Genetic diversity analysis of water lily based on transcriptome-derived EST-SSR markers

doi:10.14088/j.cnki.issn0439-8114.2026.05.021

Abstract

Abstract: The development of expressed sequence tag-simple sequence repeat (EST-SSR) markers based on transcriptome data and subsequent genetic diversity analysis provided reliable tools for germplasm identification, genetic diversity evaluation, and marker-assisted breeding in water lily (Nymphaea L.). In this study, 362 982 unigenes were assembled from the floral organ transcriptome data of Nymphaea ‘King of Siam'. From these, 29 pairs of polymorphic EST-SSR primers were developed, and 9 inter-simple sequence repeat (ISSR) primers were utilized to analyze the genetic diversity of 77 water lily accessions. The results indicated that the EST-SSR markers exhibited a high level of polymorphism, with an average number of alleles (Na) of 4.793 1 and an average expected heterozygosity (He) of 0.648 4. Cluster analysis demonstrated that the 77 water lily accessions could be clearly classified into two major groups: hardy and tropical, revealing significant genetic differentiation between them. The analytical results derived from the ISSR markers were highly consistent with those from the EST-SSRs; however, the EST-SSR markers demonstrated superior advantages in terms of polymorphism detection efficiency and resolution. Furthermore, BLAST alignment revealed that 20 SSR loci were significantly associated with functional genes involved in flowering regulation, stress response, and heavy metal accumulation. In conclusion, the 77 water lily accessions exhibited rich genetic diversity. Both EST-SSR and ISSR markers effectively identified the genetic differentiation between the hardy and tropical groups, highlighting the technical superiority of EST-SSR markers as a robust tool for genetic diversity research in water lilies.

Key words: water lily(Nymphaea L.), EST-SSR marker, ISSR marker, genetic diversity, functional gene

CLC Number:

HU Yi-hang, SHAN Song-wang, CHEN Long-qing, QIAO Zheng-lin. Genetic diversity analysis of water lily based on transcriptome-derived EST-SSR markers[J]. HUBEI AGRICULTURAL SCIENCES, 2026, 65(5): 130-141.

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