Abstract
Key message
We developed and identified a new set of polymorphic EST-SSR markers in Sorbus pohuashanensis (Hance) Hedl. and generated an optimal sampling strategy.
Abstract
Sorbus pohuashanensis (Hance) Hedl. is indigenous to northern China and prized for its graceful appearance and seasonal variations in foliage color. However, only a few molecular biology studies have been conducted on this species. Therefore, its development and increased utilization are limited. The objective of the present study was to develop expressed sequence tag-simple sequence repeat (EST-SSR) markers based on the transcriptome data of this species. A total of 167 primer pairs were designed and 24 were randomly selected from the 55 initially screened for validation. Their polymorphism was assessed using samples of the Mount Kunyu in Shandong Province (SDKYS) population. Fifteen EST-SSR markers were identified as polymorphic, with a mean number of alleles (Na) and a polymorphism information content (PIC) of 8.2 and 0.6907, respectively. Thirty EST-SSRs (including another 15 EST-SSRs being previously developed) derived from S. pohuashanensis had high transferability (90%) to another 14 Sorbus species, and there were nine EST-SSRs applicable to Sorbus species tested. These Sorbus species were divided into two main clusters by an unweighted pair-group method with the arithmetic mean (UPGMA) clustering tree based on the nine EST-SSRs and was validated by principal coordinate analysis (PCoA). The sampling strategy showed that 25 randomly selected individuals from a population of S. pohuashanensis could represent 95% of its genetic diversity level. In all, these findings would provide a powerful theoretical basis for future studies on the genetic diversity and germplasm resources of S. pohuashanensis and its related species.
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Acknowledgements
This work was supported by the National Natural Fund Project (No. 31770369) and Beijing Municipal Education Commission General Project (No. KM201810020014). The authors thank the National Forest Genetic Resources Platform (NFGRP) for providing the S. pohuashanensis resources and Editage English Editing company (https://app.editage.cn) for providing language assistance during the preparation of this manuscript.
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Table S1: The repeat motif types and the primer sequences of the 167 EST-SSRs for Sorbus pohuashanensis. Table S2: Transferability of the 30 EST-SSR markers developed from Sorbus pohuashanensisis to other Sorbus species. Table S3: Polymorphism analysis of 30 EST-SSRs in Sorbus amabilis. Table S4: Nei’s Original Measures of Genetic Identity and Genetic distance among 15 Sorbus species. Table S5: Polymorphism analysis of the 30 EST-SSR markers from Sorbus pohuashanensis in HBBS population. Table S6: The mean values and percentage from the 14 groups of subsamples for 30 loci in Sorbus pohuashanensis from HBBS population. Table S7: The gene frequency of each locus in Sorbus pohuashanensis from the HBBS population. Table S8: The mean values and percentage from the 14 groups of subsamples without null allele. Table S9: The mean values and percentage from the 14 groups of subsamples without the loci significantly deviating from Hardy–Weinberg equilibrium. (RAR 133 kb)
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Wu, Y., He, R., Lu, Y. et al. Development and evaluation of EST-SSR markers in Sorbus pohuashanensis (Hance) Hedl. and their application to other Sorbus species. Trees 34, 455–467 (2020). https://doi.org/10.1007/s00468-019-01928-0
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DOI: https://doi.org/10.1007/s00468-019-01928-0