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<p><i>Paphiopedilum</i>, comprising approximately 80 Southeast Asia distributed species, is commonly designated as Venus or lady's slipper orchids due to the slipper-shaped morphology of its labellum and synsepal. All <i>Paphiopedilum</i> species are endangered, and their conservation is therefore imperative. However, the lack of species-diagnostic markers restricts taxonomic discrimination and conservation efforts. To address this limitation, transcriptomes of <i>Paphiopedilum concolor</i> and <i>P. hirsutissimum</i> served as templates for variant detection, identifying 2,027,219 polymorphic loci (1,816,143 SNPs and 224,715 InDels). Fifty loci within <i>EcoR</i>I recognition regions were randomly selected to design cleaved amplified polymorphic sequence (CAPS) marker primer pairs. Following digestion with <i>EcoR</i>I and gel electrophoresis, 34 polymorphic single nucleotide polymorphism (SNP-CAPS) markers were developed based on the transcriptomes of <i>P. concolor</i> and <i>P. hirsutissimum</i>. These markers exhibited a polymorphism information content (<i>PIC</i>) ranging from 0.08 to 0.37. Among these, three markers were found to have the potential to be developed as species-diagnostic markers for <i>P. hirsutissimum</i>, with preliminary validation conducted using <i>P. hirsutissimum</i> and <i>P. henryanum</i> in China. With the distinct allele patterns of the remaining 31 markers, the tested individuals representing 38 species/grexes/hybrids could be discriminated, while 21 individuals of original species were accurately clustered into distinct groups based on their sections or subgenera. In summary, the developed SNPs will facilitate the conservation of <i>Paphiopedilum</i>.</p>

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Development of 34 SNP-CAPS markers for species identification and phylogenetic analysis in Paphiopedilum, an endangered orchid genus

  • 期刊论文

  • 发表日期：

    2025年12月10日

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  • Haiguang Gong,
  • Xiuping Chen,
  • Chao Hu,
  • Jianzhong Ni,
  • Zilong Liu,
  • Peishan Zou,
  • Shiou Yih Lee,
  • Manmei He,
  • Guofeng Liu

摘要

Paphiopedilum, comprising approximately 80 Southeast Asia distributed species, is commonly designated as Venus or lady's slipper orchids due to the slipper-shaped morphology of its labellum and synsepal. All Paphiopedilum species are endangered, and their conservation is therefore imperative. However, the lack of species-diagnostic markers restricts taxonomic discrimination and conservation efforts. To address this limitation, transcriptomes of Paphiopedilum concolor and P. hirsutissimum served as templates for variant detection, identifying 2,027,219 polymorphic loci (1,816,143 SNPs and 224,715 InDels). Fifty loci within EcoRI recognition regions were randomly selected to design cleaved amplified polymorphic sequence (CAPS) marker primer pairs. Following digestion with EcoRI and gel electrophoresis, 34 polymorphic single nucleotide polymorphism (SNP-CAPS) markers were developed based on the transcriptomes of P. concolor and P. hirsutissimum. These markers exhibited a polymorphism information content (PIC) ranging from 0.08 to 0.37. Among these, three markers were found to have the potential to be developed as species-diagnostic markers for P. hirsutissimum, with preliminary validation conducted using P. hirsutissimum and P. henryanum in China. With the distinct allele patterns of the remaining 31 markers, the tested individuals representing 38 species/grexes/hybrids could be discriminated, while 21 individuals of original species were accurately clustered into distinct groups based on their sections or subgenera. In summary, the developed SNPs will facilitate the conservation of Paphiopedilum.