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Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for “classical” wheat probes (pSc119.2 and Afa family) and “universal” repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.

Hemp (Cannabis sativa L.) was karyotyped using by DAPI/C-banding staining to provide chromosome measurements, and by fluorescence in situ hybridization with probes for 45 rDNA (pTa71), 5S rDNA (pCT4.2), a subtelomeric repeat (CS-1) and the Arabidopsis telomere probes. The karyotype has 18 autosomes plus a sex chromosome pair (XX in female and XY in male plants). The autosomes are difficult to distinguish morphologically, but three pairs could be distinguished using the probes. The Y chromosome is larger than the autosomes, and carries a fully heterochromatic DAPI positive arm and CS-1 repeats only on the less intensely DAPI-stained, euchromatic arm. The X is the largest chromosome of all, and carries CS-1 subtelomeric repeats on both arms. The meiotic configuration of the sex bivalent locates a pseudoautosomal region of the Y chromosome at the end of the euchromatic CS-1-carrying arm. Our molecular cytogenetic study of the C. sativa sex chromosomes is a starting point for helping to make C. sativa a promising model to study sex chromosome evolution.

The low diversity of the D-subgenome of bread wheat requires the involvement of new alleles for breeding. In grasses, the allelic state of Growth Regulating Factor (GRF) gene is correlated with nitrogen uptake. In this study, we characterized the sequence of TaGRF-2D and assessed its diversity in bread wheat and goatgrass Aegilops tauschii (genome DD). In silico analysis was performed for reference sequence searching, primer pairs design and sequence assembly. The gene sequence was obtained using Illumina and Sanger sequencing. The complete sequences of TaGRF-2D were obtained for 18 varieties of wheat. The polymorphism in the presence/absence of two GCAGCC repeats in 5' UTR was revealed and the GRF-2D-SSR marker was developed. Our results showed that the alleles 5' UTR-250 and 5' UTR-238 were present in wheat varieties, 5' UTR-250 was presented in the majority of wheat varieties. In Ae. tauschii ssp. strangulata (likely donor of the D-subgenome of polyploid wheat), most accessions carried the 5' UTR-250 allele, whilst most Ae. tauschii ssp. tauschii have 5' UTR-244. The developed GRF-2D-SSR marker can be used to study the genetic diversity of wheat and Ae. tauschii.

Background Aegilops biuncialis is tetraploid grass species with U b U b M b M b genome constitution, distributed in Mediterranean and the Middle East. It carries many valuable traits such as disease resistance, drought tolerance, high micronutrient content, which are in demand of wheat breeding. Transfer of genetic material from Ae. biuncialis is not easy due to substantial modification of U b and especially M b genomes. Cytogenetic markers permitting easy and reliable chromosome identification will be helpful for successful manipulation with alien genetic material and introgression of useful traits into wheat. Development of chromosome nomenclature is complicated by the significant karyotype diversity of Ae. biuncialis. Results We used various combinations of eleven DNA probes for studying intraspecific karyotype divergence of Ae. biuncialis by FISH; among them pTa-566, pTa713 and pSc119.2 probes proved to be most informative for chromosome identification and analysis of karyotype evolution. FISH discriminated three chromosomal groups designated A, B and C and showed that the U b genome of Ae. biuncialis is less modified relative to the parental compared to M b genome. Based on the obtained results we suggested that Ae. biuncialis originated via multiple hybridization events and the U b and M b genomes of group A, B, and C were contributed by different forms of Ae. umbellulata and Ae. comosa . The M b genome of groups A and C probably derived from Ae. comosa subsp. comosa , whereas in the B-group - from subsp. heldreichii. Divergence of chromosomal groups of Ae. biuncialis was also accompanied by structural chromosome rearrangements. Using multiple DNA probes, we showed that reciprocal translocation between chromosomes 1M b L and 7M b L followed by pericentric inversion of modified 1M b occurred in group A. Intraspecific divergence of Ae. biuncialis was also associated with amplification/ elimination/ redistribution of repetitive DNA families. Conclusions Our study revealed complex genome structure of wild tetraploid grass Ae. biuncialis which might have occurred via multiple hybridization events resulting in formation of three distinct chromosomal groups. Their divergence was accompanied by different chromosomal rearrangements which resulted in formation of highly distinct karyotypes. By using FISH markers, we evaluated the relations between chromosomes of the three groups and developed genetic nomenclature of Ae. biuncialis chromosomes.

