Genetic and Morphological Diversity in Plants

A Special Issue of Genes (ISSN 2073-4425) belonging to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 15 October 2026 | Viewed by 9727

Editor


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Guest Editor
Department of Biology, University of Nebraska at Omaha, Omaha, NE 68128, USA
Interests: genetic variation; morphological variation; classical taxonomy; massively parallel sequencing ASKDF; lasjf; molecular systematics; species identification; biodiversity; evolutionary biology; phylogeny; conservation; phylogenetic diversity; molecular; biodiversity assessment; Pediomelum

Special Issue Information

Dear Colleagues,

From genes to species, biodiversity is the great variation within and among all forms of life on Earth, and it is vital to the health and conservation of nature. Plants depend on large and heterogeneous gene pools for future adaptations to changing environments. These genetic resources are enhanced in plants by unique reproductive strategies such as outcrossing, hybridization, and polyploidization, but these features can make it difficult for researchers to characterize plant diversity. Genes manifest into morphotypes, but environmental factors and conditions can influence labile phenotypes. Morphological variation within and among populations of plant species may result from genetic variation, from varying environmental factors, or from a combination of both. Furthermore, understanding genetic and morphological diversity in plants is important for many reasons: (1) conserving healthy ecosystems and natural resources for ecosystem services such as air, water, and soil health, climate stabilization, pollination, and for the quality of recreational, cultural, and aesthetic landscapes; (2) controlling or eradicating invasive species; (3) predicting how a species may respond to a changing climate; (4) bioprospecting; (5) determining taxonomic identities or resolving taxonomic conflicts; and (6) informing crop improvement and plant breeding programs by enhancing germplasm resources and other genetic resources and identifying genotypes that result in desirable phenotypes. Currently, research is focused on investigating these topics via proven classical techniques to characterize morphologies using morphometrics and the principle component analysis (PCA) of quantitative traits and for genotyping and molecular profiling using inter-simple sequence repeats (ISSRs), random amplified polymorphism DNA (RAPD), and amplified fragment length polymorphism (AFLP) fingerprinting. Additionally, many studies employ state-of-the-art, high-throughput sequencing for simple sequence repeat (SSR; microsatellite) analysis or double-digest restriction site-associated DNA (ddRADseq) to assess the genetic structure of a population.

This Special Issue aims to provide a collection of articles highlighting current investigations that utilize and/or elucidate the links between genetic and morphological variation in plants and the numerous reasons why understanding this connection is important.

Dr. P. Roxanne Kellar
Guest Editor

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Keywords

  • biodiversity
  • conservation
  • genetic structure
  • genetics
  • genotype
  • germplasm
  • haplotype
  • high-throughput sequencing
  • invasive species
  • microsatellites
  • molecular markers
  • morphological characters
  • morphology
  • morphometrics
  • morphotype
  • next-generation sequencing
  • phenotype
  • systematics
  • taxonomy
  • variation

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Published Papers (8 papers)

