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
文献类型： 外文期刊
作者： Ye, Yuanjun 1 ; Xu, Yechun 1 ; Li, Dongmei 1 ; Tan, Jianjun 1 ; Liu, Jinmei 1 ;
作者机构： 1.Guangdong Acad Agr Sci, Environm Hort Res Inst, Guangdong Prov Key Lab Ornamental Plant Germplasm, Guangzhou, Peoples R China
2.Minist Agr, Key Lab Urban Agr South China, Guangzhou, Peoples R China
关键词： Curcuma species; Transcriptome sequencing; Marker-assisted selection (MAS); Transferability and polymorphism analysis; Genetic diversity; Core collection
期刊名称：GENETIC RESOURCES AND CROP EVOLUTION （ 影响因子：1.524； 五年影响因子：1.713 ）
ISSN： 0925-9864
年卷期： 2021 年 68 卷 4 期
页码：
收录情况： SCI
摘要： 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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