Integrating herbgenomics with systems biology approaches for sustainable utilization of medicinal plant resources.

Plant genetics can exert a strong effect on soil rhizosphere microbes. Broad-sense heritability estimates quantify the degree to which plant genotype predicts microbiome composition, enabling characterization of plant genotype effects on rhizosphere microbes. We used 16S rRNA and ITS marker gene sequencing data from rhizosphere soil from 95 field-grown sunflower (Helianthus annuus) inbred lines to test the heritability of archaeal, bacterial, and fungal rhizosphere communities, as well as alpha- and beta-diversity metrics and differences in the relative abundance of microbial zero-radius operational taxonomic units (ZOTUs). The majority of taxa passing prevalence and relative abundance cutoffs of 25% and 0.01% were heritable across all taxonomic levels for both prokaryotes (archaea and bacteria) and fungi, with higher heritabilities at finer taxonomic resolution. Metrics of alpha- and beta-diversity were also heritable, particularly for prokaryotes. Prokaryotic and fungal communities were both heritable, but there was significantly higher fungal heritability at the ZOTU, genus, and family levels. Prokaryotic and fungal richness were only weakly positively correlated, and beta-diversity was not correlated, suggesting that sunflower inbred lines affect prokaryotes and fungi in different ways. Our work provides valuable information for crop breeding and provides a general methodological framework for assessing the strength and types of genotype-microbial associations. Because of high heritability for individual microbial taxa as well as for microbial diversity metrics more broadly, sunflowers are clearly an important species to study the ecology, evolution, and genetics of plant-microbe interactions, and to use this knowledge to improve sustainability of the crop.

The genus Medicago, which includes the widely cultivated forage crop alfalfa, is of significant agricultural and ecological importance. Understanding genetic diversity in Medicago is essential for the conservation of its germplasm and its utilisation in plant breeding. This study aimed to assess the genetic diversity and population structure of the Medicago germplasm collection at the German Federal Ex situ Gene Bank. Genotyping-by-sequencing was used to analyse 1234 accessions of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), representing 40 Medicago species. After filtering, a high-quality dataset of 23,315 single nucleotide polymorphisms (SNPs) was generated. Our analyses revealed distinct genetic clusters corresponding to Medicago species and sections, with cultivated M. sativa L. and M. × varia Martyn clustering together with less genetic diversity compared to their wild counterparts. This reflects the shared genetic composition and extensive gene flow between M. sativa and M. × varia, commonly considered a hybrid between M. sativa and M. falcata L. Wild species displayed a more complex genetic structure, with polyphyletic patterns indicating higher genetic differentiation that reflects their diverse evolutionary histories and ecological adaptations. In conclusion, the comprehensive diversity analysis of the IPK Medicago collection provides valuable insights for gene bank management, targeted conservation efforts and strategic breeding initiatives.

The review highlights the main trends in the use of achievements in plant physiology in breeding and the contribution of scientists from the Institute of Plant Physiology and Genetics of the NAS of Ukraine to solving the problems of increasing plant productivity and stress resistance. In particular, as a result of many years of research into the genotypic features of morphology and functioning of the photosynthetic apparatus of a wide range of wheat varieties at the levels from chloroplast to agrocenosis, a number of physiological and morphological traits have been identified, which are recommended for use as phenotypic markers in the selection of this most important agricultural crop for productivity and drought resistance. A number of studies of the physiological and biochemical characteristics of genetically modified wheat plants with an increased proline content both under normal conditions and under the influence of drought were also conducted. A conclusion was made about the prospects of their involvement in breeding programs to increase resistance to abiotic stress factors. A wide range of highly effective strains of nodule bacteria, complementary to a number of leading legume crops, were selected, including using transposon mutagenesis. New technologies for their use in inoculums were developed, taking into account the genetic characteristics of the crop, which contribute to the maximum realization of the productivity potential of the legume-rhizobial symbiosis and protect against the negative effects of biotic and abiotic stress factors. Technologies for the use of mixtures of specially selected strains of associative and free-living nitrogen-fixing microorganisms to intensify the cultivation of various wheat varieties were also developed. It is known that in order to fully reveal the genetic potential of modern agricultural crops, it is necessary to develop new or significantly improve existing technologies for their cultivation and take care of protection against diseases, pests and weeds. Such technologies have been developed to increase the efficiency of nitrogen use by modern high-intensity wheat varieties. The use of tank mixtures for foliar feeding of plants together with protective agents and growth regulators has been scientifically substantiated and implemented in practice, which has a significant economic effect. Thus, plant physiologists and geneticists of the Institute closely cooperate both in fundamental scientific research and for the benefit of the agricultural sector of Ukraine and strengthening its food security.