Melanin is the dark polymer pigment found in all kingdoms of life. Plant allomelanin, formed through the oxidation and polymerization of phenolic compounds, does not contain nitrogen; however, it possesses similar properties to melanin of animal, fungal, or bacterial origin. The black coloration of awns, spike husk edges, and even complete spikes is well-known in wheat and occurs frequently in wild, but rarely in cultivated, wheat species. Previously, anthocyanins were considered the only pigments responsible for the black coloration of wheat ears. Recently, it has been shown that the black coloration of the husks in other cereals can be attributed to melanin or anthocyanins, or both of these pigments. In this study, using standard procedures for chemical extraction of anthocyanins and melanin, ultraviolet–visible–near-infrared spectroscopy, and hyperspectral imaging, we examined the pigment in Persian wheat (Triticum carthlicum Line 5999) black-colored spikes and found that it exhibits properties characteristic of melanin rather than anthocyanins. Also, using microscopy, we show that the dark pigment in the husks and awns of mature spikes is located mainly in the dead protoplasts of epiderma and sub-epidermal sclerenchyma cells. The localization of the pigment suggests that melanin may perform some protective or sunlight-to-heat transforming function.

Background Plant height is an important wheat trait that is regulated by multiple genes, among which Rht is of the utmost value. In wheat, Rht-B1p (= Rht17 ) is a mutant allele of the Rht gene that encodes for a DELLA-protein and results in the development of gibberellin-insensitive plants with a dwarfing phenotype. The pleiotropic effects of dwarfing genes on yield are highly dependent on both the genetic background and the environmental conditions. In Russia, the Central Non-Black Earth Region and Krasnodar Krai are two economically important regions that require differing management for sustainable wheat production for food, feed and industry. The purpose of our study was to compare the pleiotropic effects of Rht-B1p on the main valuable agronomic traits in the F 3:4 families of the spring bread wheat Chris Mutant/Novosibirskaya 67 in the genetic background of Vrn-B1a / vrn-B1 (spring/winter phenotype) and Ppd-D1a / Ppd-D1b (insensitivity/sensitivity to photoperiod) alleles in a field experiment in Moscow and Krasnodar Krai. Results Plant height was reduced on average by 21 cm (28%) and 25 cm (30%), respectively; Ppd-D1a slightly strengthened the dwarfing effect in Moscow and mitigated it in Krasnodar Krai. Grain weight of the main spike was reduced by Rht-B1p in Moscow and to lesser extent in Krasnodar; Ppd-D1a and Vrn-B1a tended to partially compensate for this loss in Krasnodar Krai. Thousand grain weight was reduced on average by 5.3 g (16%) and 2.9 g (10%) in Moscow and Krasnodar Krai, respectively, but was partially compensated for by Ppd-D1a in Krasnodar Krai. Harvest index was increased due to Rht-B1p by 6 and 10% in Moscow and Krasnodar Krai, respectively. Rht-B1p resulted in a delay of heading by 1–2 days in Moscow. Ppd-D1a accelerated heading by 1 day and 6 days in Moscow and in Krasnodar Krai, respectively. Conclusions Rht-B1p could be introduced into wheat breeding along with dwarfing genes such as Rht-B1b and Rht-D1b . Special attention should be paid to its combination with Ppd-D1a and Vrn-B1a as regulators of developmental rates, compensators of adverse effects of Rht-B1p on productivity and enhancers of positive effect of Rht-B1p on harvest index.

The production and productivity of cereal crops, which form the foundation of global food security, are increasingly threatened by unstable water regimes and recurring droughts linked to climate change. Fortunately, a wide diversity of cereal crops is endowed with natural resilience to drought and heat stress, enabling them to survive under conditions that are critical for other plants. Understanding the key morphological, genetic, physiological, biochemical, and ecological mechanisms—and their interactions—is crucial for unraveling the processes involved in drought tolerance in these species. A comprehensive study of cereal crops, their variability, and their ability to survive and thrive under arid conditions will unlock new opportunities for breeding drought-resistant agricultural varieties. This review highlights the role of root system architecture (RSA) and gravitropic mechanisms (e.g., EGT1, DRO1), the integration of phytohormonal crosstalk, the potential of wild relatives and genome editing, and the emerging role of plant growth-promoting rhizobacteria (PGPR) in enhancing drought resilience. We propose a novel synthesizing concept focused on overcoming the fundamental yield-survival trade-off by framing drought resilience through the lens of optimizing three interconnected functional modules: water budget architecture, metabolic homeostasis, and integrative signaling networks. The central advance of this framework is its systems-level perspective that redefines these well-studied components as dynamically interacting, tunable modules, providing a practical blueprint for designing crop ideotypes that break the yield-survival trade-off.

