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<p>Almond is a globally important nut crop. We investigated genome-wide diversity and structure in 36 genotypes grown in Jordan: 24 cultivated and 12 wild types, using Inter-Simple Sequence Repeat (ISSR) and Start Codon Targeted (SCoT) markers. Thirteen ISSR primers amplified 188 polymorphic bands (93% polymorphism), and ten SCoT primers generated 174 polymorphic bands (90% polymorphism), with both systems showing an average PIC of 0.25. Jaccard’s similarity coefficients ranged from 0.281 to 0.899 (ISSR) and 0.289–0.818 (SCoT), indicating greater variability among wild genotypes. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrograms grouped all genotypes into three main clusters, clearly separating cultivated and wild groups, with <i>Amygdalus arabica</i> consistently forming an isolated clade. Principal Coordinate Analysis (PCoA) based on ISSR and SCoT markers supported the dendrogram results: ISSR PCoA resolved cultivated and wild genotypes into two main groups, while SCoT PCoA showed a clearer separation, with <i>Amygdalus arabica</i> positioned separately from <i>A. communis</i> and <i>A. korschinskyi</i>. Despite their diverse geographic origins, cultivated genotypes exhibited high genetic similarity and clustered together, suggesting a narrow genetic base that was likely shaped by historical breeding and gene flow. In contrast, wild genotypes clustered approximately by regional origin within Jordan, suggesting localized differentiation. The distinct genetic profile of <i>A. arabica</i>, together with the overall high polymorphism observed, underscores the value of wild almond germplasm as a reservoir of novel alleles for almond improvement. This study delineates the genetic landscape of Jordanian almonds, emphasizing the conservation of wild genetic resources for future breeding and stress-resilience strategies.</p>

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Genetic diversity and structure of cultivated and wild almond genotypes in Jordan revealed by inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) markers

  • 期刊论文

  • 发表日期：

    2025年12月19日

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  • Ghina Al-Hmoud,
  • Emel Sözen

摘要

Almond is a globally important nut crop. We investigated genome-wide diversity and structure in 36 genotypes grown in Jordan: 24 cultivated and 12 wild types, using Inter-Simple Sequence Repeat (ISSR) and Start Codon Targeted (SCoT) markers. Thirteen ISSR primers amplified 188 polymorphic bands (93% polymorphism), and ten SCoT primers generated 174 polymorphic bands (90% polymorphism), with both systems showing an average PIC of 0.25. Jaccard’s similarity coefficients ranged from 0.281 to 0.899 (ISSR) and 0.289–0.818 (SCoT), indicating greater variability among wild genotypes. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrograms grouped all genotypes into three main clusters, clearly separating cultivated and wild groups, with Amygdalus arabica consistently forming an isolated clade. Principal Coordinate Analysis (PCoA) based on ISSR and SCoT markers supported the dendrogram results: ISSR PCoA resolved cultivated and wild genotypes into two main groups, while SCoT PCoA showed a clearer separation, with Amygdalus arabica positioned separately from A. communis and A. korschinskyi. Despite their diverse geographic origins, cultivated genotypes exhibited high genetic similarity and clustered together, suggesting a narrow genetic base that was likely shaped by historical breeding and gene flow. In contrast, wild genotypes clustered approximately by regional origin within Jordan, suggesting localized differentiation. The distinct genetic profile of A. arabica, together with the overall high polymorphism observed, underscores the value of wild almond germplasm as a reservoir of novel alleles for almond improvement. This study delineates the genetic landscape of Jordanian almonds, emphasizing the conservation of wild genetic resources for future breeding and stress-resilience strategies.