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Research

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24 pages, 12724 KB  
Article
Morphological and Genetic Variation in Strychnos madgascariensis Poir (Loganiaceae) at Bonamanzi Game Reserve, KwaZulu-Natal, South Africa
by Luyanda A. Mbongwe, Nontuthuko R. Ntuli and Zoliswa Mbhele
Genes 2026, 17(7), 732; https://doi.org/10.3390/genes17070732 - 24 Jun 2026
Viewed by 391
Abstract
Background: Strychnos madagascariensis Poir (Loganiaceae) is a drought-tolerant indigenous fruit tree of East and southern Africa, valued for its food, medicinal, and socio-economic contributions to rural communities. Despite its importance as a candidate food crop, intraspecific morphological and genetic diversity had not previously [...] Read more.
Background: Strychnos madagascariensis Poir (Loganiaceae) is a drought-tolerant indigenous fruit tree of East and southern Africa, valued for its food, medicinal, and socio-economic contributions to rural communities. Despite its importance as a candidate food crop, intraspecific morphological and genetic diversity had not previously been characterized, and no simple sequence repeat (SSR) markers had been developed for this species, leaving breeders and conservation planners without the basic diversity baseline needed to prioritize material for domestication. Methods: This study assessed vegetative and reproductive trait variation, variance components, and broad-sense heritability, and SSR-based genetic diversity among 27 morphologically defined S. madagascariensis morphotypes at Bonamanzi Game Reserve, KwaZulu-Natal, South Africa. Three trees were measured per morphotype (81 trees total), over two growing seasons. Genetic diversity was characterized in one representative tree per morphotype using seventeen newly developed SSR loci, the first such markers reported for this species, and analyzed with population structure (STRUCTURE version 2.3.4), PCA, and Nei’s genetic distance. Results: Twenty-seven morphotypes were identified based on leaf colour, shape, hairiness and size, dominated by grey (41%), elongated (59%), less hairy (48%), and medium-sized (>50–90 mm) leaves. Fruit diameter and mass showed the highest inter-morphotype variation (r = 0.949) and also the highest broad-sense heritability (H2 = 55.3% and 47.8%, respectively), indicating strong genetic control of these traits and their suitability as targets for selective breeding. Environmental variance exceeded genotypic variance for most traits. A total of 144 alleles were identified across 17 SSR loci (mean 4.24 alleles/locus; mean PIC = 0.31). Population structure gave a preliminary, tentative signal of two genetic clusters (K = 2) with substantial admixture, which we interpret cautiously, given the limited sampling depth. Conclusions: This is the first study to characterize intraspecific morphological variation in S. madagascariensis and the first to develop SSR markers for the species. The results provide a preliminary, single-site framework for conservation genetics and crop improvement that should be validated with larger, multi-site samples. Grey morphotypes GyEvH1, GyEvH2, GyEvH3, GyRlH1 and GyEH2 combined consistent fruiting performance with favourable fruit-trait values and are proposed as priority candidates for further evaluation in domestication and breeding programmes. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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17 pages, 2679 KB  
Article
Genetic Variation and Spatial Genetic Structure of Eleocharis ussuriensis Zinserl. in South Korea: Implications for Ecological Monitoring and Resource Management
by Eun-Hye Kim, Kang-Rae Kim, Mi-Hwa Lee, Jaeduk Goh and Jeong-Nam Yu
Genes 2026, 17(5), 513; https://doi.org/10.3390/genes17050513 - 26 Apr 2026
Viewed by 832
Abstract
Background/Objectives: Eleocharis ussuriensis Zinserl. is a perennial riparian sedge widely distributed in Northeast Asia and a dominant component of freshwater vegetation in South Korea. However, the intraspecific genetic structure of this species across contrasting hydrological habitats remains insufficiently understood. This study aimed [...] Read more.
Background/Objectives: Eleocharis ussuriensis Zinserl. is a perennial riparian sedge widely distributed in Northeast Asia and a dominant component of freshwater vegetation in South Korea. However, the intraspecific genetic structure of this species across contrasting hydrological habitats remains insufficiently understood. This study aimed to develop novel SSR markers from whole-genome data and investigate genetic variation and population structure among E. ussuriensis populations in South Korea. Methods: Twenty-one novel simple sequence repeat (SSR) markers were developed from whole-genome sequence data and applied to analyze genetic variation in 120 individuals from 6 populations. Genetic diversity, differentiation, and gene flow were estimated using allele-frequency-based metrics, and population genetic structure was further evaluated using spatial information derived from geographic coordinates. Results: A total of 201 alleles were detected, with a mean polymorphism information content (PIC) of 0.759, indicating high marker informativeness. Mean genetic diversity across populations showed observed heterozygosity (Ho = 0.360) and expected heterozygosity (He = 0.281), while multilocus genotype ratios (G/N) ranged from 0.30 to 1.00 among populations. Genetic differentiation was substantial (FST = 0.373–0.669; Jost’s D = 0.540–0.997). Mantel tests revealed that genetic differentiation was significantly correlated with geographic distance (r = 0.67, p < 0.001). Both allele-frequency-based and spatially explicit approaches suggested genetic structuring among populations. Conclusions: The results suggest spatial tendencies in genetic structure among populations, reflecting patterns of allele distribution across regions. These findings provide baseline information on genetic variation in E. ussuriensis and may contribute to a better understanding of its ecological dynamics. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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17 pages, 2811 KB  
Article
Genetic Diversity and Phylogenetic Relationships Among Accessions of Pediomelum tenuiflorum (Pursh) A.N. Egan
by Cynthia O. Anukege, Mark Schoenbeck and P. Roxanne Kellar
Genes 2026, 17(4), 490; https://doi.org/10.3390/genes17040490 - 20 Apr 2026
Viewed by 688
Abstract
Background: Differentiating plant species is complex, complicated by morphological similarities that confound species’ delineation. For hundreds of years, researchers have used herbarium specimens to study plant morphology, and over the last forty years, these samples have also served as material for molecular phylogenetic [...] Read more.
