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<p>Black pepper (<i>Piper nigrum</i> L.) is a globally significant spice, with Phu-Quoc Island in Vietnam being renowned for its premium genotypes. This study evaluated the genetic diversity and relationships among 21 black pepper samples from Phu-Quoc and other regions using Start Codon Targeted (SCoT) markers and DNA barcoding. SCoT markers revealed high genetic diversity, amplifying 132 amplicons, of which 129 were polymorphic (97.73% polymorphism). The analysis clustered the samples into six groups, where the Phu-Quoc and Ha-Tien genotypes exhibited high genetic similarity. In contrast, DNA barcoding employed six regions—<i>rbc</i>L, ITS1-ITS4, <i>mat</i>K, <i>psb</i>A-<i>trn</i>H, <i>rpo</i>C, and <i>atp</i>F-<i>atp</i>H—to provide finer resolution. Among these, ITS1-ITS4 exhibited the highest variability (60/739 variable sites, 8.12%), followed by <i>mat</i>K (39/828, 4.71%) and <i>rbc</i>L (14/527, 2.66%), while <i>psb</i>A-<i>trn</i>H, <i>rpo</i>C, and <i>atp</i>F-<i>atp</i>H showed lower variability (&lt; 2.0%) due to the low resolution of these plastid markers. ITS1-ITS4 effectively distinguished Vinh-Linh from Phu-Quoc and Ha-Tien genotypes, whereas multilocus analysis combining all six regions was less clear. These findings highlight the complementary roles of SCoT markers for broad diversity assessment and DNA barcoding, particularly ITS1-ITS4, for precise genotype identification. The results support breeding, conservation, and authentication strategies for Phu-Quoc black pepper, ensuring its sustainable management and market competitiveness.</p>

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Genetic Diversity of Black Pepper Genotypes in Phu-Quoc Island Using SCoT Markers and DNA Barcodes

  • 期刊论文

  • 发表日期：

    2026年2月12日

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  • Nguyen Van An,
  • Le Tran Quoc Anh,
  • Ngo Thi Thanh Tuyen,
  • Tran Kim Ngoc,
  • Ngo Minh Dung,
  • Truong Vinh Hai,
  • Nguyen Vu Phong

摘要

Black pepper (Piper nigrum L.) is a globally significant spice, with Phu-Quoc Island in Vietnam being renowned for its premium genotypes. This study evaluated the genetic diversity and relationships among 21 black pepper samples from Phu-Quoc and other regions using Start Codon Targeted (SCoT) markers and DNA barcoding. SCoT markers revealed high genetic diversity, amplifying 132 amplicons, of which 129 were polymorphic (97.73% polymorphism). The analysis clustered the samples into six groups, where the Phu-Quoc and Ha-Tien genotypes exhibited high genetic similarity. In contrast, DNA barcoding employed six regions—rbcL, ITS1-ITS4, matK, psbA-trnH, rpoC, and atpF-atpH—to provide finer resolution. Among these, ITS1-ITS4 exhibited the highest variability (60/739 variable sites, 8.12%), followed by matK (39/828, 4.71%) and rbcL (14/527, 2.66%), while psbA-trnH, rpoC, and atpF-atpH showed lower variability (< 2.0%) due to the low resolution of these plastid markers. ITS1-ITS4 effectively distinguished Vinh-Linh from Phu-Quoc and Ha-Tien genotypes, whereas multilocus analysis combining all six regions was less clear. These findings highlight the complementary roles of SCoT markers for broad diversity assessment and DNA barcoding, particularly ITS1-ITS4, for precise genotype identification. The results support breeding, conservation, and authentication strategies for Phu-Quoc black pepper, ensuring its sustainable management and market competitiveness.