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Article

KASP Markers for Identifying Roselle (Hibiscus sabdariffa L.) Key Varieties Based on Genetic Polymorphisms Revealed by ddRAD-Seq

by
Shih-Jie Huang
1,†,
Jheng-Yang Ou
2,3,†,
Yao-Cheng Lin
2,3,†,
Jing-Wen Chen
4,
Kai-Yi Chen
5,
Yu-Lin Wu
1,2,3,
Chun-Hao Hu
1,3,
Ju-Yin Lee
1,
Jia-Wei Wu
1 and
Fu-Chiun Hsu
1,*
1
Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106319, Taiwan
2
Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
3
Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115201, Taiwan
4
Taitung District Agricultural Research and Extension Station, Ministry of Agriculture, Taitung 950244, Taiwan
5
Department of Agronomy, National Taiwan University, Taipei 106319, Taiwan
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Horticulturae 2024, 10(12), 1325; https://doi.org/10.3390/horticulturae10121325
Submission received: 30 October 2024 / Revised: 29 November 2024 / Accepted: 9 December 2024 / Published: 11 December 2024
(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))
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Abstract

Variety characterization is crucial in the seed trade, particularly for protecting variety rights. However, the identification of roselle (Hibiscus sabdariffa L.) varieties, known for their beneficial effects on human health and high processing potential, has traditionally relied on morphological traits due to limited genetic information. To investigate genetic polymorphisms of roselle germplasms and to develop breeder-accessible genotyping tools, this study first phenotyped a roselle collection from diverse geographical origins for the selection of core varieties, and then utilized double-digest restriction-associated DNA sequencing (ddRAD-seq) to identify 53,746 single nucleotide polymorphisms (SNPs) across 17 core varieties. Cluster analysis of the SNP data effectively grouped varieties with similar genetic backgrounds. From this genetic information, we selected nine SNPs as a toolkit to simplify core variety discrimination. These SNPs were then converted into breeder-friendly kompetitive allele-specific PCR (KASP) markers, facilitating the classification of an additional 54 roselle accessions. In conclusion, this research contributes novel insights into the genetic relationships among roselle varieties, and establishes a robust framework utilizing ddRAD-seq and KASP markers for improved genetic resource identification and application in breeding programs.
Keywords: variety identification; genotyping; double-digest restriction-associated DNA sequencing (ddRAD-seq); kompetitive allele-specific PCR (KASP); genetic diversity; SNP genotyping variety identification; genotyping; double-digest restriction-associated DNA sequencing (ddRAD-seq); kompetitive allele-specific PCR (KASP); genetic diversity; SNP genotyping
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MDPI and ACS Style

Huang, S.-J.; Ou, J.-Y.; Lin, Y.-C.; Chen, J.-W.; Chen, K.-Y.; Wu, Y.-L.; Hu, C.-H.; Lee, J.-Y.; Wu, J.-W.; Hsu, F.-C. KASP Markers for Identifying Roselle (Hibiscus sabdariffa L.) Key Varieties Based on Genetic Polymorphisms Revealed by ddRAD-Seq. Horticulturae 2024, 10, 1325. https://doi.org/10.3390/horticulturae10121325

AMA Style

Huang S-J, Ou J-Y, Lin Y-C, Chen J-W, Chen K-Y, Wu Y-L, Hu C-H, Lee J-Y, Wu J-W, Hsu F-C. KASP Markers for Identifying Roselle (Hibiscus sabdariffa L.) Key Varieties Based on Genetic Polymorphisms Revealed by ddRAD-Seq. Horticulturae. 2024; 10(12):1325. https://doi.org/10.3390/horticulturae10121325

Chicago/Turabian Style

Huang, Shih-Jie, Jheng-Yang Ou, Yao-Cheng Lin, Jing-Wen Chen, Kai-Yi Chen, Yu-Lin Wu, Chun-Hao Hu, Ju-Yin Lee, Jia-Wei Wu, and Fu-Chiun Hsu. 2024. "KASP Markers for Identifying Roselle (Hibiscus sabdariffa L.) Key Varieties Based on Genetic Polymorphisms Revealed by ddRAD-Seq" Horticulturae 10, no. 12: 1325. https://doi.org/10.3390/horticulturae10121325

APA Style

Huang, S.-J., Ou, J.-Y., Lin, Y.-C., Chen, J.-W., Chen, K.-Y., Wu, Y.-L., Hu, C.-H., Lee, J.-Y., Wu, J.-W., & Hsu, F.-C. (2024). KASP Markers for Identifying Roselle (Hibiscus sabdariffa L.) Key Varieties Based on Genetic Polymorphisms Revealed by ddRAD-Seq. Horticulturae, 10(12), 1325. https://doi.org/10.3390/horticulturae10121325

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