SSR markers development and genetic diversity assessment in Rubus chingii

JI yueling, JIANG xinyuan, LING mengting, CHEN bei, FU shunhua, ZHOU xiaohong

Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 0

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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 (Natural Sciences Edition） ›› 0 DOI: 10.12302/j.issn.1000-2006.202601024

SSR markers development and genetic diversity assessment in Rubus chingii

  • JI yueling1, JIANG xinyuan1, LING mengting1, CHEN bei1, FU shunhua1,2, ZHOU xiaohong1,2
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Abstract

【Objective】Rubus chingii Hu is a traditional medicinal and edible plant in China with significant economic value. This study focuses on the genetic differentiation characteristics within a local small population of R. chingii using 50 germplasm accessions collected from Fuyang, Zhejiang, aiming to provide references for germplasm utilization and molecular breeding.【Method】We used transcriptome datasets from the thornless cultivar 'Meici' and a common genotype to mine SSR loci and design primers via MISA software. Fifty R. chingii germplasm accessions collected from Fuyang, Zhejiang were genotyped to screen polymorphic SSR markers and to assess genetic diversity. 【Result】A total of 2,507 SSR loci were identified from the transcriptome data. Of the eight SSR primer pairs designed, seven showed high polymorphism (PIC≥0.50). Population structure analyses (Structure, UPGMA, and PCoA) consistently revealed two well-defined groups. AMOVA showed that 99.09% of genetic variation occurred within groups, while differentiation among groups was low (Fst=0.019) with high gene flow (Nm=17.954), indicating weak differentiation but extensive exchange. The observed heterozygosity (0.601) was slightly higher than the expected heterozygosity (0.584), and the mean Shannon's information index was 1.225, suggesting rich within-population genetic diversity.【Conclusion】The eight SSR markers developed in this study can effectively evaluate the genetic diversity of R. chingii. The local small population exhibits abundant genetic variation, providing support for elite individual selection, thornless cultivar breeding, and germplasm innovation.

Key words

Rubus chingii Hu / SSR markers / Genetic diversity / Small population

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JI yueling, JIANG xinyuan, LING mengting, CHEN bei, FU shunhua, ZHOU xiaohong. SSR markers development and genetic diversity assessment in Rubus chingii[J]. Journal of Nanjing Forestry University (Natural Sciences Edition）. 0 https://doi.org/10.12302/j.issn.1000-2006.202601024

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