are normally distributed around a mean of zero, with a low variance between pairs of individuals. (PDF 121 kb)

Fig. S2

Modeling of number of genepools in P. pyrifolia using STRUCTURE. Ln P(D) and delta K, calculated according to Evanno et al. (2005), plotted against the number of modeled genepools (K). (JPG 170 kb)

Fig. S3

Inference of the number of clusters. Bayesian information criterion (BIC) is provided for different numbers of clusters (from 1 to 50). The chosen number of clusters (8) is crossed in black. (PDF 310 kb)

Fig. S4

Scatterplots of DAPC. Groups are shown by different colors and inertia ellipses; dots represent individual strains. (PDF 368 kb)

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Xue, L., Liu, Q., Hu, H. et al. The southwestern origin and eastward dispersal of pear (Pyrus pyrifolia) in East Asia revealed by comprehensive genetic structure analysis with SSR markers. Tree Genetics & Genomes 14, 48 (2018). https://doi.org/10.1007/s11295-018-1255-z

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