The genetic diversity analysis and molecular ID establishment of Chaenomeles speciosa based on SSR markers

LI Hui, HOU Lina, WANG Tianqi, BI Ningning, LI Shengbo, LIU Zhonghua

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2025, Vol. 49 ›› Issue (1) : 59-68.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2025, Vol. 49 ›› Issue (1) : 59-68. DOI: 10.12302/j.issn.1000-2006.202301027

The genetic diversity analysis and molecular ID establishment of Chaenomeles speciosa based on SSR markers

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Abstract

【Objective】Chaenomeles speciosa has high ornamental, edible, and medicinal values. China is the origin and distribution center of C. speciosa. The genetic diversity of Chaenomeles speciosa germplasm resources was studied, and the molecular identity card of varieties was constructed to solve the problems of lack of unified classification criteria among varieties, homonymous and synoonymous, and unclear origin and evolution among varieties in recent years.【Method】A total of 168 C. speciosa varieties and SSR (simple sequence repeats) markers were combined with capillary electrophoresis to analyze the genetic diversity and the degree of genetic differentiation. The observed number of alleles (Na), Shannon’s information index (I), and the polymorphism information content (PIC) were employed to screen primer combinations that can distinguish the entire germplasm and construct DNA molecular IDs based on string codes. 【Result】The results showed that 26 pairs of primers amplified 304 alleles in 168 C. speciosa varieties, with an average of 11.577 per locus. The average expected heterozygosity (He), I and PIC were determined as 0.748, 1.731 and 0.607, respectively. Based on the cluster analysis, the population could be divided into two groups, and further into six groups. Moreover, based on population structure analysis, the tested materials was divided into two subgroups. Four pairs of core primers were selected from 26 pairs of primers to construct barcode and two-dimensional code identification cards of C. speciosa varieties. 【Conclusion】The selected amplification loci have a high degree of variation and strong discrimination, and are thus suitable for applications in genetic diversity analysis, core primer screening, and fingerprint construction. The results can provide a reference for the variety identification, genetic resource management, and the construction of a germplasm resource database of C. speciosa.

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Chaenomeles speciosa / genetic diversity / SSR / molecular ID

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LI Hui , HOU Lina , WANG Tianqi , et al . The genetic diversity analysis and molecular ID establishment of Chaenomeles speciosa based on SSR markers[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2025, 49(1): 59-68 https://doi.org/10.12302/j.issn.1000-2006.202301027

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