Genetic Diversity and Population Structure of Plants

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

Deadline for manuscript submissions: 30 May 2025 | Viewed by 3199

Special Issue Editors


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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

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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 (3 papers)

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Research

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16 pages, 1631 KiB  
Article
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
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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 [...] Read more.
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  
Article
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
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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 [...] Read more.
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  
Review
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
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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 [...] Read more.
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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