Research Article
Large-scale advances in SSR markers with high-throughput sequencing in Euphorbia fischeriana Steud

https://doi.org/10.1016/j.ejbt.2020.11.004Get rights and content
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Abstract

Background

Euphorbia fischeriana Steud is a very important medicinal herb and has significant medical value for healing cancer, edema and tuberculosis in China. The lack of molecular markers for Euphorbia fischeriana Steud is a dominant barrier to genetic research. For the purpose of developing many simple sequence repeat (SSR) molecular markers, we completed transcriptome analysis with the Illumina HiSeq 2000 platform.

Results

Approximately 9.1 million clean reads were acquired and then assembled into approximately 186.3 thousand nonredundant unigenes, 53,146 of which were SSR-containing unigenes. A total of 76,193 SSR loci were identified. Of these SSR loci, 28,491 were detected at the terminal position of ESTs, which made it difficult to design SSR primers for these SSR-containing sequences, and the residual SSRs were thus used to design primer pairs. Analyzing the results of these markers revealed that the mononucleotide motif A/T (44,067, 57.83% of all SSRs) was the most abundant, followed by the dinucleotide type AG/CT (9430, 12.38%). Using 100 randomly selected primer pairs, 77 primers were successfully amplified in Euphorbia fischeriana Steud, and 79 were successfully amplified in three other related species. The markers developed displayed relatively high quality and cross-species transferability.

Conclusions

The large number of EST-SSRs exploited successfully in Euphorbia fischeriana Steud for the first time could provide genetic information for research on linkage maps, variety identification, genetic diversity analysis, and molecular marker-assisted breeding.

How to cite: Li H, Ma Y, Pei F, et al. Large-scale advances in SSR markers with high-throughput sequencing in Euphorbia fischeriana Steud. Electron J Biotechnol 2021;49. https://doi.org/10.1016/j.ejbt.2020.11.004

Keywords

Cross-species
EST-SSRs
Euphorbia fischeriana Steud
Genetic diversity analysis
High-throughput sequencing
Linkage maps
Medicinal herb
Molecular marker-assisted breeding
Molecular markers
SSR

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