The research, led by Dalia Youssef El-Berawey of the University of Alexandria together with colleagues from the university’s Faculty of Education and Faculty of Science, focused on four widespread native species: prickly lettuce (Lactuca serriola), London rocket (Sisymbrium irio), nettle-leaved goosefoot (Chenopodium murale), and swallow-wort (Cynanchum acutum). These plants were not chosen at random. All four thrive in disturbed, degraded habitats and are known to tolerate harsh growing conditions, making them natural candidates for phytoremediation — the use of plants to extract, stabilize, or detoxify pollutants from soil and water. Unlike conventional remediation techniques, which rely on excavation, chemical washing, or landfilling of contaminated earth, phytoremediation is inexpensive, solar-powered, and environmentally benign, though its success depends entirely on selecting the right plant for the right pollutant.

To identify those candidates, the researchers sampled both soils and plants from industrial locations that they classified into two categories: low-pollution and highly polluted sites. Soil and plant tissues were analyzed for three of the most problematic metals — cadmium, lead, and copper — establishing a gradient of exposure across the study sites. The team then measured a suite of biochemical indicators in the plant tissues, including soluble sugars, proteins, secondary metabolites, total phenolics, malondialdehyde (MDA), and hydrogen peroxide (H2O2). Each of these molecules tells a story about stress. Hydrogen peroxide and MDA, for example, are classic signatures of oxidative damage: when heavy metals interfere with cellular metabolism, plants produce reactive oxygen species that attack membranes and proteins, and MDA accumulates as a byproduct of that lipid peroxidation.

The results showed a clear and consistent pattern. In the heavily polluted areas, all four species exhibited elevated levels of soluble sugars, proteins, hydrogen peroxide, MDA, and secondary metabolites compared with plants growing in less contaminated soil. Rising sugar and protein content reflects the plants’ attempt to fuel repair mechanisms and maintain osmotic balance under stress, while the surge in secondary metabolites points to an intensified antioxidant arsenal. The increase in H2O2 and MDA confirms that even these hardy weeds were experiencing genuine oxidative stress at the most contaminated sites — they were not immune to the toxicity, but they were actively fighting it. This combination of damage markers and defense responses provides a physiological portrait of plants pushed to their metabolic limits yet still functioning.

One of the most intriguing findings concerned total phenolic compounds, which displayed a unique interaction between plant species and location. Cynanchum acutum, the vigorous vine sometimes regarded as an invasive weed, responded to severe contamination with what the authors describe as hyper-stress phenolic accumulation — a massive surge in these antioxidant compounds to cope with the toxicity. Chenopodium murale, by contrast, maintained a balanced phenolic level while preserving the integrity of its genome. This divergence suggests two distinct survival strategies: one species throws overwhelming chemical defenses at the problem, while the other appears to buffer the stress more gently, avoiding both runaway oxidative damage and genetic injury. Understanding these strategies matters because a plant that keeps its genome stable under pollution pressure is more likely to grow, reproduce, and accumulate metals reliably across seasons.

That genetic dimension is where the study becomes particularly novel. Beyond the biochemical assays, the team employed two molecular marker systems — inter simple sequence repeats (ISSR) and start codon targeted (SCoT) markers — to probe the plants’ DNA directly. These polymerase chain reaction-based techniques generate banding patterns that reveal genetic variation and, crucially, detect DNA damage caused by environmental stress. From the marker profiles, the researchers calculated genomic template stability (GTS), a measure of how much the DNA banding pattern of stressed plants deviates from that of unstressed references. A high GTS means the genome has remained essentially intact; a low GTS signals genotoxic damage, with altered or lost bands reflecting mutations, rearrangements, or strand breaks induced by metal exposure.

The molecular data added a decisive layer to the physiological picture. While all species showed biochemical signs of stress in the highly polluted sites, Chenopodium murale stood out for maintaining genomic stability alongside its balanced phenolic profile. This is significant because DNA damage in a remediating plant can compromise growth and seed production, undermining the long-term viability of a phytoremediation program. A species that can tolerate heavy metals without suffering genetic erosion offers both immediate cleanup capacity and the resilience to persist across generations. The ISSR and SCoT markers thus serve a dual purpose: they act as sensitive biosensors of pollution-induced genotoxicity, and they help identify which plants possess the underlying genetic robustness needed for sustained field deployment.

