Genome-Wide Identification of SNP and SSR Markers from Cymbidium goeringii and C. faberi for Their Potential Application in Breeding

Cheng, Mengya; Liu, Yingqi; Jin, Chentai; Jiang, Xiao; Chen, Xiuming; Wang, Fei; Duan, Yanru; Zhuo, Xiaokang; Peng, Donghui

doi:10.3390/horticulturae11060622

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Genome-Wide Identification of SNP and SSR Markers from Cymbidium goeringii and C. faberi for Their Potential Application in Breeding

by

Mengya Cheng

^1,†,

Yingqi Liu

^1,2,†,

Chentai Jin

^1,2,

Xiao Jiang

¹,

Xiuming Chen

¹,

Fei Wang

¹,

Yanru Duan

¹,

Xiaokang Zhuo

^1,2,* and

Donghui Peng

^1,*

¹

Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, The Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, National Long Term Scientific Research Base for Fujian Orchid Conservation, Fujian Agriculture and Forestry University, Fuzhou 350002, China

²

Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops at College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Horticulturae 2025, 11(6), 622; https://doi.org/10.3390/horticulturae11060622

Submission received: 2 May 2025 / Revised: 27 May 2025 / Accepted: 28 May 2025 / Published: 1 June 2025

(This article belongs to the Special Issue Orchids: Advances in Propagation, Cultivation and Breeding)

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Abstract

Chinese Cymbidium are prized for their ornamental beauty, ecological significance, and economic value. However, genomic resources crucial for breeding studies within this genus remain scarce, which has hindered the identification of key genes controlling economically important traits and posed challenges for conservation efforts. We performed a comprehensive identification of whole-genome simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers using the restriction-site associated DNA sequencing (RADseq) on C. goeringii and C. faberi. A total of 49,640 SSR loci were identified across both species, with an average density of 12.7 SSRs/Mb. Among these, 17,637 SSRs were common to both C. goeringii and C. faber, while 17,676 and 14,329 SSRs were uniquely identified in C. goeringii and C. faberi, respectively. Additionally, we identified 405,416 SNPs and 26,870 InDels, with average densities of 105.2/Mb and 6.5/Mb. Furthermore, we validated two SSRs (located at Chr01:78857480-78860461 and Chr01:93382182-93384869) and developed an efficient method for identifying hybrids among the progeny resulting from crosses between C. goeringii and C. faberi. We also validated two SNP markers that showed a close association with the petal and lip length using Sanger sequencing. Our findings revealed that the Chr01_99657375 SNP achieved 73% predictive accuracy for identifying long-petal/lip phenotypes. The results are expected to greatly benefit marker-assisted breeding efforts in Cymbidium orchids and lay a solid foundation for the molecular breeding process of improving flower shape traits in orchid plants.

Keywords: Cymbidium orchids; molecular marker; RAD-seq; flower shape traits

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MDPI and ACS Style

Cheng, M.; Liu, Y.; Jin, C.; Jiang, X.; Chen, X.; Wang, F.; Duan, Y.; Zhuo, X.; Peng, D. Genome-Wide Identification of SNP and SSR Markers from Cymbidium goeringii and C. faberi for Their Potential Application in Breeding. Horticulturae 2025, 11, 622. https://doi.org/10.3390/horticulturae11060622

AMA Style

Cheng M, Liu Y, Jin C, Jiang X, Chen X, Wang F, Duan Y, Zhuo X, Peng D. Genome-Wide Identification of SNP and SSR Markers from Cymbidium goeringii and C. faberi for Their Potential Application in Breeding. Horticulturae. 2025; 11(6):622. https://doi.org/10.3390/horticulturae11060622

Chicago/Turabian Style

Cheng, Mengya, Yingqi Liu, Chentai Jin, Xiao Jiang, Xiuming Chen, Fei Wang, Yanru Duan, Xiaokang Zhuo, and Donghui Peng. 2025. "Genome-Wide Identification of SNP and SSR Markers from Cymbidium goeringii and C. faberi for Their Potential Application in Breeding" Horticulturae 11, no. 6: 622. https://doi.org/10.3390/horticulturae11060622

APA Style

Cheng, M., Liu, Y., Jin, C., Jiang, X., Chen, X., Wang, F., Duan, Y., Zhuo, X., & Peng, D. (2025). Genome-Wide Identification of SNP and SSR Markers from Cymbidium goeringii and C. faberi for Their Potential Application in Breeding. Horticulturae, 11(6), 622. https://doi.org/10.3390/horticulturae11060622

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Genome-Wide Identification of SNP and SSR Markers from Cymbidium goeringii and C. faberi for Their Potential Application in Breeding

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