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Genetic Diversity and Population Structure of Plants

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 January 2026 | Viewed by 5578

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Special Issue Editors

Dr. Mario Ciaffi

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Guest Editor

Department for the Innovation in Biological, Agrofood and Forestal Systems, Tuscia University,01100 Viterbo, Italy
Interests: plant genetics; plant biotechnology; molecular markers (ISSRs, SSRs, and SNPs); phenotypic and genetic characterization of plant genetic resources in crop and forest species; plant transcriptomics; common bean; globe artichoke; wheat; forest tree species

Dr. Enrica Alicandri

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Guest Editor

Department for the Innovation in Biological, Agrofood and Forestal Systems, Tuscia University, 01100 Viterbo, Italy
Interests: forest genetics; plant diversity; plant biotechnology

Special Issue Information

Dear Colleagues,

At present, the global community faces the formidable challenges of population growth, food insecurity, and the pervasive impacts of climate change. The latter phenomenon poses a substantial threat to global food security by impeding food production through disruptions in cropping patterns and diminishing crop resilience to both biotic and abiotic stresses. Research widely advocates plant breeding as a pivotal strategy in addressing these challenges. Nonetheless, it is universally acknowledged that plant breeding also contributes to genetic erosion. Consequently, extant food cultivars exhibit suboptimal performance under unprecedented climatic conditions, primarily due to a genetic bottleneck. To address these complex issues, there is an urgent need to harness plant diversity.

The collection, preservation, and characterization of plant genetic resources represent a valid strategy, as it facilitates the exploration of genotypic and phenotypic diversities that are potentially beneficial for breeding endeavors. The limited genetic diversity inherent in our agricultural crops can be expanded by integrating landraces, wild progenitors of cultivated species, as well as underutilized and neglected plant species. Assessing the genetic diversity and population structure of available genetic resources represents a starting point and a crucial topic for crop improvement and food security, allowing their evolution and adaptation to diverse environments to be understood and useful traits for disease resistance and environmental stress tolerance, as well as higher nutitional quality, to be identified. Additionally, such analyses are essential for developing effective conservation strategies and managing genetic resources.

This Special Issue aims to underscore the significance of plant biodiversity and genetic resources in fostering sustainable agricultural production systems. We invite submissions of short communications, original research articles, reviews, and modeling methodologies addressing various aspects of plant genetic diversity, including its utilization in breeding programs, its characterization using omics and biotechnological technologies, and advanced approaches used for its in situ and ex situ conservation.

Dr. Mario Ciaffi
Dr. Enrica Alicandri
Guest Editors

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Keywords

genetic diversity
population genetics
population structure
germplasm characterization
phenotypic markers
molecular markers
genotyping by sequencing
molecular breeding
omics and biotechnological technologies
climate change resilience
biodiversity conservation
genetic erosion
in situ and ex situ conservation strategies
cereals
legumes
horticultural crops
fruit crops
plant wild relatives
endangered species

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Published Papers (9 papers)

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17 pages, 1438 KiB

Open AccessArticle

Endangered with High Dispersal Abilities: Conservation Genetics of Himantoglossum metlesicsianum (Teschner) P. Delforge (Orchidaceae) in the Canary Islands

by Rocío González Negrín, Victoria Eugenia Martín Osorio, Pedro A. Sosa and Priscila Rodríguez-Rodríguez