Synthesizing the physiological, biochemical, and molecular evidence, the authors conclude that two of the four species demonstrate superior potential for phytoremediation: Cynanchum acutum and Chenopodium murale. Cynanchum’s aggressive phenolic response and robust growth habit suggest it can withstand and perhaps sequester high metal loads, while Chenopodium’s combination of stress tolerance and genomic stability makes it an exceptionally reliable candidate. The finding aligns with earlier field evidence from other regions — including studies in Pakistan that identified Chenopodium murale as a promising cadmium accumulator — and reinforces a growing consensus that native weeds, often dismissed as agricultural nuisances, may be among the most practical tools for restoring contaminated land in resource-limited settings.

The implications extend beyond Egypt. Rapid industrialization across many emerging economies has outpaced environmental regulation, leaving a legacy of metal-contaminated soils that conventional cleanup cannot afford to address at scale. Phytoremediation with locally adapted native species offers a low-cost alternative that also restores vegetation cover, prevents erosion, and can be combined with careful harvesting and disposal of metal-laden biomass. The Egyptian study’s integrated approach — pairing classic stress biochemistry with modern DNA markers — provides a template other researchers can follow to screen regional floras quickly and rigorously, identifying the plants best suited to each pollution profile before committing to large-scale restoration projects.

There remain important caveats and next steps. The authors themselves emphasize that Cynanchum acutum and Chenopodium murale warrant further investigation for ecological restoration, and field-scale trials will be needed to confirm accumulation rates, biomass yields, and safe disposal of contaminated plant material. Questions about whether these species hyperaccumulate metals or merely stabilize them in their roots, and how their performance varies with soil chemistry and climate, remain open. Still, the study delivers a compelling message: the solution to industrial pollution may already be growing in the contaminated soil itself. By listening to the molecular signals of these unassuming weeds, scientists are learning which plants can turn toxic ground into living, self-repairing landscape — a quiet revolution in green technology rooted in some of nature’s most persistent survivors.

Subject of Research: Phytoremediation potential of native plant species under heavy metal stress assessed through physiological and ISSR/SCoT molecular markers

Article Title: Heavy metal stress in native plant species: investigating phytoremediation potential through physiological and ISSR/SCoT molecular assessments

Article References: El-Berawey, D. Y., Nouby, A. E., Megahed, S. M., & Fawzy, E. E. (2026). Heavy metal stress in native plant species: investigating phytoremediation potential through physiological and ISSR/SCoT molecular assessments. Environmental Science and Pollution Research, 33(30), 15728-15742. https://doi.org/10.1007/s11356-026-38207-8

Image Credits: AI Generated

DOI: 10.1007/s11356-026-38207-8

Keywords: phytoremediation, heavy metals, Chenopodium murale, Cynanchum acutum, ISSR markers, SCoT markers, genomic template stability, oxidative stress, cadmium, lead, copper, soil pollution

The team used inter-simple sequence repeat markers, known as ISSR markers, to probe the genomes of the collected trees. ISSR markers target short repeated DNA sequences scattered throughout the genome, amplifying the stretches between them to produce a fingerprint of bands that can be compared across individuals. Because these microsatellite-flanking regions mutate relatively quickly, ISSR markers are sensitive tools for detecting variation even among closely related cultivars of the same crop. In this study, 14 ISSR primers generated 214 scorable bands across the 93 cultivars, and a striking 184 of those bands, or 85.98 percent, were polymorphic, meaning they differed among at least some of the trees sampled.

Those numbers translate into exceptionally high genetic diversity for a cultivated fruit tree. The researchers calculated a resolving power of 8.00 for their marker set, a Nei’s gene diversity index of 0.34, a polymorphism information content of 0.52, and a Shannon information index of 0.34. Each of these metrics describes a different facet of variation, from how well the markers distinguish individual genotypes to how much uncertainty remains when guessing the genetic makeup of a randomly chosen tree. A PIC value above 0.5 is generally considered highly informative, indicating that the ISSR system captured substantial discriminating power across the Moroccan fig collection.

