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Diversity
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Genetic Diversity, Breeding and Adaption Evolution of Plants
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Genetic Diversity, Breeding and Adaption Evolution of Plants

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Plant Diversity".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 1981

Special Issue Editor

Dr. Qiuyue Chen

E-Mail Website
Guest Editor
Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
Interests: genetic architecture; crop genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic diversity is the cornerstone of successful plant breeding programs, serving as a raw material for the development of new crop varieties with improved traits. By harnessing the rich reservoir of genetic resources that is available in plant populations, breeders can enhance traits such as yield, stress tolerance, nutritional quality, and adaptability to changing environmental conditions. This Special Issue, entitled “Genetic Diversity, Breeding and Adaption Evolution of Plants”, aims to explore the crucial interplay between genetic diversity and the advancement of plant breeding strategies.

This Special Issue aims to bring together insights from genetics, genomics, breeding, agronomy, and biotechnology to provide a comprehensive understanding of the role of genetic diversity in relation to plant improvement. The contributions included within this Special Issue cover a wide range of topics, including the characterization and utilization of genetic resources, the development and application of molecular markers for trait mapping and marker-assisted selection, the utilization of genomic selection for predicting breeding values, and the application of genomic technologies like genome editing and transgenics in breeding programs. Additionally, this Special Issue will explore the role of genetic diversity in addressing various biotic and abiotic stresses, such as pest and disease resistance, drought tolerance, and heat tolerance.

This Special Issue will highlight the importance of preserving and utilizing genetic diversity in breeding programs to ensure the sustainability and resilience of agricultural systems in the face of climate change, population growth, and evolving pest and disease pressures. By addressing different biotic and abiotic stresses, this Special Issue aims to provide valuable insights and strategies for developing resilient crop varieties that can thrive in diverse and challenging environments.

Dr. Qiuyue Chen
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diversity is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic diversity
  • plant breeding
  • evolution

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Published Papers (3 papers)

