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<p>Wild pomegranate (<i>Punica granatum</i> L.) represents an important reservoir of genetic diversity for conservation and breeding; however, information on its population genetic structure in the Himalayan region remains scarce. This study provides the first detailed assessment from the Pir Panjal range, examining genetic diversity, population structure, and differentiation among 80 wild pomegranate samples using 25 SSR (PgSSR) markers. The research revealed considerable allelic diversity, with 4–11 alleles per marker and average effective allele numbers (Ne) ranging from 4.17 to 4.82. The PgSSR markers were highly informative, with polymorphic information content (PIC) values ranging from 0.439 to 0.875 and mean PIC values of 0.740–0.778 across populations. Both Shannon’s information index (I = 1.55–1.66) and observed heterozygosity (Ho = 0.78–0.81) were high, demonstrating substantial genetic variation and the strong discriminatory power of the markers. Negative fixation indices (Fis = − 0.020 to − 0.056) indicated an excess of heterozygotes, implying a predominantly outcrossing breeding system and low inbreeding. Bayesian clustering separated the accessions into four distinct genetic groups (K = 4), supported by a pronounced ΔK value (ΔK = 1830.5). Most samples exhibited high membership coefficients (&gt; 0.80), indicating clear genetic differentiation with limited admixture. Additional analyses, including Principal Coordinates Analysis, UPGMA clustering, and Nei’s genetic identity, corroborated these findings. Analysis of molecular variance showed that 78% of total genetic variation resided within populations and 22% among populations, indicating moderate differentiation (average FST = 0.113). Estimated gene flow (Nm = 2.13) suggests sufficient historical exchange to counteract strong genetic drift. Overall, wild pomegranate germplasm from the Pir Panjal Himalayas possesses high genetic diversity and moderate population structure, underscoring its value for in situ conservation, evolutionary studies, and future breeding programs.</p>

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Genetic mosaic and population stratification of wild pomegranate (Punica granatum) across the Pir Panjal range

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月2日

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  • Parshant Bakshi,
  • Kiran Kour,
  • Zafir Ahmad Naik,
  • Neha Sharma,
  • Zahid Nabi Sheikh,
  • Bader Alsubaie,
  • Jameel M. Al-Khayri,
  • Othman Al-Dossary,
  • Wael F. Shehata,
  • Adel A. Rezk

摘要

Wild pomegranate (Punica granatum L.) represents an important reservoir of genetic diversity for conservation and breeding; however, information on its population genetic structure in the Himalayan region remains scarce. This study provides the first detailed assessment from the Pir Panjal range, examining genetic diversity, population structure, and differentiation among 80 wild pomegranate samples using 25 SSR (PgSSR) markers. The research revealed considerable allelic diversity, with 4–11 alleles per marker and average effective allele numbers (Ne) ranging from 4.17 to 4.82. The PgSSR markers were highly informative, with polymorphic information content (PIC) values ranging from 0.439 to 0.875 and mean PIC values of 0.740–0.778 across populations. Both Shannon’s information index (I = 1.55–1.66) and observed heterozygosity (Ho = 0.78–0.81) were high, demonstrating substantial genetic variation and the strong discriminatory power of the markers. Negative fixation indices (Fis = − 0.020 to − 0.056) indicated an excess of heterozygotes, implying a predominantly outcrossing breeding system and low inbreeding. Bayesian clustering separated the accessions into four distinct genetic groups (K = 4), supported by a pronounced ΔK value (ΔK = 1830.5). Most samples exhibited high membership coefficients (> 0.80), indicating clear genetic differentiation with limited admixture. Additional analyses, including Principal Coordinates Analysis, UPGMA clustering, and Nei’s genetic identity, corroborated these findings. Analysis of molecular variance showed that 78% of total genetic variation resided within populations and 22% among populations, indicating moderate differentiation (average FST = 0.113). Estimated gene flow (Nm = 2.13) suggests sufficient historical exchange to counteract strong genetic drift. Overall, wild pomegranate germplasm from the Pir Panjal Himalayas possesses high genetic diversity and moderate population structure, underscoring its value for in situ conservation, evolutionary studies, and future breeding programs.