Perhaps the most consequential finding came from the analysis of molecular variance, or AMOVA, a statistical framework that partitions genetic variation into components within and between groups. The results showed that 89 percent of the total genetic variation resided within groups of cultivars, while only 11 percent was found between groups. In practical terms, this means that a farmer’s orchard in one valley may contain nearly as much hidden genetic variation as an entire region hundreds of kilometers away. Traditional agroecosystems, where multiple varieties are grown side by side and exchanged informally among neighbors, appear to be incubators of diversity rather than mere repositories of it.

Cluster analysis reinforced this picture of diffuse, locally rich diversity. Using UPGMA, a hierarchical clustering method that groups genotypes according to overall band-sharing similarity, the researchers organized the 93 cultivars into five main groups. The edible female figs from the Beni Mellal-Khenifra region showed particularly high genetic dispersion, scattering across the clustering diagram rather than gathering into a tight regional cluster. That dispersion suggests extensive exchange of planting material, seedling selection by farmers, and possibly multiple historical introductions of fig germplasm into the region, which historically served as a crossroads for trans-Saharan trade routes.

The caprifigs told a very different story. Caprifigs are the male, inedible figs that produce pollen and host the tiny fig wasp, Blastophaga psenes, which pollinates female fig flowers in a symbiosis so ancient and so intimate that neither partner can reproduce without the other. In the study, caprifigs formed a distinct and homogeneous cluster regardless of where they had been collected, separating cleanly from the edible female cultivars. This clear genetic split mirrors the gynodioecious breeding system of Ficus carica, in which male and female functional forms are genetically differentiated, and it validates the use of molecular markers to distinguish caprifig germplasm for breeding and pollination management.

The significance of this work extends well beyond Morocco’s borders. The fig is one of the oldest domesticated fruit trees in the world, and its center of diversity lies in the Middle East and Mediterranean basin, with Morocco recognized as a rich secondary reservoir. Earlier studies using microsatellite and other marker systems have documented diversity in Turkish, Tunisian, Algerian, and Jordanian fig germplasm, and Moroccan collections have been characterized morphologically and with SSR markers in previous work. What this new study adds is a broad, marker-based survey that explicitly spans both the mountain agroecosystems of the Atlas and the desert oases of the south, two environments that impose very different pressures on the trees growing in them.

That environmental breadth matters for conservation planning. Oases are fragile systems threatened by water scarcity, salinization, and rural depopulation, while mountain terraces face their own pressures from land abandonment and climate shifts. When genetic variation is distributed mostly within rather than between sites, losing any single site erodes a meaningful slice of the species’ total diversity. The authors argue that their results underline the value of ISSR markers for conservation and breeding programs, providing a cost-effective way to identify unique genotypes, avoid duplicating accessions in germplasm collections, and select parents for crosses that maximize genetic gain in fruit quality, drought tolerance, or disease resistance.

The study also fits into a growing body of work by the same research group at Sultan Moulay Slimane University, which has applied ISSR markers to Moroccan walnuts, plums, apples, and the endemic resin spurge Euphorbia resinifera. Together with companion studies by Mardoume and colleagues on the sugar profiles, organic acids, antioxidant activity, and phenotypic variability of Moroccan figs, the molecular data sketch a crop that is not only genetically rich but also chemically and morphologically diverse. For breeders seeking climate-resilient cultivars, such multidimensional diversity is raw material that cannot be recreated once lost.

For now, the message from the oases and mountains of Morocco is a hopeful one: centuries of traditional farming have quietly assembled one of the most genetically diverse fig populations ever surveyed with molecular markers. The challenge ahead is to document and conserve that diversity before the agroecosystems that sustain it disappear. With 85.98 percent of their marker bands polymorphic and nearly nine-tenths of the variation locked within local groups, Moroccan figs demonstrate that the future of food security under global change may depend as much on the smallholdings of traditional farmers as on any high-tech gene bank.

