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Development of polymorphic SSR markers and their applicability in genetic diversity evaluation in Euptelea pleiosperma

XIAOJUN ZHOU*, XIAOYU LU, XUBO WANG
College of Life Science, Luoyang Normal University, Luoyang, 471934, China
* Corresponding Author: Xiaojun Zhou,

BIOCELL 2022, 46(11), 2489-2495. https://doi.org/10.32604/biocell.2022.020311

Received 16 November 2021; Accepted 13 March 2022; Issue published 07 July 2022

Abstract

Euptelea pleiosperma is a characteristic species of East Asian flora with both ornamental and scientific values. Based on the reduced-representation sequencing (RRS) technology of RAD-Seq, this study conducted high-throughput Illumina paired-end sequencing to find SSR marker information in the genome of E. pleiosperma, and to screen and verify polymorphism of SSR markers. We obtained 5.5G of high-quality data using RAD-Seq. The total number of contigs of the RAD tags was 299,376, with the maximum contig length of 2,062 bp and the average length of 445 bp. From these sequences, we identified 20,718 SSR loci, with a distribution density of one SSR per 6.45 kb (1/6.45 kb). Among all SSRs, dinucleotides (52.00%) were the most detected SSRs, followed by mononucleotides (21.63%). AG/CT was the dominant motif in the SSR loci, accounting for 34.8%. Primers were successfully designed for 14,593 loci, and 100 pairs of these primers were randomly selected for chemical synthesis and validated by SSR-PCR amplification in 20 individuals of E. pleiosperma. Seventy-nine primers were able to amplify the target bands. Cervus 3.0 software was used to analyze the selected 20 SSR loci with good polymorphism. For the 20 SSR markers, the number of alleles ranged from 4 to 9, and the observed heterozygosity and expected heterozygosity were from 0.35 to 0.75 and 0.541 to 0.875, respectively. The information content of polymorphic loci ranged from 0.463 to 0.848, with an average value of 0.638. Among them, there were 18 highly polymorphic loci, and 20 SSR loci did not deviate from the HardyWeinberg equilibrium. Furthermore, the 20 pairs of SSR primers were used to conduct PCoA analysis based on Nei’s genetic distance of 51 individuals from three populations. The results showed that these SSR markers could distinguish genetic differences based on different geographical locations.

Keywords

Cluster analysis, E. pleiosperma, RAD-Seq, Rare species, SSR markers

Cite This Article

ZHOU, X., LU, X., WANG, X. (2022). Development of polymorphic SSR markers and their applicability in genetic diversity evaluation in Euptelea pleiosperma. BIOCELL, 46(11), 2489–2495.



This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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