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<p>Shallot (<i>Allium cepa</i> L. var. <i>aggregatum</i>) is essential for maintaining economic stability in Indonesia, and it serves as a vital and nutrient-rich vegetable. It is important to conduct a genetic study of Indonesia’s shallot germplasm collection, focusing on both morphological and molecular levels, to identify beneficial traits for parental selection in hybridization programs. The study aimed to analyze the genetic diversity of thirteen Indonesia’s shallot genotypes using morphological, microsatellite, and Start Codon Targeted (SCoT) markers, and to compare the efficacy of these markers in distinguishing the genotypes. Morphological traits examined included bulb dry skin color, bulb flesh color, bulb shape, bulb stem-end shape, and bulb root-end shape, which were observed qualitatively after harvesting. DNA from 13 shallot genotypes was amplified using 10 microsatellite primers and 30 SCoT primers. The results indicated that SCoT markers produced significantly more alleles (176) than microsatellite markers (55). Additionally, SCoT markers exhibited higher major allele frequency (0.27–0.81), gene diversity (0.31–0.83), observed heterozygosity (0.08–1.00), and polymorphism information content (PIC) (0.37–0.82). These findings indicate that SCoT markers are more effective than microsatellite markers for genetic analysis in shallots, reflected by their higher informativeness and diversity metrics. Eight microsatellite markers and twenty-four SCoT markers were identified as highly informative (PIC &gt; 0.5), making them suitable for selection tools in shallot breeding programs. The phylogenetic analysis and principal coordinate analysis (PCoA) biplots showed that shallot genotypes clustered by genetic background rather than by geographical origin. Genotypes with low genetic similarity (e.g. Rubaru and Kuning, Bima and Sumenep, Batu Ijo and Rubaru) were identified as promising candidates for future hybridization programs.</p>

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Morphological and molecular assessment of Indonesia’s shallot (Allium cepa L. var. aggregatum) genotypes based on microsatellite and start codon targeted markers

  • 期刊论文

  • 发表日期：

    2026年2月24日

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  • Tri Joko Santoso,
  • Kristianto Nugroho,
  • Tri Handayani,
  • Alberta Dinar Ambarwati,
  • Chotimatul Azmi,
  • Rini Murtiningsih,
  • Atmitri Sisharmini,
  • Aniversari Apriana,
  • Zeeshan Ali,
  • Dwinita Wikan Utami,
  • Reflinur Reflinur

摘要

Shallot (Allium cepa L. var. aggregatum) is essential for maintaining economic stability in Indonesia, and it serves as a vital and nutrient-rich vegetable. It is important to conduct a genetic study of Indonesia’s shallot germplasm collection, focusing on both morphological and molecular levels, to identify beneficial traits for parental selection in hybridization programs. The study aimed to analyze the genetic diversity of thirteen Indonesia’s shallot genotypes using morphological, microsatellite, and Start Codon Targeted (SCoT) markers, and to compare the efficacy of these markers in distinguishing the genotypes. Morphological traits examined included bulb dry skin color, bulb flesh color, bulb shape, bulb stem-end shape, and bulb root-end shape, which were observed qualitatively after harvesting. DNA from 13 shallot genotypes was amplified using 10 microsatellite primers and 30 SCoT primers. The results indicated that SCoT markers produced significantly more alleles (176) than microsatellite markers (55). Additionally, SCoT markers exhibited higher major allele frequency (0.27–0.81), gene diversity (0.31–0.83), observed heterozygosity (0.08–1.00), and polymorphism information content (PIC) (0.37–0.82). These findings indicate that SCoT markers are more effective than microsatellite markers for genetic analysis in shallots, reflected by their higher informativeness and diversity metrics. Eight microsatellite markers and twenty-four SCoT markers were identified as highly informative (PIC > 0.5), making them suitable for selection tools in shallot breeding programs. The phylogenetic analysis and principal coordinate analysis (PCoA) biplots showed that shallot genotypes clustered by genetic background rather than by geographical origin. Genotypes with low genetic similarity (e.g. Rubaru and Kuning, Bima and Sumenep, Batu Ijo and Rubaru) were identified as promising candidates for future hybridization programs.