Subject of Research: Genetic diversity of fig tree (Ficus carica) cultivars and caprifigs in Moroccan oases and Atlas regions assessed with ISSR molecular markers

Article Title: Genetic diversity of Caprifigs and female fig (Ficus carica) from Moroccan oases and Atlas Regions revealed by ISSR markers

Article References: Mardoume, I., Bouda, S., Khachtib, Y., Zaggoumi, H., Neg, I., Ait Bella, Y., & Haddioui, A. (2026). Genetic diversity of Caprifigs and female fig (Ficus carica) from Moroccan oases and Atlas Regions revealed by ISSR markers. Plant Biosystems, 160(4), Article 216. https://doi.org/10.1007/s44473-026-00221-6

Image Credits: AI Generated

DOI: 10.1007/s44473-026-00221-6

Keywords: Ficus carica, genetic diversity, ISSR markers, Morocco, caprifigs, oases, Atlas Mountains, AMOVA, agroecosystems, germplasm conservation, plant breeding, molecular markers

The research team, led by Abhishek Gupta and Baleshwar Meena of CSIR-National Botanical Research Institute in Lucknow, together with colleagues from Banaras Hindu University and the Academy of Scientific and Innovative Research, sampled seven natural populations comprising 71 individual plants across the Western Himalayan Region. Rather than relying on a single line of evidence, the researchers integrated molecular marker data with species distribution modelling, an approach that conservation biologists increasingly favour because it captures both the biological richness of populations and the environmental context in which that richness evolved. The work was supported by a grant from the Department of Science and Technology’s Science and Engineering Research Board.

At the molecular level, the team deployed two complementary marker systems: 22 inter-simple sequence repeat markers, known as ISSR, and 11 directed amplification of minisatellite DNA markers, abbreviated DAMD. Both techniques amplify variable regions scattered across the genome, providing a rapid and cost-effective snapshot of genetic variation without requiring prior knowledge of the species’ DNA sequence. Together, the 33 markers revealed a cumulative polymorphism of 75.90 percent across the sampled individuals, meaning that roughly three-quarters of the detected genetic loci showed more than one variant. That figure suggests the species retains a meaningful reservoir of genetic diversity in the region, even though its populations are scattered across steep, fragmented terrain.

That overall diversity, however, was not evenly distributed. Populations designated KOK, BDR, and TND exhibited relatively higher genetic diversity, while populations SNM, GMK, and UDP showed comparatively lower levels. This unevenness matters for conservation because populations with reduced genetic diversity are more vulnerable to disease, environmental stress, and inbreeding depression, and they carry less raw material for adaptation to changing conditions. The researchers also quantified how genetic variation is partitioned across the landscape. A coefficient of genetic differentiation, GST, of 0.35 indicated substantial differentiation among populations, while an estimated gene flow value, Nm, of 0.88 pointed to only moderate exchange of genes between them. An analysis of molecular variance, or AMOVA, sharpened the picture further: about 70 percent of the total genetic variation resides within populations, with the remaining 30 percent occurring among them.

To visualize how the populations relate to one another, the team applied three independent clustering approaches: UPGMA, a distance-based tree-building method; principal coordinate analysis, which compresses genetic distances into a two-dimensional map; and Bayesian clustering, a statistical framework that assigns individuals to genetic groups based on allele frequencies. All three methods converged on the same answer: the sampled junipers belong to two major genetic clusters. The agreement among methods strengthens confidence in the result, since each technique carries different assumptions and potential biases. For conservation planners, the existence of two distinct clusters means that protecting representatives of both lineages is essential to preserve the full breadth of evolutionary heritage in the region.

The study went a step further by embedding the genetic data in a landscape context. Landscape genetics analysis supported isolation by distance as the primary driver of genetic differentiation, meaning that populations separated by greater geographic distances are also more genetically distinct, most likely because pollen and seed dispersal are limited over long distances in this rugged environment. Crucially, the analysis also identified potential dispersal corridors linking populations, pathways through the mountain landscape where gene flow could plausibly occur. These corridors offer a practical blueprint for conservation: maintaining or restoring connectivity along them could help counteract the genetic isolation that threatens small, fragmented populations.

On the environmental side, the researchers used ecological niche modelling to map where the species finds suitable habitat today and where it might persist in the future. The models identified four principal environmental determinants of the species’ distribution: precipitation of the driest month, elevation, isothermality, which measures how stable day-to-night temperatures are relative to seasonal variation, and the mean temperature of the wettest quarter. In plain terms, the alpine juniper depends on a delicate combination of winter-dry conditions, high altitude, and moderate thermal variability, precisely the conditions that climate change is expected to disrupt most rapidly in mountain systems, where species often have nowhere higher to go.

