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<p><i>Rhododendron</i> L. is one of the most popular flower around the world. Nevertheless, the species classification and evolution of <i>Rhododendron</i> based on morphological characteristics have a highly debated and limited the parent selection for breeding of new cultivars. In order to solve these problems, single nucleotide polymorphism (SNP) primers were developed for chloroplast genomes that exhibit high polymorphism and well&#xa0;universality in <i>Rhododendron</i> germplasm in this study. Eleven pairs of primers were used for selection, in which four pairs were from previously published literature, and seven were newly designed in this study based on the analysis of 19 released complete chloroplast genomes of <i>Rhododendron</i> species. A total of 45 <i>Rhododendron</i> germplasms were used for test, comprising 21 wild species for universality and polymorphism test, and 24 cultivars for further transferability test. The results showed that the <i>psbE-petL</i> and <i>rbcL</i> primers exhibited better specificity, higher polymorphism, and better transferability compared to the other nine primers. Among them, <i>psbE-petL</i> was newly developed in this study with a fragment length ranged from 682 to 689&#xa0;bp and a nucleotide diversity of 0.09902, and <i>rbcL</i> was from previous reports with a fragment length ranged from 536 to 539&#xa0;bp and a nucleotide diversity of 0.07849. Phylogenetic analysis and haplotype analysis based on the <i>psbE-petL</i> and <i>rbcL</i> concatenate sequences can effectively differentiate wild types of <i>Rhododendrons</i> across various subgenera while also distinguishing between cultivars of groups Azalea and <i>Rhododendron</i>. The development of SNP primers in this study provide references for future maternal identification and phylogenetic analysis among <i>Rhododendron</i> cultivars and species.</p>

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Development of universal polymorphic SNPs primers for chloroplast genome of Rhododendron plants

  • 期刊论文

  • 发表日期：

    2025年3月17日

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  • Zonbin Yang,
  • Huie Li,
  • Xiaozhe Tong,
  • Chuanjiang Tan

摘要

Rhododendron L. is one of the most popular flower around the world. Nevertheless, the species classification and evolution of Rhododendron based on morphological characteristics have a highly debated and limited the parent selection for breeding of new cultivars. In order to solve these problems, single nucleotide polymorphism (SNP) primers were developed for chloroplast genomes that exhibit high polymorphism and well universality in Rhododendron germplasm in this study. Eleven pairs of primers were used for selection, in which four pairs were from previously published literature, and seven were newly designed in this study based on the analysis of 19 released complete chloroplast genomes of Rhododendron species. A total of 45 Rhododendron germplasms were used for test, comprising 21 wild species for universality and polymorphism test, and 24 cultivars for further transferability test. The results showed that the psbE-petL and rbcL primers exhibited better specificity, higher polymorphism, and better transferability compared to the other nine primers. Among them, psbE-petL was newly developed in this study with a fragment length ranged from 682 to 689 bp and a nucleotide diversity of 0.09902, and rbcL was from previous reports with a fragment length ranged from 536 to 539 bp and a nucleotide diversity of 0.07849. Phylogenetic analysis and haplotype analysis based on the psbE-petL and rbcL concatenate sequences can effectively differentiate wild types of Rhododendrons across various subgenera while also distinguishing between cultivars of groups Azalea and Rhododendron. The development of SNP primers in this study provide references for future maternal identification and phylogenetic analysis among Rhododendron cultivars and species.