Plants 2025, 14(12), 1862; https://doi.org/10.3390/plants14121862 - 17 Jun 2025

Viewed by 101

Abstract

Himantoglossum metlesicsianum is a threatened orchid with low population numbers and fragmented distribution, present in four of the Canary Islands. This study focused on assessing the genetic variability and population genetic structure of the natural populations known to date, identifying those characteristics of the species that condition the flow and genetic variation. For that purpose, we collected samples from eight sites in its distribution range and developed 14 polymorphic microsatellite markers. Despite its rarity, this orchid presents high levels of genetic diversity and a homogeneous population structure, characterised by a low degree of genetic differentiation and patterns consistent with high genetic connectivity among populations. Our results suggest that the species might show dichotomy in seed dispersal, combining long- and short-distance events. In addition, it is possible that pollen cross-pollination (pollinia) between adjacent sites may also be involved. In conclusion, these findings reveal unexpectedly high genetic diversity and connectivity among populations, despite the species’ rarity and fragmented distribution, highlighting key biological traits that should be considered in future conservation and recovery plans. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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16 pages, 1512 KiB

Open AccessArticle

Microsatellite Genotyping and Genetic Diversity of a Greek Pear (Pyrus communis L.) Germplasm Collection

by Eleftheria Deligiannidou, Anastasia Boutsika, Ioannis Plesias, Aliki Xanthopoulou, Theodoros Moysiadis, Ifigeneia Mellidou, Ioannis Manthos, Thomas Sotiropoulos and Ioannis Ganopoulos

Plants 2025, 14(12), 1816; https://doi.org/10.3390/plants14121816 - 13 Jun 2025

Viewed by 262

Abstract

Pear (Pyrus communis L.) is a widely cultivated fruit tree species, valued for its significant economic impact and cultural relevance. The rise in commercial cultivars, characterized by genetic uniformity and high yield, is increasingly displacing traditional landraces. However, traditional varieties are highly adapted to local environmental conditions, having resulted from centuries of selection. In this study, 51 pear (Pyrus communis L.) accessions conserved in the Greek national germplasm collection were genotyped using eight SSR markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR). A total of 44 alleles were detected, including several private alleles, indicative of localized adaptation or potential genetic isolation. Analyses of population structure and genetic diversity, using Principal Coordinate Analysis (PCoA), UPGMA clustering, and Bayesian inference via STRUCTURE, uncovered distinct genetic groupings within the collection. The results revealed moderate genetic variability among the 51 accessions and identified some accessions with significant genetic divergence. These findings underscore the importance of conserving Greek pear germplasm, as it represents an ideal source of desirable traits, such as stress tolerance and fruit quality, which can be utilized in breeding programs. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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16 pages, 3846 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Wild Ancient Camellia tetracocca in Pu’an, Guizhou, China

by Deqin Li, Lushan Li, Shukui Chang, Shunrong Zhang, Jian Feng, Lifei Wang, Xiaoxia Huang, Huizhen Hu, Feng Zu and Xiaomao Cheng

Plants 2025, 14(11), 1709; https://doi.org/10.3390/plants14111709 - 4 Jun 2025

Viewed by 381

Abstract

Pu’an County, located in southwestern Guizhou Province, China, is one of the original habitats for wild tea plants. It is renowned not only as the “Home of Ancient Tea Trees in China” but also as the “Core Production Area for High-Quality Early Tea in China”. The wild ancient Camellia tetracocca tea trees are considered “living fossil”. Understanding the genetic diversity of wild ancient C. tetracocca in Pu’an, Guizhou, is of great significance for addressing conservation concerns and mitigating genetic erosion in this endemic species. This study investigates the genetic diversity and population structure of wild ancient C. tetracocca tea plants in Pu’an County to support the development of conservation strategies. We genotyped 138 ancient wild C. tetracocca specimens using 40 intron-length polymorphism markers. A total of 180 alleles were detected, with the allele numbers per locus ranging from 2 to 10 and an average of 4.50. The number of effective alleles varied from 1.36 to 8.01, with an average of 2.86. The Shannon information index ranged from 0.28 to 2.19, with an average of 1.10. Nei’s gene diversity index ranged from 0.14 to 0.88, with an average of 0.58. The polymorphic information content (PIC) varied from 0.14 to 0.85, with an average of 0.58. Our findings indicate that the genetic diversity of wild ancient C. tetracocca tea plants in Pu’an is high. Specifically, the genetic diversity in Qingshan Township surpassed that in Xindian Township. Analysis of molecular variance indicated that 91.59% of the genetic variation occurred within the subpopulations, suggesting limited differentiation. Despite their geographical separation, populations from Qingshan and Xindian showed a complex genetic relationship (F_ST = 0.04). STRUCTURE analysis identified three distinct genetic clusters, indicating a complex demographic history. These findings underscore the conservation significance of wild C. tetracocca populations in Pu’an and highlight the need for conservation strategies that prioritize the protection of genetically diverse subpopulations, especially in the Qingshan region. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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18 pages, 2348 KiB