The present study was undertaken to evaluate eleven green gram (Vigna radiata (L.) Wilczek) accessions to identify superior genotypes based on yield and key yield-associated traits. The experiment was conducted in the Experimental Field of Department of Plant Breeding and Genetics, College of Agriculture, Vellanikkara, Kerala Agricultural University, Thrissur, Kerala (10°32’11’’N and 76°16’43’’E and 97m above mean sea level) during June to August, 2024. The experiment was laid out in randomized complete block design with three replications. Significant genotypic correlations were observed between yield per plant and number of pods per plant, number of primary branches, number of clusters per plant, and pod length. Path coefficient analysis revealed that number of pods per plant and pod length exerted strong positive and direct effects on yield indicating their values as primary selection criteria. Superior accessions were identified by integrating yield performance with favourable trait expression. Results obtained from the two approaches were almost comparable. Among the different multivariate approaches examined for constructing a selection index, the PCA biplot proved particularly effective for visualizing trait relationships and discriminating high-performing accessions. The findings provide a practical framework for trait-based selection in green gram improvement programs.

As one of the flagship databases of the U.S. Department of Agriculture, GrainGenes is positioned at the critical juncture of agricultural data crossroads. GrainGenes (https://graingenes.org; https://wheat.pw.usda.gov) is a centralized location for curated data and web-based tools for wheat, barley, rye, and oat in the service of a global user base. Since 1992, GrainGenes has been serving plant researchers in their quest to improve traits, including biotic and abiotic resistance, as well as high nutrition content. Starting with genetic markers and maps, GrainGenes has evolved to acquire genomic sequences, assemblies, and annotations, leading to an ever-increasing number of pangenomes. Over the years, new web-based tools and capabilities were added to the website to increase the access and utility of peer-reviewed datasets for researchers, plant geneticists and breeders at various stages of their careers, from high school students to emeritus professors. Here we provide a comprehensive overview of the curated content and customized tools available in GrainGenes, whose resources are designed to benefit researchers, growers, and farmers in their efforts to develop more nutritious food for the growing human population and high-quality animal feed.

Microbes secrete structurally diverse secondary metabolites during plant infection, some of which are detected by plant cells, which trigger stress responses. In this method, the induction of ion leakage, peroxidase activity, and callose production is measured in the same leaf disk sample. First, Arabidopsis or barley leaf disks are vacuum infiltrated in a 96-well plate. After 4-6 hours, conductivity is measured, followed by peroxidase activity and callose deposition at 24 hours. The flg22 peptide induces all three responses and is an affordable positive control. Surfactin and gramillin cyclic lipopeptides induce peroxidase activity and ion leakage, respectively, while the phytotoxic T-2 trichothecene suppresses peroxidase activity. Overall, this approach enables multiple comparisons across either plant genotypes or metabolite treatments. This approach can be applied to chemical genetics or bioprotection to identify stress-modulating compounds for further study. In plant genetics, this approach can be used to compare responses across plant populations for genetic mapping and to improve our understanding of plant-microbe interactions.

Plant ribosomopathies: New insights and a critical re-evaluation of ribosomal protein gene mutants in plants.

Meiotic recombination and advances in quantitative trait locus mapping.

Understanding genetic variability and selection indices are the essentials for the program of rice improvement. This study assessed 80 genetically diverse rice (Oryza sativa L.) genotypes during Kharif 2021 at the Seed Breeding Farm, Department of Plant Breeding and Genetics, JNKVV, Jabalpur, India, arranged in a randomized complete block design with three replications. The significant (p < 0.01) differences were found in all the characters studied, which is an indication of the large genetic diversity in the experimental material. The phenological traits like days to 50% flowering (98.90 days) and days to maturity (125.98 days) showed that the tested genotypes covered the whole range of early to late maturity groups, while plant height had a broad range (67.36 to 149.78 cm). Likewise, considerable variation was recorded for yield‐related characters such as 1000‐grain weight (12.32 to 34.75 g), fertile spikelets per panicle (mean 173.25), and grain yield per plant, thus providing significant scope for selection. The comparison of PCV and GCV gave a hint of moderate to high variability for the majority of the traits, with characters related to spikelets, flag leaf traits, and yield components being the most influenced by the genotypic factors. Heritability in the broad sense was high for the majority of the traits, especially for flag leaf length (97.90%), total spikelets per panicle (97.20%), fertile spikelets per panicle (96.80%), and 1000‐grain weight (93.50%), indicating the dominance of additive gene effects. The genetic advance as a percentage of the mean was the highest for spikelet density (78.71%), total spikelets per panicle (66.05%), fertile spikelets per panicle (67.05%), and sterile spikelets per panicle (65.18%), thus demonstrating strong selection potential. The high heritability together with the high genetic advance for the most important traits such as spikelet density, 1000‐grain weight, and grain yield per plant, supported further the direct selection efficiency. The research has reconfirmed the large genetic variability and has pointed out the traits whose changes depend mainly on the additive gene effects; thus the traits are open for the improvement by simple genotypic selection. The results of this investigation shed light on trait inheritance and selection efficiency to a great extent, thereby they provide a lot of useful guidance in breeding high-yielding rice cultivars adapted to subtropical ecosystems.

