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Characterization of EST-SSR markers in Curcuma kwangsiensis S. K. Lee & C. F. Liang based on RNA sequencing and its application for phylogenetic relationship analysis and core collection construction

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Abstract

Curcuma kwangsiensis S. K. Lee & C. F. Liang, a traditional herb in southern China, accumulates substantial amounts of active components, curcuminoids and volatile oil. However, the limited hereditary information and SSR markers have hindered its breeding program and genetic analysis. Here, we examined the transcriptome of C. kwangsiensis using next-generation sequencing (NGS) technology. A dataset with 8.17 Gb of raw reads was generated and assembled into 77,976 unigenes. Moreover, 11,678 EST-SSR markers were screened from transcriptome data. Of the 800 synthesized primer pairs, 486 (60.8%) exhibited successful amplification and 115 (23.7%) were polymorphic. A set of 24 selected markers showed high cross-species transferabilities among 13 Curcuma species. In total, 277 alleles (6–19 alleles per locus) were discovered, and the polymorphic information content (PIC) ranged from 0.496 to 0.905. Based on the results of cluster and structure analyses, the 75 accessions were classified into four major groups with some admixtures. Finally, a core collection (22 accessions) was identified, exhibiting Na, Ne, I, and PIC values with retention rates of 87.7%, 107.8%, 102.5% and 102%, respectively. All these unigenes and EST-SSRs will be useful for germplasm resource evaluation and for diversifying the potential of product derivatives from Curcuma.

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Acknowledgements

The financial support is from Key-Area Research and Development Program of Guangdong Province (2020B020220007).

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Authors and Affiliations

  1. Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China

    Yuanjun Ye, Yechun Xu, Dongmei Li, Jianjun Tan & Jinmei Liu

  2. Key Laboratory of Urban Agriculture in South China, Ministry of Agriculture, Guangzhou, China

    Yuanjun Ye, Yechun Xu, Dongmei Li, Jianjun Tan & Jinmei Liu

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  1. Yuanjun Ye
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  2. Yechun Xu
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  3. Dongmei Li
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Correspondence to Jinmei Liu.

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Ye, Y., Xu, Y., Li, D. et al. Characterization of EST-SSR markers in Curcuma kwangsiensis S. K. Lee & C. F. Liang based on RNA sequencing and its application for phylogenetic relationship analysis and core collection construction. Genet Resour Crop Evol 68, 1503–1516 (2021). https://doi.org/10.1007/s10722-020-01079-z

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