The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

in Journal of the American Society for Horticultural Science

Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In Pyrus, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from Pyrus species. A total of 49,147 SSR loci were identified in Pyrus, and their genotypes were evaluated by whole-genome resequencing data of 30 Pyrus accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all Pyrus accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of Pyrus species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in Pyrus.

Contributor Notes

This work was financed by a grant from Shanghai Science and Technology Committee Rising-Star Program (19QB1403500) rewarded to JS, a grant for Discipline Construction in Shanghai Academy of Agricultural Sciences (2018-31701886) rewarded to JS, and a specialized research fund for Major Science and Technique of Zhejiang Province of China (no. 2016C02052-4) rewarded to TU.

Shuang Jiang and Haishan An performed the experiments and wrote the manuscript. Xiaoqing Wang, Chunhui Shi and Fangjie Xu helped to analyze the data and revise the manuscript. Jun Luo and Yuanwen Teng were involved in designing the research and revised the manuscript. All authors read and approved the manuscript.

The chromosome data of ‘Dangshansuli’ were downloaded from the Center of Pear Engineering Technology Research of Nanjing Agricultural University, China ( The whole-genome resequencing data of the 30 Pyrus accessions were downloaded from BIG Data Center and National Center for Biotechnology Information (Table 1). The remaining data supporting our findings are contained within the article and supplementary files.

These authors contributed equally to this work.

Corresponding author. E-mail:

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    The workflow diagram in the identification of genotypes of simple sequence repeat (SSR) loci revealed by whole-genome resequencing data. The sequence of all SSR loci and their left and right flanking region of 120 bp were reserved as a database (SSRDB).

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    The type and distribution of microsatellites in the genome of Pyrus. (A) Type of repeat motifs. (B) Microsatellite length distribution. (C) Number of microsatellites. (D) Percent of different repeat motifs. P2, dinucleotide repeats; P3, trinucleotide repeats; P456, tetranucleotide repeats, pentanucleotide repeats, and hexanucleotide repeats; SSRs, simple sequence repeats.

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    The characteristics of the microsatellites in the 30 Pyrus accessions. (A) Percentage of simple sequence repeat (SSR) loci detected with fragments. (B) Number of alleles in 23,209 SSR loci. (C) Value of observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) in 23,209 SSR loci.

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    The percentage of simple sequence repeat (SSR) loci with more than two fragments in 30 Pyrus accessions.

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    Genetic relationship among the 30 accessions of Pyrus revealed by dendrogram based on the neighbor-joining method and STRUCTURE (Evanno et al., 2005) under K = 3 (right) and K = 2 (left).

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