The projections are sobering. Under current climate conditions, the model estimates roughly 64,568 square kilometres of climatically suitable habitat across the region. When the models were projected onto future climate scenarios for the years 2060 and 2080, that suitable area declined, indicating an increased risk of habitat contraction. For a species already exhibiting high genetic differentiation and limited gene flow, shrinking habitat could trap populations on ever-smaller mountaintop islands, accelerating the loss of genetic diversity and raising local extinction risk. The findings echo a broader pattern documented for montane juniper species elsewhere in Asia, where endemic mountain conifers face elevated extinction risk under warming scenarios.

What makes this study valuable is not any single number but the convergence of evidence. The genetics reveal which populations are genetically rich and which are vulnerable; the niche models reveal where habitat is secure and where it is slipping away; and the landscape analysis reveals where corridors could reconnect fragmented populations. Together, these threads give conservation managers a prioritized action list: protect the genetically diverse populations at KOK, BDR, and TND as reservoirs of adaptive potential, closely monitor the low-diversity populations at SNM, GMK, and UDP, and safeguard the climatically suitable habitats identified by the models, particularly those that overlap with dispersal corridors.

The stakes extend beyond a single shrub. Juniperus communis has a long history of medicinal use, and its essential oils have been studied for antioxidant, antimicrobial, and neuroprotective properties, with prior work by members of the same research group documenting chemical variability among the western Himalayan populations. As a dominant element of alpine vegetation, the species also stabilizes soils and shelters other high-altitude organisms. Losing its genetic diversity would mean losing options, for ecosystem resilience, for future phytochemical discovery, and for the species’ own capacity to adapt. The study’s authors frame their results as a scientific basis for conservation prioritization in the western Himalaya, and in an era of rapid mountain warming, that basis could not have arrived at a more urgent moment.

Subject of Research: Population genetics and ecological niche modelling of common juniper in the western Himalaya

Article Title: Integrative analysis of population genetics and ecological niche modelling of common juniper (Juniperus communis L. var. saxatilis Pall.) in the western Himalaya, India

Article References: Gupta, A., Singh, H. C., Wairokpam, B., Singh, L. A., Dwivedy, A. K., Rana, T. S., & Meena, B. (2026). Integrative analysis of population genetics and ecological niche modelling of common juniper (Juniperus communis L. var. saxatilis Pall.) in the western Himalaya, India. 3 Biotech, 16(9), Article 403. https://doi.org/10.1007/s13205-026-05023-3

Image Credits: AI Generated

DOI: 10.1007/s13205-026-05023-3

Keywords: Juniperus communis, population genetics, ecological niche modelling, western Himalaya, ISSR markers, DAMD markers, genetic diversity, climate change, habitat suitability, conservation genetics, gene flow, alpine plants

The fieldwork relied on an augmented block design, a statistical layout that allows large numbers of genetically distinct accessions to be evaluated even when seed or planting material is limited. The researchers scored 20 morphological descriptors covering traits that farmers and consumers actually notice: leaf shape and colour, stem pigmentation, petiole characteristics and the colour patterns of the flowering shoots. Every one of the 20 traits showed a wide range of variation across the collection. Some of what the team found was genuinely unusual. Alongside the familiar green-leaved types, the germplasm included novel leaf shapes, stems in white and pink, striking petiole pigmentation and distinct inflorescence colour patterns that had not previously been catalogued in Indian material at this scale.

To quantify that visual diversity, the team turned to the Shannon-Weaver index, a measure borrowed from information theory that ecologists and geneticists use to describe how evenly traits are distributed within a collection. Values in the study ranged from 0.00, meaning no variation at a given descriptor, to 1.48, indicating near-maximal diversity for a trait scored across many categories. Eleven of the traits showed statistically significant morphological variation, confirming that the apparent visual differences among accessions were not random noise but genuine, heritable diversity. For breeders, such qualitative descriptors matter because they are easy to score in the field, they often mark traits with market value, and they can serve as anchors when distinguishing varieties for registration and protection.