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Research

19 pages, 3457 KB  
Article
Revealing the Diversity and Varietal Relationships of Regional Cacao and Close Relatives in the Northwestern Colombian Amazon: Insights for Conservation and Agroforestry Resilience
by Armando Sterling, Félix H. Polo-Munar, Ginna P. Velasco-Anacona, Diego F. Caicedo-Rodríguez, Sebastián Valderrama-Cuspian, Sidney do Rosário Costa, Juan C. Suárez-Salazar and Carlos H. Rodríguez-León
Diversity 2026, 18(1), 20; https://doi.org/10.3390/d18010020 - 27 Dec 2025
Viewed by 466
Abstract
Understanding the genetic diversity and structure of regional cacao and its close relatives is essential for strengthening conservation strategies and enhancing the resilience of Amazonian agroforestry systems. This study evaluated the genetic diversity, population structure, and varietal relationships of 48 sexually derived regional [...] Read more.
Understanding the genetic diversity and structure of regional cacao and its close relatives is essential for strengthening conservation strategies and enhancing the resilience of Amazonian agroforestry systems. This study evaluated the genetic diversity, population structure, and varietal relationships of 48 sexually derived regional accessions of Theobroma cacao, T. grandiflorum, and T. bicolor with desirable morpho-agronomic traits, together with eight universal T. cacao reference clones, all cultivated in farmer-managed agroforests of the northwestern Colombian Amazon, using a panel of 15 SSR markers. The loci exhibited substantial allelic richness (mean Na = 8.53) and consistently high expected heterozygosity (Hexp = 0.74), with numerous private alleles indicating species- and lineage-specific divergence. Bayesian clustering, ΔK inference, and minimum spanning networks identified four genetically coherent subpopulations corresponding to the three species and a distinct lineage within T. cacao, strongly aligned with the discriminant analysis of principal components (DAPC) results. Analysis of Molecular Variance (AMOVA) revealed that most genetic variation occurred among subpopulations (56.68%), while pairwise FST (Wright’s fixation index) values confirmed strong interspecific differentiation and significant divergence within T. cacao. No isolation-by-distance pattern was detected. These findings demonstrate that regional Theobroma germplasm maintained in smallholder agroforests constitutes a valuable reservoir of genetic diversity that complements universal reference clones. By documenting species-level divergence and lineage-specific variation, this study supports the integration of farmer-managed genetic resources into conservation planning and highlights their importance for the long-term resilience of Amazonian cacao-based agroforestry landscapes. Full article
(This article belongs to the Special Issue Genetic Diversity, Breeding and Adaption Evolution of Plants)
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19 pages, 3687 KB  
Article
Species-Specific Transcriptome in Xerophytes Atriplex halimus (L.) and Atriplex leucoclada (Boiss.)
by Monther T. Sadder, Mohammad Brake, Mohammad K. Al-Rifaee, Mahfouz M. Abu-Zanat, Saeid Abu-Romman, Anas Musallam, Mohammad A. Alabdallah, Bayan Alkharabsheh, Fatima A. Bani Khaled, Abdulrahman K. Kharouf, Seif D. Alsuraikhat, Hutheyfah Al-Sawalmah and Hassan R. Hamasha
Diversity 2026, 18(1), 10; https://doi.org/10.3390/d18010010 - 23 Dec 2025
Viewed by 746
Abstract
Climate change and global warming are deeply impacting natural foraging dependent upon rain fall. To understand how xerophytes cope with these dramatic changes, comparative transcriptomic profiling of Atriplex halimus and Atriplex leucoclada was investigated under drought stress. The data revealed both shared and [...] Read more.
Climate change and global warming are deeply impacting natural foraging dependent upon rain fall. To understand how xerophytes cope with these dramatic changes, comparative transcriptomic profiling of Atriplex halimus and Atriplex leucoclada was investigated under drought stress. The data revealed both shared and species-specific adaptive mechanisms. Differentially expressed genes (DEGs) clustered into major conserved gene families, including stress signaling, transcriptional regulation, antioxidant defense, metabolism, transport, and hormone signaling. In A. halimus, drought tolerance was characterized by strong transcriptional regulation, redox balance, and energy homeostasis, highlighted by the up-regulation of WRKY, MYB, and SET-domain transcription factors, calcium transporters, SnRK1 kinases, and stress-protective proteins such as HSPs and LEAs. On the other hand, A. leucoclada exhibited broader signaling flexibility and structural reinforcement through enrichment of MAPKs, CDPKs, 14-3-3 proteins, and cell wall-modifying enzymes (XTHs, expansins, chitinase-like proteins), as well as high expression of transporters and hormone-responsive genes. Such patterns indicated distinct drought adaptation strategies: A. halimus relied on rapid transcriptional and redox adjustments suited for fluctuating moisture regimes, while A. leucoclada employed multi-layered, constitutive defenses for persistent arid conditions. Together, these results elucidate complementary molecular strategies enabling ecological divergence and drought resilience among closely related halophytes. Full article
(This article belongs to the Special Issue Genetic Diversity, Breeding and Adaption Evolution of Plants)
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21 pages, 10278 KB  
Article
DNA Barcoding for Managing Blackberry Genetic Resources on Black Sea Coast (Russia)
by Igor Yu. Zhuravlev, Anton V. Korzhuk, Elena S. Tyurina, Nadezhda A. Dobarkina, Elena N. Markova, Evgenija I. Gereeva, Ioanna M. Protasova, Mikhail T. Menkov, Irina V. Rozanova, Lilija Yu. Shipilina, Elena K. Khlestkina and Alexey S. Rozanov
Diversity 2025, 17(12), 869; https://doi.org/10.3390/d17120869 - 18 Dec 2025
Viewed by 474
Abstract
Accurate species identification in blackberries (Rubus spp.) is difficult because of morphological similarity and frequent hybridization. We studied 56 wild accessions from the Sirius Federal Territory (Russia), representing coastal and foothill ecosystems of the Black Sea region. Multilocus DNA barcoding with the [...] Read more.
Accurate species identification in blackberries (Rubus spp.) is difficult because of morphological similarity and frequent hybridization. We studied 56 wild accessions from the Sirius Federal Territory (Russia), representing coastal and foothill ecosystems of the Black Sea region. Multilocus DNA barcoding with the plastid rbcL gene and nuclear ITS1 and ITS2 regions revealed signals of hybridization and hidden diversity. The rbcL marker showed low variation, grouping most accessions into two clusters with several singletons, which limited its use for distinguishing species. In contrast, ITS1 and ITS2 showed higher variation, forming six clusters and eight singletons, and allowed for clear separation of taxa such as Rubus caesius L., R. irritans Focke, and R. amabilis Focke. Accession 3 carried a raspberry (closely to R. corchorifolius L.fil) plastid haplotype, pointing to a hybrid origin. We also found groups of nearby plants with identical mutations, which likely reflect clonal spread with fixed somatic changes or the persistence of recent hybrid lineages. At the same time, accessions collected up to 140 km apart did not form separate clusters, showing weak geographic structuring along the coast. The results demonstrate that multilocus barcoding can reveal not only species boundaries but also evolutionary processes among Rubus such as hybridization, clonal propagation, and early stages of speciation. Full article
(This article belongs to the Special Issue Genetic Diversity, Breeding and Adaption Evolution of Plants)
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