Open AccessArticle

Genetic Diversity and Phenotypic Variation of Indigenous Wild Cherry Species in Kazakhstan and Uzbekistan

by Ulzhan Manapkanova, Nazgul Rymkhanova, Stefanie Reim, Eric Fritzsche, Monika Höfer, Natalya Beshko, Yeskendir Satekov and Svetlana V. Kushnarenko

Plants 2025, 14(11), 1676; https://doi.org/10.3390/plants14111676 - 30 May 2025

Viewed by 339

Abstract

This study investigates the phenotypic characteristics, genetic diversity, and population structure of four wild cherry species collected from various regions of Kazakhstan and Uzbekistan: Prunus fruticosa Pall., Ptunus erythrocarpa (Nevski) Gilli, Prunus griffithii var. tianshanica (Pojark.) Ingram, and Prunus verrucosa (Franch.). A total of 163 accessions were characterized morphologically using standardized descriptors for plant, leaf, and fruit traits. Genetic diversity was assessed using 13 simple sequence repeat (SSR) markers. STRUCTURE analysis revealed that 87.7% of the accessions were assigned to pure species. However, hybrid accessions were identified in P. griffithii var. tianshanica (34.4%), P. erythrocarpa (18.5%), and P. verrucosa (8.0%). Identical genotypes were found across all species, with P. fruticosa showing the highest proportion (54.8%), likely due to clonal propagation via root suckers. Among the four species, P. verrucosa exhibited the highest genetic diversity, while P. fruticosa had the lowest. Analysis of molecular variance (AMOVA) showed that genetic variation within the species (81%) was substantially greater than variation among the species (19%). These findings enhance our understanding of the genetic relationships among wild cherry species in Central Asia and provide valuable data for conservation planning and breeding programs aimed at improving drought and frost tolerance in Prunus species. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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15 pages, 3400 KiB

Open AccessArticle

Genetic Diversity and Conservation of Bomarea ovallei (Phil.) Ravenna: Microsatellite Markers Reveal Population Vulnerability in the Atacama Desert

by Valeska Rozas-Lazcano, Mariel Mamani-Gómez, Irina Rojas-Jopia, Mariana Arias-Aburto and Roberto Contreras-Díaz

Plants 2025, 14(10), 1468; https://doi.org/10.3390/plants14101468 - 14 May 2025

Viewed by 353

Abstract

The Atacama Desert, the driest and oldest desert on Earth, hosts a unique floral phenomenon known as the Desierto Florido (Flowering Desert), which occurs sporadically in response to rare rainfall events. Bomarea ovallei (Phil.) Ravenna is an endemic and endangered species of the Atacama Desert. However, its populations are geographically restricted and potentially vulnerable to genetic erosion due to isolation and extreme environmental conditions. This study aims to assess the genetic diversity of B. ovallei populations and develop microsatellite markers using next-generation sequencing (NGS) technology. A total of 268 microsatellite loci were identified, and 34 co-dominant markers were successfully developed for the first time in B. ovallei. Genetic diversity analysis using eight fluorescently labeled SSR markers revealed low genetic diversity across four populations, with the highest diversity observed in the QCA population, located within Llanos de Challe National Park, and the lowest in the TOTO population, which is highly exposed to anthropogenic activities. UPGMA and STRUCTURE analyses revealed three genetic clusters and high admixture among populations, suggesting historical or ongoing gene flow despite geographical separation. The presence of non-polymorphic loci and low PIC values in some markers further supports limited genetic variation. The newly developed microsatellite markers offer a valuable tool for future genetic studies, enabling the monitoring of genetic diversity and informing strategies for the preservation of this rare and ecologically significant species. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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26 pages, 6832 KiB

