ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1514213
This article is part of the Research TopicFrom Genomics to Genome Editing: Crop Improvement Innovations for Farmers WorldwideView all 6 articles
The Genomic potential of Iranian pomegranate germplasm for future breeding ١ programs revealed through the GBS technique ٢
Provisionally accepted
Sara Razi1
Ali Soleimani1*
Mehrshad Zeinalabedini2
Mohammad Reza Vazifeshenas3
Pedro Martinez-Gomez4
Pedro José Martínez-García4- 1University of Zanjan, Zanjan, Iran
- 2Agricultural Research, Education and Extension Organization (AREEO), Tehran, Alborz, Iran
- 3Agriculture and Natural Resources Research Center of Yazd, Yazd, Yazd, Iran
- 4Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Murcia, Spain
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٢٣ Pomegranate (Punica granatum L.) is a perennial fruit tree native to Iran and the Himalayan ٢٤ Mountains in northern India. In this study, a genotyping-by-sequencing (GBS) approach was used to ٢٥ call single nucleotide polymorphisms (SNPs) and analyze genetic variation in a collection of 214 ٢٦ Iranian accessions from different regions. These individuals were grouped into commercial, wild, ٢٧ base, and ornamental-pharmaceutical categories. A total of 281,514 variants (259,268 SNPs, 11,311 ٢٨ insertions, and 10,935 deletions) were identified. The average values of expected heterozygosity (He) ٢٩ and observed heterozygosity (Ho) were 0.22 and 0.26, respectively. The commercial and base groups ٣٠ exhibited the highest allelic richness. Harmonized results of genetic diversity, allelic richness, and ٣١ genetic differentiation strengthen the hypothesis that most current commercial trees originated ٣٢ directly from wild genotypes through selection and introduction processes rather than classic parental ٣٣ breeding or inbreeding programs. The structure and principal component analyses (PCA) clustered ٣٤ all accessions into three main groups, with no clear relationship to their geographical origin. For the ٣٥ first time, the LD pattern was investigated in this population, revealing a partially rapid LD decay ٣٦ with a short range (~250 bp) across all pseudochromosomes. This study provides new insights for ٣٧ future marker-assisted selection and genome-wide association studies in pomegranate trees. ٣٨
Keywords: pomegranate, molecular marker, Linkage disequilibrium mapping, Genotyping-by-٢١ sequencing, Single nucleotide polymorphisms ٢٢
Received: 20 Oct 2024; Accepted: 04 Apr 2025.
Copyright: © 2025 Razi, Soleimani, Zeinalabedini, Vazifeshenas, Martinez-Gomez and Martínez-García. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Ali Soleimani, University of Zanjan, Zanjan, Iran
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