The Green Revolution of the 20th century was largely sustained by the intensive application of synthetic nitrogen (N) fertilizers and phosphorus (P)-based fertilizers. However, the economic and environmental costs of this dependency are untenable in the long term, contributing significantly to greenhouse gas emissions, aquatic eutrophication, and soil degradation. In contrast, nature has evolved sophisticated plant-microbe symbioses, most notably legume-rhizobia interactions for biological nitrogen fixation (BNF) and arbuscular mycorrhizal (AM) fungi associations for phosphorus acquisition, which operate with high efficiency and minimal environmental impact. This review posits that the strategic engineering of these symbiotic systems represents the most promising pathway to developing the next generation of sustainable agricultural practices. We synthesize recent advances in our understanding of the molecular dialogues, genetic networks, and metabolic cross-talk that underpin these symbioses. A core focus is on the emerging strategies to "de-orphan" non-legume crops, such as cereals, by equipping them with the genetic machinery to initiate and maintain nitrogen-fixing nodules with rhizobia. Concurrently, we explore the engineering of enhanced phosphorus scavenging and uptake through the optimization of mycorrhizal associations and the plant's own P-starvation response (PSR) machinery. We discuss synthetic biology approaches, including the design of minimal genetic modules for symbiosis, the manipulation of phytohormone signaling, and the engineering of microbial communities (microbiomes) to create synergistic, beneficial consortia. Furthermore, we critically evaluate the challenges of ensuring the stability, efficiency, and field-level robustness of these engineered symbioses. By integrating insights from plant genetics, microbiology, and synthetic biology, this article charts a course toward a new era of agriculture where crops are empowered to harness atmospheric nitrogen and soil phosphorus through tailored symbiotic partnerships, drastically reducing the need for chemical inputs and enhancing global food security.

The Mediterranean Germplasm Gene Bank (MGG) of the CNR-IBBR in Bari (Italy) is the oldest gene bank of the Mediterranean area. Thanks to Vavilov, this area is considered an important gene centre. The first safeguarding activities of the MGG began in 1969 and continue today following traditional and innovative approaches. The strategy followed by the MGG for safeguarding plant genetic resources of Mediterranean origin and of agricultural interest is described in detail together with the activities and methods used. Some examples of rare agrobiodiversity discovered in the area are reported and described. The MGG seed collection (as ex situ conservation) contains about 59,000 accessions from 34 families, 208 genera and 872 species. Over 13,000 samples have been directly collected over time by exploration teams, while others have been acquired from 314 donor institutions through a seed exchange. MGG studies in the Mediterranean region show a severe genetic erosion of about 75%. The approach adopted by the CNR-IBBR research group to combat this phenomenon can be broken down into two main areas. Firstly, new collecting missions could secure still available valuable material as old landraces cultivated in the fields and gardens of less anthropized areas; the considerable experience and knowledge acquired over the span of five decades, accumulated through this endeavour, undoubtedly plays a pivotal role. Moreover, the integration of conservation methods, ex situ and on farm, for cultivated material, and predominantly in situ for wild species, is necessary for the sustainable development and use of Mediterranean plant genetics resources. In pursuit of this objective, the international standing of the MGG and its extensive network of collaborations represent a foundational element.