Morphology alone, however, can be misleading. Visible traits are shaped by environment as much as by genes, and closely related plants can look alike while carrying very different DNA. So the team profiled the same 96 genotypes with two classes of molecular markers: inter-simple sequence repeats, or ISSRs, and simple sequence repeats, or SSRs. Both target the short, tandemly repeated DNA motifs scattered through plant genomes. ISSR markers use a single primer designed to anchor on one microsatellite and amplify the stretch of DNA between neighbouring repeats, producing dominant fingerprints. SSR markers, by contrast, amplify specific microsatellite loci flanked by known sequences, and because they are co-dominant they can distinguish homozygotes from heterozygotes. Of the 13 ISSR primers tested, six proved polymorphic, and of the 22 SSR markers screened, nine were polymorphic, giving the researchers a solid panel for comparing genotypes across the collection.

The molecular data told a story that the field observations alone could not. Within individual populations, genetic diversity was low, with an expected heterozygosity among subpopulations, denoted Hs, of just 0.15. But when diversity was measured across the whole set of populations, total genetic diversity, Ht, rose to 0.26. That gap is the signature of strong population structuring: the variation exists, but it is partitioned among groups rather than mixed within them. A differentiation statistic, Gst, of 0.42 confirmed moderate-to-high separation between populations, and an estimated gene flow, Nm, of only 0.34 indicated that alleles rarely move from one group to another. In practical terms, the Indian amaranth collection is not a single blended pool but a set of partially isolated lineages, each carrying its own slice of the species’ genetic heritage.

Two complementary ordination and clustering approaches reinforced that picture. Principal coordinate analysis, which compresses pairwise genetic distances into a few visual axes, revealed substantial overall variation, partial clustering of accessions from the same populations and clear evidence of admixture, meaning some genotypes carry ancestry from more than one group. Marker-based clustering then divided the entire collection into five clusters, while a formal population structure analysis, of the kind pioneered by Pritchard and colleagues, identified four admixed subpopulations. The fact that different methods converged on a similar number of groups, while still detecting individuals of mixed ancestry, suggests the structure is real but porous, the result of historical seed exchange, overlapping cultivation and the outcrossing tendencies of the genus.

Why does this matter beyond the herbarium and the molecular lab? Amaranth is a nutritional powerhouse. Its leaves are rich in iron, calcium and vitamins, and the grain types produce gluten-free seeds with an unusually high lysine content, an essential amino acid that cereals typically lack. Reviews have described amaranth as a new-millennium crop of nutraceutical value, and interest in it is growing as consumers seek resilient, nutrient-dense foods. Yet crop improvement depends on having genetically distinct parental lines to cross. If all breeding material derives from a narrow genetic base, gains from selection stall and vulnerability to pests and diseases rises. The new study demonstrates that Indian germplasm contains exactly the kind of structured, exploitable variation that breeding programmes need.

The population structure revealed by the markers offers a practical roadmap. Breeders selecting parents for crossing schemes can now choose lines from different clusters or subpopulations to maximise heterosis, the hybrid vigour that often appears when divergent lineages are combined. Conversely, the low gene flow estimate warns that desirable alleles confined to one group will not spread on their own; deliberate introgression will be required. The rare phenotypes documented in the field, from pink stems to novel leaf shapes, could serve as visible markers in breeding programmes aimed at ornamental or specialty markets, while the quantitative diversity indices identify which descriptors are most informative for future germplasm characterisation.

The study also adds to a growing global literature on amaranth genetics. Earlier work had used ISSR markers to assess grain amaranth in India, SSR markers to profile core collections and single nucleotide polymorphisms to study Peruvian amaranth landraces. What distinguishes the new analysis is its dual approach at scale, pairing a full suite of morphological descriptors with both ISSR and SSR panels on a single large collection, and its focus on India, the crop’s centre of diversity. The work formed part of a doctoral programme at the Varanasi institute and was supported by the Indian Council of Agricultural Research, reflecting a broader national effort to characterise and conserve underutilised vegetable crops before their wild and traditional diversity erodes.