Background: Differentiating plant species is complex, complicated by morphological similarities that confound species’ delineation. For hundreds of years, researchers have used herbarium specimens to study plant morphology, and over the last forty years, these samples have also served as material for molecular phylogenetic research. Taxonomists have alternately split and combined morphotypes of Pediomelum tenuiflorum for two centuries. With samples of P. tenuiflorum from across its distribution, this research aimed to (1) infer a robust phylogeny using molecular data, i.e., gene sequences from chloroplast and nuclear genomes; (2) assess genetic diversity using molecular markers, specifically Inter Simple Sequence Repeats (ISSRs); (3) provide evidence to support the taxonomic placement and possible splitting of P. tenuiflorum; and (4) identify consistent morphological characteristics using a correlation matrix to distinguish among the morphotypes. Results: Striking morphological differences among the individuals of P. tenuiflorum from across the species’ distribution resulted in more than two morphotypes. Phylogenetic data suggest hybridization is occurring among genetically and morphologically distinct members of P. tenuiflorum and with other species in the genus Pediomelum, whereas ISSR results indicate detectable genetic variation but do not resolve discrete clusters. This study reports the first ISSR markers used to assess genetic diversity in Pediomelum species. Conclusions: Morphological and genetic variation exist across individuals of P. tenuiflorum but not in monophyletic groups that support splitting the morphotypes into multiple species. Future investigations into chromosome numbers might reveal polyploidization in the lineage, and phylogenies estimated from low-copy nuclear genes could elucidate hybridization pathways. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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21 pages, 3289 KB  
Article
Genetic Interrelationship Among Newly-Bred Mutant Lines of Wheat Using Diagnostic Simple Sequence Repeat Markers and Phenotypic Traits Under Drought
by Athenkosi Makebe, Hussein Shimelis and Jacob Mashilo
Genes 2025, 16(10), 1210; https://doi.org/10.3390/genes16101210 - 14 Oct 2025
Cited by 1 | Viewed by 1166
Abstract
Background/Objectives: Induced mutagenesis is vital in genetic enhancement and trait discovery, for genetic analysis and breeding of novel crop varieties with desirable product profiles. Understanding the genetic relationships among newly developed mutant genotypes enables targeted selection and genetic recombination. Therefore, the objective of [...] Read more.
Background/Objectives: Induced mutagenesis is vital in genetic enhancement and trait discovery, for genetic analysis and breeding of novel crop varieties with desirable product profiles. Understanding the genetic relationships among newly developed mutant genotypes enables targeted selection and genetic recombination. Therefore, the objective of the current study was to assess the genetic diversity among mutant bread wheat genotypes developed through ethyl methanesulfonate (EMS) mutagenesis using phenotypic traits and diagnostic simple sequence repeat (SSR) markers to identify novel mutants and traits for breeding. Methods: Sixteen advanced (M6) mutant lines, one parental genotype, and three check varieties were genetically profiled using ten diagnostic SSR markers. The genotypes were evaluated for agronomic traits under drought-stressed (DS) and non-stressed (NS) conditions using a 10 × 2 alpha lattice design with two replications. Results: The SSR markers revealed a total of 21 alleles, with an average of 2.10 alleles per locus. An average polymorphic information content (PIC) of 0.51 was computed, revealing moderate informativeness of the genetic markers. Significant (p < 0.05) differences were observed among the test genotypes for key agronomic traits under NS and DS conditions. Grain yield positively and significantly (p < 0.001) correlated with plant height (r = 0.79), number of productive tillers (r = 0.82), root biomass (r = 0.77), shoot biomass (r = 0.74), spike length (r = 0.74), total biomass (r = 0.74), and thousand-seed weight (r = 0.64), under DS conditions. Principal component analysis explained 78.03 and 87.14% genotype variation for assessed agronomic traits under DS and NS conditions, with total biomass, shoot biomass, root biomass, productive tiller, plant height and grain yield as key traits contributing the most variation in the test genotypes. Conclusions: Wheat mutants LMA16, LMA44, and LMA53 were identified as genetically distinct and high yielders under drought stress conditions and recommended for production in rain-fed environments. The selected mutants are a valuable source of genes for wheat improvement programs. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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10 pages, 2899 KB  
Article
Genetic Characterization of Wild Soybean Collected from Zhejiang Province in China
by Xiaomin Yu, Xujun Fu, Qinghua Yang, Hangxia Jin and Longming Zhu
Genes 2025, 16(7), 776; https://doi.org/10.3390/genes16070776 - 30 Jun 2025
Viewed by 1191
Abstract
Background/Objectives: Wild soybean could grow in different soil types and under diverse climate conditions, which provides rich genetic resources in the locality. It is important to understand the genetic diversity as well as phenotypic variation for soybean breeding. The objective of this [...] Read more.
Background/Objectives: Wild soybean could grow in different soil types and under diverse climate conditions, which provides rich genetic resources in the locality. It is important to understand the genetic diversity as well as phenotypic variation for soybean breeding. The objective of this study was to analyze the genetic and phenotypic characteristics of 96 wild soybean accessions collected in Zhejiang Province, and to explore the potential advantage of germplasm resources for further application. Methods: These 96 annual type soybean resources have been propagated, identified and evaluated in both 2022 and 2023. In addition, their agronomic, quality and genetic traits have been characterized. Results: Most of the accessions exhibited sooty seed coats with different stem and leaf shapes. The means of seed protein and oil contents were 45.4% and 10.0%, respectively. There were significant differences in both protein and oil contents based upon the seed size. The average number of alleles per loci was 3.96, and the average PIC value was 0.619. The 96 accessions were clustered into three different groups. Each group had a consistency with both the geographical sources and the seed quality traits. Conclusions: There were agronomic, quality and genetic variations of these wild soybean accessions by the comprehensive analyses. This study gave us a combined understanding of both phenotypic variation and genetic diversity of wild soybean accessions in Zhejiang. Therefore, both reasonable exchanging and crossing between different soybean types is highly recommended. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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Review