Cutting-edge nanotechnology in plant physiology and genetics

The current study was carried out to find the better performing and widely adapted lines of pea (Pisum sativum L.) using multi-location trials at four diverse locations spanning central, northern, and southern Punjab, Pakistan. A total of 103 genotypes were collected from the gene pool of the Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, and the Vegetable Research Institute, Faisalabad including commonly commercially cultivated varieties. This research focused on selecting pea genotypes that combine stability with wide adaptation across Punjab. These genotypes were evaluated across four diverse agro-climatic zones including Faisalabad, Sahiwal, Bahawalpur, and Chakwal using a split-plot design. Eight plants were randomly selected from each treatment in each replication, and data on yield/per plant were recorded across four locations. The recorded data was analyzed through analysis of variance and GGE biplot analysis to explore genetic variability and genotype × environment interactions. The GGE biplot analysis, accounting for 93.33% of the total variation, effectively identified both discriminating and representative environments for pea cultivation. Sahiwal emerged as the most discriminating location, making it suitable for identifying specifically adapted genotypes, while Faisalabad and Bahawalpur were found to be more representative of average growing conditions. Genotypes such as Supreme, Pea-09, Champion, Classic, Green cross and 1800-6 were identified as stable and high-yielding across multiple environments. The findings of the study elaborate that by the cultivation of these stable genotypes in Punjab, the average pea yield of the country can be enhanced.

This research aimed to assess common bean genotypes for genetic diversity, heritability, and genetic advancement under varying concentrations of sodium chloride (NaCl) in hydroponic systems. Eight common bean genotypes were grown and evaluated in a two-factor completely randomized design with three replications in three NaCl concentrations (0 mM, 150 mM, 300 mM) at the Molecular lab of the Department of Plant Breeding and Genetics, The University of Agriculture, Peshawar, during 2022. Analysis showed substantial differences among eight genotypes for all traits across three NaCl levels. Mean ranges under 0, 150, and 300 mM NaCl concentration 10.93 to 20.87 cm, 8.71 to 21.43 cm, and 11.64 to 21.58 cm for hypocotyl length, and from 13.02 to 23.63, 10.51 to 15.9, and 6.96 to 12.99 for chlorophyll content, and from 32.33 to 46.67 cm, 34.00 to 57.33 cm and 33.50 to 45.67 cm for plant height, and from 10.73 to 15.30 cm, and 11.10 to 15.30 cm and 10.00 to 15.70 cm for epicotyl length. Heritability estimates ranged from 0.62 to 0.93 for various traits of common bean genotypes in all three levels of NaCl. The highest heritability was recorded for hypocotyl length (0.93) in 150mM NaCl concentrations, while the lowest heritability was recorded for plant height (0.62) in 300mM NaCl and also for hypocotyl length in 0mM 0.62 NaCl concentrations. The highest genetic advance value was estimated for plant height (8.26) in all NaCl concentrations, i.e., 4.10 in 0 mM NaCl, 8.26 in 150 mM NaCl, and 3.96 in 300 mM NaCl, respectively. Based on the current experiment, genotypes SW-32, GL299, and GL-287 appeared to be superior, with the highest values for plant height, chlorophyll content, and hypocotyl length. These results are recommended for future breeding programs aimed at improving salt tolerance in common bean genotypes.

Tools showing best conservation practices are becoming critical for rare plant conservation as populations become isolated through habitat fragmentation and changing ecosystem processes. We illustrate the importance of reintroduction and assisted gene flow, using reintroduction of the USA federally threatened Pitcher's thistle (Cirsium pitcheri), a monocarpic perennial endemic to the western Great Lakes sand dunes. We evaluate the success of experimental reintroductions of this species into its dynamic coastal environment and address fundamental issues for rare plant reintroduction, including questions of maintenance of genetic diversity, founder size, introduction methods and assisted gene flow effectiveness. In 1994 we initiated experimental reintroductions at three new locations along a habitat successional gradient using 4200 seeds collected from 54 maternal lines. At each site, seed sources were distributed among replicate blocks that were split by sowing method (sowing vs broadcasting) to examine establishment success. We monitored population demography for 30 years, assessing genetic variation in 2009 and regionally from 1997 to 2014. Two of three populations persisted for 30 years from a single-seeding founder event. Reintroduction populations had greater expected heterozygosity than regional native populations. Despite persistence, moderate inbreeding coefficients showed that reintroduction populations have not achieved an effective size to reduce the likelihood of inbreeding depression. However, the mid-successional reintroduction had the lowest kinship of all populations sampled, indicating a healthy restoration. Seed sowing produced three times as many seedlings as broadcasting, but seed source did not affect germination success. Persistence has been facilitated by local migration to suitable habitat patches, an important metapopulation process. Seeds can be an effective method for reintroducing monocarpic plants in high-quality habitats. However, low numbers of reproductive adults and moderate inbreeding illustrate the need for repeated additions of plants or seed to reduce inbreeding to improve rare plant genetic evolutionary potential.