Open AccessArticle

Identification of Indigenous Thai Phlegmariurus Genotypic Population by Integrating Morphological and Molecular Studies

by Nusanisa Chedao, Avinash Chandra Pandey and Potjamarn Suraninpong

Plants 2025, 14(9), 1400; https://doi.org/10.3390/plants14091400 - 7 May 2025

Viewed by 416

Abstract

Phlegmariurus, a diverse genus within the Lycopodiaceae family, has wide diversity in tropical regions, including Thailand. Accurate species delimitation in the tropical clubmoss genus Phlegmariurus is challenged by high morphological plasticity and genetic complexity. This study applied an integrative multilocus approach combining morphometric analysis of 27 complete specimens, 35 Phlegmariurus and one Lycopodiella accessions for AFLP genotyping (926 loci; PIC 0.32), SSR profiling (44 loci; PIC 0.57; expected heterozygosity 0.35), and chloroplast barcoding using rbcL (1308 bp; bootstrap 89–99%) and the psbA-trnH intergenic spacer (308 bp; bootstrap ≥ 94%). A total of 13 were identified as belonging to seven known species, including P. nummulariifolius (NST01, NST15, NST36), P. goebelii (JP04), P. phlegmaria (NST13), P. verticillatus (PHI16), P. squarrosus (NST21, NST22, MY31), P. tetrastichus (NST30), and P. carinatus (MY32, MY33, NST34). Morphological clustering and molecular markers consistently distinguished Phlegmariurus accessions from the Lycopodiella outgroup. Additionally, 19 previously unclassified Phlegmariurus accessions were successfully identified as belonging to the species P. nummulariifolius (NST23), P. goebelii (NST03, JP05, STN12, PNA14, SKA25, CPN26, KRB27, PNA28), P. phlegmaria (NWT07, STN08, NST09, NST10, PHI29), P. squarrosus (NST17), and P. carinatus (PNA06, STN18, CPN19, JP24). Moreover, this study identified three novel lineages (NST02, STN11, NST20) with strong support across datasets. The combination of broad genomic coverage (AFLP), fine-scale allelic resolution (SSR), deep-branch backbone (rbcL), and terminal-branch discrimination (psbA-trnH) yields a robust framework for species identification. These results define clear operational units for conservation prioritization and establish a foundation for marker-assisted development of ornamental Phlegmariurus cultivars. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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16 pages, 1631 KiB

Open AccessArticle

The Characterization of the Morphological and Molecular Traits of Phaseolus coccineus in the Aniene Valley: Insights into Genetic Diversity and Adaptation

by Mario Ciaffi, Anna Rita Paolacci, Martina Marcomeni, Lorenzo Coluccia, Paola Taviani and Enrica Alicandri

