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Genome-wide genetic diversity and IBD analysis reveals historic dissemination routes of pear in China

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Abstract

Pear (Pyrus) is an important temperate fruit, which originates in the southwestern region of China and has more than 3000 year’s cultivation history. However, the historic routes of pear dissemination in China have not been fully elucidated. In this study, a total of 2,412,930 single nucleotide polymorphisms (SNPs) at a density of 4.74 SNP/kb were identified by resequencing. The SNP-based phylogenetic analysis revealed that 102 pear samples from 23 provinces in China were divided into two major clades and eight geographic groups, and these divisions were supported by results of a population structure analysis and principal component analysis (PCA). Combined with the results of population diversity and identity-by-descent (IBD) analysis, it was revealed that the dissemination direction of pear was from southwest to southeast and from south to north. In the southern region, the dispersal pattern of pear spreading from west to east was generally in line with the course of the Yangtze River and Pearl River. The southern pear spread by multiple routes to its north neighboring areas, and regions in the middle and lower reaches of the Yellow River played important roles in the further dissemination of pear in the northern region of China. Moreover, we identified comparative higher genetic diversity of Ussurian pear than other populations, which might be due to low degree of domestication and closely resembled the high diversity of its wild counterpart. Our study provides new information to further our understanding of pear evolution in China, while laying a foundation of data for population genetic research, germplasm protection, and utilization for pear breeding in the future.

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Data availability

The datasets generated and analyzed during the current study are available from the corresponding author upon request. Raw genome resequencing reads have been deposited into the NCBI sequence read archive (SRA) under BioProject accession PRJNA782471.

Code availability

The software application during the current study is downloaded from its official website, and custom codes are available from the corresponding author upon request.

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Acknowledgements

This project was supported by the Bioinformatics Center of Nanjing Agricultural University.

Funding

This work was funded by the Earmarked Fund for Jiangsu Agricultural Industry Technology System (JATS [2020]401]), the National Science Foundation of China (31820103012, 31725024, 31801835, 31901983), and China Agriculture Research System of MOF and MARA.

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Author notes

  1. Xuening Chen and Mingyue Zhang contributed equally to this work.

  2. Xuening Chen and Mingyue Zhang are co-first authors.

Authors and Affiliations

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

    Xuening Chen, Manyi Sun, Yueyuan Liu, Shengnan Li, Bobo Song, Mengyan Li, Shaoling Zhang, Runze Wang, Jiaming Li, Kejiao Zhao & Jun Wu

  2. State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018, Shandong, China

    Mingyue Zhang

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  1. Xuening Chen
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Contributions

JW designed this project. XNC and MYZ drafted the manuscript. XNC collected the public dataset and performed bioinformatics analysis. MYZ and MYS contributed to results analysis. BBS contributed to data analysis. SNL worked with data collection. YYL and MYL reviewed the manuscript. SLZ provided help to the platform. RZW, JML, and KJZ provided the suggestion to do this study. All authors read and approved the final manuscript.

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Correspondence to Jun Wu.

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Chen, X., Zhang, M., Sun, M. et al. Genome-wide genetic diversity and IBD analysis reveals historic dissemination routes of pear in China. Tree Genetics & Genomes 18, 1 (2022). https://doi.org/10.1007/s11295-021-01530-x

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