Abstract Rhizosheath formation—the adhesion of soil particles to root surfaces—has gained attention in sustainable agriculture due to its diverse contributions to plant health and productivity. This process is driven by root hairs, root exudates, and rhizosheath-associated microbial communities and shaped by plant genetics, and soil physical and chemical properties. Despite recent advances, the mechanisms underlying root–soil–microbe interactions remain poorly understood, especially in intercropping systems. Intercropping can alter belowground traits such as root system architecture, exudate profiles, and rhizosheath microbial communities, but direct links between these changes and rhizosheath formation remain unclear. We advocate incorporating rhizosheath-related traits into intercropping design to enhance crop resilience and productivity. This commentary highlights key research gaps, outlines future directions, and discusses applied perspectives for agronomy and breeding. Advancing rhizosheath biology could translate fundamental knowledge into practical innovations for sustainable agriculture.

Tobacco (Nicotiana tabacum L.) is a crop of major economic importance worldwide and also a widely used model in plant biology and genetics. Leaf number (LN) is a key agronomic trait that determines yield. To elucidate its genetic basis, we developed a mapping population by crossing the low-leaf, high-quality cultivar 'NC82' with the high-leaf cultivar 'Jiucaiping No.2' (JCP2). Bulked segregant analysis initially placed the locus controlling LN within a 6.16 Mb region on chromosome 9. The integration of competitive allele-specific PCR markers with RNA sequencing data narrowed down this region and identified a single candidate gene, NtDEAH1. Overexpression of NtDEAH1 in both NC82 and JCP2 backgrounds significantly reduced LN, whereas CRISPR/Cas9-mediated knockout increased LN, indicating that NtDEAH1 acts as a negative regulator of LN and is a previously unreported control factor. Transcriptomic profiling and phytohormone analyses revealed that NtDEAH1 modulates the expression of genes in the gibberellin pathway. Specifically, NtDEAH1 binds to the 5'-untranslated region of the gibberellin receptor gene NtGID1, thereby influencing mRNA stability and translational efficiency to regulate LN. These findings provide new insights into genetic and molecular mechanisms underlying LN determination, and suggest that NtDEAH1 may serve as a target for future breeding aimed at optimising plant architecture and enhancing yield.

Abiotic and biotic stresses, whether occurring individually or in combination, have profound effects on plant growth, development and overall productivity. Abiotic stresses such as drought, salinity and extreme temperatures disrupt physiological processes, while biotic stresses from pathogens, pests and herbivores impair plant defenses and nutrient dynamics. When these stressors act simultaneously, they interact in complex ways, often exacerbating damage and creating unique challenges for plants. Research has shown that plants employ sophisticated signalling networks involving hormones such as abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA) and ethylene to coordinate responses to these stress combinations. These signalling pathways can have synergistic or antagonistic effects on stress tolerance, depending on the nature and timing of the stresses. Recent advancements in plant genetics, metabolomics, transcriptomics and genome-editing tools such as CRISPR-Cas (clustered regularly interspaced short palindromic repeats) are providing new insights into how plants adapt to dynamic environments and cope with concurrent stresses. Additionally, microbial inoculations, including arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR), are emerging as effective strategies to mitigate stress impacts by enhancing nutrient uptake, regulating hormone levels and improving overall plant resilience. This review emphasizes the need for an integrated approach to understanding the interactions between biotic and abiotic stressors. It highlights innovative strategies such as microbial applications, advanced breeding programs and biotechnological interventions to improve stress tolerance. Addressing these challenges is critical for developing resilient crop varieties capable of withstanding the impacts of climate change and ensuring sustainable agricultural productivity.

Gene-editing tools enable precise, targeted genome modifications, providing new approach for the rapid and sustainable improvement of tea plant (Camellia sinensis (L.) Kuntze). Developing such an approach is especially important due to the perennial nature and complex genetics of the tea plant, which make traditional breeding slow and inefficient. To validate a gene editing protocol in the elite local tea cultivar Kolkhida three candidate genes were selected. Two guide RNAs (gRNAs) were designed for each gene, and corresponding constructs for targeted genome modification in tea were generated. Successful modifications of the target sequences in cv. Kolkhida tea protoplasts were achieved for all three target genes. The high mutagenic efficiency of the selected gRNAs was observed for two out of three genes, including induction of precise deletions between target motifs. gRNAs were delivered in protoplasts via co-transfection technique, and combined gRNA activity was observed when transfection efficiency exceeded 28%. The genome modification method for tea protoplasts established in this study can serve as a screening protocol to evaluate the in vivo efficiency of different genome editing approaches in the tea plant.