Plants 2024, 13(23), 3320; https://doi.org/10.3390/plants13233320 - 26 Nov 2024

Viewed by 649

Abstract

This study aimed to characterize the genetic diversity and morphological traits of 32 populations of Phaseolus coccineus collected from the Aniene Valley. Quantitative seed trait analyses revealed that Mandolone accessions exhibited significantly higher seed weights and dimensions compared to Fagiolone accessions. Specifically, Mandolone accessions showed an average weight of 189.48 g per 100 seeds, with seed heights and lengths averaging 14.38 mm and 23.84 mm, respectively. In contrast, Fagiolone accessions had an average seed weight of 174.13 g, with seed heights and lengths of 13.95 mm and 22.58 mm, respectively. Molecular analysis, conducted using 9 polymorphic SSR loci, identified 53 alleles across 320 genotypes, with a mean expected heterozygosity (He) of 0.695. This indicated that there was high genetic variability within the Aniene Valley populations. The genetic diversity analysis revealed two genetic clusters corresponding to the Mandolone and Fagiolone landraces. This was supported by UPGMA, PCoA, and STRUCTURE analyses. This study highlights the need to conserve the genetic diversity within these landraces and provides a basis for the development of conservation strategies for P. coccineus germplasms in the singular ecological context of the Aniene Valley. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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12 pages, 3022 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Endangered Orchid Cypripedium flavum in Fragmented Habitat Using Fluorescent AFLP Markers

by Shijun Hu, Meizhen Wang, Xiaohui Yan and Xiaomao Cheng

Plants 2024, 13(20), 2851; https://doi.org/10.3390/plants13202851 - 11 Oct 2024

Viewed by 1136

Abstract

Genetic diversity is crucial for determining the evolutionary potential of a species and is essential for developing optimal conservation strategies. The impact of habitat fragmentation on the genetic diversity of food-deceptive orchids seems to be unpredictable because of their specialized seed and pollen dispersal mechanisms. The habitat of deceptive Cypripedium flavum was severely fragmented during the past half century. This study investigated the genetic diversity and structure of seven fragmented Cypripedium flavum populations in Shangrila County using AFLP markers. A total of 376 alleles were identified, with a range of 70 to 81 alleles per locus. The species exhibited considerable genetic diversity, as evidenced by an average Nei’s gene diversity (H) of 0.339 and a Shannon’s information index (I) of 0.505, with all loci being polymorphic. Based on Molecular Variance (AMOVA), 8.75% of the genetic differentiation was found among populations, while the remaining 91.25% of genetic variation occurred within populations. Population structure analysis revealed that the C. flavum germplasm can be categorized into 2 distinct groups, among which there was significant gene flow. Despite habitat fragmentation, C. flavum still retained a high level of genetic diversity, and the substantial gene flow (5.0826) is a key factor in maintaining the genetic diversity. These findings offer valuable insights for the conservation and potential use of C. flavum genetic resources. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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Review

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17 pages, 1374 KiB

Open AccessReview

Using Quantitative Trait Locus Mapping and Genomic Resources to Improve Breeding Precision in Peaches: Current Insights and Future Prospects

by Umar Hayat, Cao Ke, Lirong Wang, Gengrui Zhu, Weichao Fang, Xinwei Wang, Changwen Chen, Yong Li and Jinlong Wu

Plants 2025, 14(2), 175; https://doi.org/10.3390/plants14020175 - 10 Jan 2025

Cited by 1 | Viewed by 1111

Abstract

Modern breeding technologies and the development of quantitative trait locus (QTL) mapping have brought about a new era in peach breeding. This study examines the complex genetic structure that underlies the morphology of peach fruits, paying special attention to the interaction between genome editing, genomic selection, and marker-assisted selection. Breeders now have access to precise tools that enhance crop resilience, productivity, and quality, facilitated by QTL mapping, which has significantly advanced our understanding of the genetic determinants underlying essential traits such as fruit shape, size, and firmness. New technologies like CRISPR/Cas9 and genomic selection enable the development of cultivars that can withstand climate change and satisfy consumer demands with unprecedented precision in trait modification. Genotype–environment interactions remain a critical challenge for modern breeding efforts, which can be addressed through high-throughput phenotyping and multi-environment trials. This work shows how combining genome-wide association studies and machine learning can improve the synthesis of multi-omics data and result in faster breeding cycles while preserving genetic diversity. This study outlines a roadmap that prioritizes the development of superior cultivars utilizing cutting-edge methods and technologies in order to address evolving agricultural and environmental challenges. Full article

(This article belongs to the Special Issue Genetic Diversity and Population Structure of Plants)

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