Digital phenotyping is a fast-growing area of hardware and software research and development. Phenotypic studies usually require determining whether there is a difference in some trait between plants with different genotypes or under different conditions. We developed StatFaRmer, a user-friendly tool tailored for analyzing time series of plant phenotypic parameters, ensuring seamless integration with common tasks in phenotypic studies. For maximum versatility across phenotypic methods and platforms, it uses data in the form of a set of spreadsheets (XLSX and CSV files). StatFaRmer is designed to handle measurements that have variation in timestamps between plants and the presence of outliers, which is common in digital phenotyping. Data preparation is automated and well-documented, leading to customizable ANOVA tests that include diagnostics and significance estimation for effects between user-defined groups. Users can download the results from each stage and reproduce their analysis. It was tested and shown to work reliably for large datasets across various experimental designs with a wide range of plants, including bread wheat ( Triticum aestivum ), durum wheat ( Triticum durum ), and triticale (× Triticosecale ); sugar beet ( Beta vulgaris ), cocklebur ( Xanthium strumarium ) and lettuce ( Lactuca sativa ), corn ( Zea mays ) and sunflower ( Helianthus annuus ), and soybean ( Glycine max ). StatFaRmer is created as an open-source Shiny dashboard, and simple instructions on installation and operation on Windows and Linux are provided.

The rapid and widespread development of technology is in line with global trends of population growth and increasing demand for food. Significant breakthroughs in science have not yet fully met the needs of agriculture for increased food production and higher yields. The aim of this work is to discuss the current advancements in the application of beneficial microorganisms for crop cultivation and their integration into speed breeding technology to create optimal growing conditions and achieve the ultimate goal of developing new plant varieties. New breeding techniques, such as speed breeding—now a critical component of the breeding process—allow multiple plant generations to be produced in a much shorter time, facilitating the development of new plant varieties. By reducing the time required to obtain new generations, breeders and geneticists can optimize their efforts to obtain the required crop genotypes for both agriculture and industry. This helps to meet the demand for food, animal feed and plant raw materials for industrial use. One potential aspect of speed breeding technology is the incorporation of effective beneficial microorganisms that inhabit both the above-ground and below-ground parts of plants. These microorganisms have the potential to enhance the speed breeding method. Microorganisms can stimulate growth and development, promote overall fitness and rapid maturation, prevent disease, and impart stress resistance in speed breeding plants. Utilizing the positive effects of beneficial microorganisms offers a pathway to enhance speed breeding technology, an approach not yet explored in the literature. The controlled practical use of microorganisms under speed breeding conditions should contribute to producing programmable results. The use of beneficial microorganisms in speed breeding technology is considered an indispensable part of future precision agriculture. Drawing attention to their practical and effective utilization is an urgent task in modern research.

The optimization of all constituent conditions to obtain high and even maximum yields is a recent trend in agriculture. Legumes play a special role in this process, as they have unique characteristics with respect to storing protein and many other important components in their seeds that are useful for human and animal nutrition as well as industry and agriculture. A great advantage of legumes is the nitrogen fixation activity of their symbiotic nodule bacteria. This nitrogen self-sufficiency contributes directly to the challenging issue of feeding the world’s growing population. Molybdenum is one of the most sought-after nutrients because it provides optimal conditions for the maximum efficiency of the enzymes involved in nitrogen assimilation as well as other molybdenum-containing enzymes in the host plant and symbiotic nodule bacteria. In this review, we consider the most optimal way of providing legume plants with molybdenum, its distribution in ontogeny throughout the plant, and its accumulation at the end of the growing season in the seeds. Overall, molybdenum supply improves seed quality and allows for the efficient use of the micronutrient by molybdenum-containing enzymes in the plant and subsequently the nodules at the initial stages of growth after germination. A sufficient supply of molybdenum avoids competition for this trace element between nitrogenase and nodule nitrate reductase, which enhances the supply of nitrogen to the plant. Finally, we also consider the possibility of regulating molybdenum homeostasis using modern genetic approaches.