For a genus that includes both cherished vegetables and notorious weeds, the message of this study is that amaranth’s genetic resources are neither uniform nor random. They are organised into discernible populations, laced with rare and beautiful phenotypes, and accessible to any breeder with the right markers and crossing plan. As climate stress pushes farmers toward hardy, fast-growing greens, the structured diversity documented across these 96 Indian genotypes may prove to be one of the most valuable untapped assets in the vegetable world, waiting in plain sight in fields and markets across the subcontinent.

Subject of Research: Genetic diversity characterization of Indian Amaranthus germplasm using morphological descriptors and ISSR and SSR molecular markers

Article Title: Characterization of Genetic Diversity in Amaranthus Species Using Morpho-Molecular Markers

Article References: Sharma, A. K., Sagar, V., Dwivedi, S. V., Devi, J., Neetu, Tiwari, S. K., Singh, S. K., Rai, N., Kumar, R., & Behera, T. K. (2026). Characterization of Genetic Diversity in Amaranthus Species Using Morpho-Molecular Markers. Indian Journal of Genetics and Plant Breeding, 86(2), 224-240. https://doi.org/10.1007/s44489-026-00011-6

Image Credits: AI Generated

DOI: 10.1007/s44489-026-00011-6

Keywords: Amaranthus, genetic diversity, germplasm, ISSR markers, SSR markers, population structure, plant breeding, leafy vegetable, morphological descriptors, Shannon-Weaver index, India, crop improvement

Researchers at the National Horticultural Research Institute (NIHORT) in Ibadan set out to assess the genetic diversity of fifteen avocado accessions conserved in the institute’s genebank. The seeds behind these accessions were originally collected from smallholder farmers across four states in south-eastern Nigeria — Imo, Enugu, Anambra and Abia — during successive collection missions, and were registered with NIHORT accession numbers upon entry into the genebank. Because avocado is highly heterozygous and predominantly outcrossing, with a protogynous–protandrous flowering system that promotes cross-pollination, the seedlings raised from these seeds represent open-pollinated half-sib progenies rather than clones of the maternal trees, and were treated as independent accessions in the analysis.

The team, led by Omolara I. Akinyoola and published in the journal Discover Plants, employed two complementary DNA marker systems: inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) markers. ISSR primers amplify DNA fragments lying between simple sequence repeats in the genome and require no prior knowledge of the species’ DNA sequence, making them accessible and inexpensive. SCoT markers, first developed in rice by Collard and Mackill, target regions surrounding the start codons of genes, giving them a functional bias that often makes them more informative. After a pilot screen of twenty ISSR and fifteen SCoT primers on three representative accessions, the researchers selected five primers of each type based on band clarity, polymorphism and reproducibility.

The laboratory work began with fresh young leaflets collected from the field and preserved in liquid nitrogen. Genomic DNA was extracted from approximately 100 milligrams of leaf tissue per accession using a modified CTAB protocol, in which polyvinylpyrrolidone and 2-mercaptoethanol were added to suppress polyphenols and oxidation, and the chloroform–isoamyl alcohol extraction step was repeated twice to remove residual protein and lipid. DNA was precipitated overnight with ice-cold isopropanol, washed with 70 percent ethanol and re-suspended in buffer containing RNase A. Quality checks on 1 percent agarose gels confirmed sharp, high-molecular-weight bands with no shearing, and Nanodrop spectrophotometry gave A260/A280 purity ratios between 1.80 and 2.00 before samples were diluted to a working concentration of 30 nanograms per microlitre.

Polymerase chain reactions were carried out in 25-microlitre volumes on an Applied Biosystems GeneAmp 9700 thermal cycler. ISSR amplification used a touchdown profile in which the annealing temperature dropped from 65 to 56 degrees Celsius over ten cycles before thirty standard cycles at 55 degrees, while SCoT amplification used thirty-five cycles with a 50-degree annealing temperature. Amplified fragments were separated on 2 percent agarose gels, visualised under ultraviolet transillumination and scored manually against a 50-base-pair ladder, with faint or ambiguous bands excluded. The convergence of results across two independent marker systems, and across multiple analysis platforms, provided a form of internal validation that strengthens confidence in the findings.