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19 pages, 1757 KB  
Review
Integrative Assessment of Evidence for Anagenetic Speciation in Ulleungdo Endemic Plants: Plastid, Nuclear, and Morphological Perspectives
by Sajid Ali and Adnan Amin
Genes 2026, 17(9), 1109; https://doi.org/10.3390/genes17091109 - 12 Sep 2026
Viewed by 120
Abstract
Ulleungdo Island harbors several endemic plant lineages commonly interpreted as products of anagenetic speciation following long-distance colonization. Yet plastome phylogenies represent a single organellar genealogy and may conflict with nuclear genomic structure, morphology, or taxonomic boundaries. This critical mini-review evaluates whether plastid-based hypotheses [...] Read more.
Ulleungdo Island harbors several endemic plant lineages commonly interpreted as products of anagenetic speciation following long-distance colonization. Yet plastome phylogenies represent a single organellar genealogy and may conflict with nuclear genomic structure, morphology, or taxonomic boundaries. This critical mini-review evaluates whether plastid-based hypotheses for the origin and diversification of Ulleungdo endemics are supported by independent molecular and phenotypic evidence. We synthesize findings from comparative plastomics, chloroplast haplotype and network analyses, nuclear microsatellites, nrDNA sequencing, genome-wide multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) single-nucleotide polymorphisms (SNP), cytogenetics, morphology, and multicompartment phylogenomics. The evidence reveals heterogeneous evolutionary outcomes. Prunus takesimensis and Phedimus takesimensis are broadly consistent with probable single-origin scenarios, although confidence is constrained by progenitor sampling and marker resolution. Rubus takesimensis exhibits chloroplast non-monophyly and elevated haplotype diversity consistent with multiple maternal origins, whereas Acer takesimense shows signatures of historical drift and loss of rare nuclear alleles. Morphological, chromosomal, plastid, and nuclear–ribosomal evidence strongly support Allium ulleungense, while the delimitation of Viola ulleungdoensis remains unresolved. Plastid–nuclear incongruence in Hepatica maxima and Fagus multinervis further indicates that introgression, hybridization, incomplete lineage sorting, and restricted taxon sampling can complicate evolutionary inference. This comparative framework distinguishes species histories from provisional interpretations based on limited accessions or uniparentally inherited markers. The novelty of this review lies in its cross-taxon assessment of plastome–nuclear–morphological congruence rather than a descriptive plastome inventory. Ulleungdo lineages interpreted as products of anagenetic speciation do not exhibit a uniform genomic signature and that robust taxonomic, evolutionary, and conservation inference requires population-level integration of independently inherited genomic compartments with standardized morphological and reproductive data. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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Other