The results revealed a moderate but meaningful reservoir of variation. The ten loci detected a total of 41 polymorphic alleles, averaging 4.1 alleles per locus — higher than the 3.1 alleles per locus reported in a previous avocado study using EST-SSR primers. The polymorphism information content, a measure of a locus’s discriminating power, ranged from 0.509 to 0.825 with a mean of 0.654, and gene diversity averaged 0.708 across the ten loci. Genetic similarity coefficients between accessions ranged from 0.59 to 0.84. Notably, SCoT markers outperformed ISSR markers, generating a higher mean number of alleles per locus (4.4 versus 3.8) and higher mean PIC values (0.671 versus 0.637), leading the authors to recommend the combined use of both systems rather than either alone.

When the researchers clustered the accessions using the unweighted pair group method with arithmetic mean (UPGMA) on Jaccard dissimilarities, supported by 1000 bootstrap resamplings, the fifteen accessions split into two main clusters — one containing six accessions and the other nine — with membership broadly reflecting the south-eastern states of origin. A factorial coordinate analysis performed in DARwin software resolved four geographic groups along the first two factorial axes, with groups dominated respectively by accessions from Imo, Enugu and Anambra, while the single Abia accession stood apart. Some accessions, however, were interwoven between groups, a pattern the authors attribute to informal farmer-to-farmer seed exchange across state boundaries.

The most striking result came from the analysis of molecular variance. AMOVA partitioned 99.3 percent of the genetic variation within the UPGMA clusters and only 0.7 percent between them, with a Phi statistic of 0.007 that was statistically non-significant (P = 0.395, based on 9999 random permutations). Cross-validation in a second R package yielded an essentially identical result (P = 0.390), confirming the robustness of the partitioning. In other words, the two clusters represent dissimilarity gradients within a single, largely panmictic gene pool rather than genetically isolated subpopulations. The authors attribute this to two interacting forces: avocado’s strongly outcrossing reproductive biology, which maintains high heterozygosity within genotypes, and widespread informal seed exchange among smallholder farmers, which has homogenised allele frequencies across the sampled states.

The study is not without limitations, which the authors acknowledge candidly. The sample of fifteen accessions, while reflecting the current holdings of the NIHORT avocado germplasm at the time of sampling, is modest for inferring fine-scale population structure and limits the statistical power of subgroup analyses. Marker-trait associations were not pursued, and the dominant nature of ISSR and SCoT markers means each accession had to be treated as a single haploid genotype. Future work, the team suggests, should integrate SNP-based platforms such as genotyping-by-sequencing with phenotypic and biochemical fruit characterisation, to link the genetic variation documented here to agronomically relevant traits such as fruit quality, pest resistance and climate resilience.

Even so, the significance of the work extends well beyond a single genebank. Nigeria’s avocado industry is growing rapidly and holds considerable potential in the global market, but it faces threats from pests including the avocado lace bug, the Persea mite and the western avocado leaf roller, as well as diseases such as anthracnose and avocado black streak. The moderate diversity documented in the NIHORT collection provides a baseline molecular dataset for future curation, hybridisation and selection, and underscores a broader truth for crop science: genetic diversity is the raw currency of breeding, and knowing exactly what a genebank holds is the first step towards spending it wisely. The identified variation can now be deployed in breeding programmes aimed at developing better varieties with desirable traits, while the finding that most variation lies within rather than between geographic groupings offers a caution against assuming that provenance alone guarantees genetic distinctiveness in conserved germplasm.

Subject of Research: Genetic diversity assessment of avocado germplasm using ISSR and SCoT molecular markers

Article Title: Genetic diversity assessment of avocado (Persea americana Mill.) germplasm from NIHORT genebank

Article References: Akinyoola, O. I., Olagunju, Y. O., Matthew, J. O., Akin-Idowu, P. E., & Ajayi, E. O. (2026). Genetic diversity assessment of avocado (Persea americana Mill.) germplasm from NIHORT genebank. Discover Plants, 3(1), Article 414. https://doi.org/10.1007/s44372-026-00866-9

Image Credits: AI Generated

DOI: 10.1007/s44372-026-00866-9

Keywords: avocado, Persea americana, genetic diversity, ISSR markers, SCoT markers, germplasm, genebank, Nigeria, NIHORT, molecular markers, AMOVA, plant breeding