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31 pages, 1676 KB  
Systematic Review
Phenotypic Diversity in Maize Landraces: A Systematic Review of Global Patterns, Methodological Approaches, and Implications for Breeding
by Suwilanji Nanyangwe, Arsenio Daniel Ndeve, Pedro Fato, Paulino Munisse, Kolawole Peter Oladiran, Constantino Francisco Lhamine and Mable Chebichii Kipkoech
Genes 2026, 17(4), 413; https://doi.org/10.3390/genes17040413 - 31 Mar 2026
Viewed by 2006
Abstract
Background/Objective: Maize (Zea mays L.) is a globally important cereal crop widely cultivated for food, feed, fodder, biofuel production, and various industrial applications. Maize landraces represent a valuable source of genetic diversity that supports adaptationand resilience across diverse agroecological environments. However, evidence [...] Read more.
Background/Objective: Maize (Zea mays L.) is a globally important cereal crop widely cultivated for food, feed, fodder, biofuel production, and various industrial applications. Maize landraces represent a valuable source of genetic diversity that supports adaptationand resilience across diverse agroecological environments. However, evidence on phenotypic diversity based on agro-morphological traits in these landraces remains fragmented across regions and varying analytical approaches. This review synthesized global evidence on phenotypic variation, heritability patterns, experimental designs, statistical methods, and the extent of integration between phenotypic and molecular data. Methods: A systematic literature search was conducted in GoogleScholar, ScienceDirect, PubMed and AGRIS for studies published between 2000 and 2025 evaluating phenotypic diversity in maize landraces. The review followed PRISMA 2020 guidelines, and f50 studies from 30 countries met the eligibility criteria. Results: Substantial and structured phenotypic diversity was consistently reported across studies, with flowering time, plant architecture, and ear and kernel traits emerging as major contributors to landrace differentiation. Traits with moderate to high heritability were mainly morphological and phenological, suggesting relative genetic control and potential suitability for phenotypic selection. In contrast, grain yield showed greater environmental sensitivity and variable heritability, reflecting complex inheritance and genotype × environment interactions. Although molecular markers were incorporated in a some studies, integrative analyses linking phenotypic and genetic data remained limited. Conclusions: Phenotypic evaluation remains a reliable approach for characterizing maize landrace diversity. However, standardized methodologies, greater integration with molecular data and cross-environment validation are needed to strengthen inference and utilization in breeding and conservation. The review also provides recommendations for improving agro-morphological assessment in maize landraces. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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25 pages, 3767 KB  
Systematic Review
The Genetic Diversity of African Common Bean Germplasm: A Systematic Review of Reported Molecular Studies
by Tatenda Ephraim Chikasha, Rogerio Marcos Chiulele, Wilson Nkhata and Bernado Lazaro Muatinte
Genes 2026, 17(1), 75; https://doi.org/10.3390/genes17010075 - 9 Jan 2026
Cited by 1 | Viewed by 1741
Abstract
Background: Common bean (Phaseolus vulgaris L.) is an important grain legume crop of nutritional and economic value across Africa. Genetic improvements of the crop to enhance productivity and resilience depend on understanding the diversity within the African germplasm. Methods: Following [...] Read more.
Background: Common bean (Phaseolus vulgaris L.) is an important grain legume crop of nutritional and economic value across Africa. Genetic improvements of the crop to enhance productivity and resilience depend on understanding the diversity within the African germplasm. Methods: Following PRISMA guidelines, the genetic diversity and population structure of common bean in Africa were reviewed systematically based on existing research. A protocol for conducting the systematic review was developed registered in OSF. Twenty-nine studies met the inclusion criteria after a comprehensive search in ScienceDirect, PubMed, Google Scholar, PubMed, AGRICOLA, Taylor & Francis, and SpringerLink. Data on molecular markers and diversity metrics, thus PIC, He, and AMOVA, were extracted and synthesized qualitatively. Results: Despite substantial heterogeneity in panel sizes, reporting completeness, and marker systems (SSR, SNP, POX, ISSR), consistent patterns emerged. Studies revealed moderate to high levels of genetic diversity. Population-structure analyses recovered the canonical Andean and Mesoamerican gene pools with extensive admixture and high gene flow. AMOVA results indicated that a substantial proportion of total genetic variation was attributed to within-population components. Conclusions: The results are consistent with previous studies, but the sample size and types of markers make direct comparisons impossible. More future studies should use standardized genotyping approaches to increase data consistency. These insights are useful for yield improvement under both non-stress and stress conditions and for developing Africa’s diverse environments. Full article
(This article belongs to the Special Issue Genetic and Morphological Diversity in Plants)
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