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Transcriptomic Characterization of Candidate Genes for Fusarium Resistance in Maize (Zea mays L.)
Fusarium diseases are among the most dangerous fungal diseases of plants. To date, there are no plant protectants that completely prevent fusariosis. Current breeding trends are therefore focused on increasing genetic resistance. While global modern maize breeding relies on various molecular genetics techniques, they are useless without a precise characterization of genomic regions that determine plant physiological responses to fungi. The aim of this study was thus to characterize the expression of candidate genes that were previously reported by our team as harboring markers linked to fusarium resistance in maize. The plant material included one susceptible and four resistant varieties. Biotic stress was induced in adult plants by inoculation with fungal spores under controlled conditions. qRT-PCR was performed. The analysis focused on four genes that encode for GDSL esterase/lipase (LOC100273960), putrescine hydroxycinnamyltransferase (LOC103649226), peroxidase 72 (LOC100282124), and uncharacterized protein (LOC100501166). Their expression showed differences between analyzed time points and varieties, peaking at 6 hpi. The resistant varieties consistently showed higher levels of expression compared to the susceptible variety, indicating their stronger defense responses. Moreover, to better understand the function of these genes, their expression in various organs and tissues was also evaluated using publicly available transcriptomic data. Our results are consistent with literature reports that clearly indicate the involvement of these genes in the resistance response to fusarium. Thus, they further emphasize the high usefulness of the previously selected markers in breeding programs to select fusarium-resistant maize genotypes.
Associative and Physical Mapping of Markers Related to Fusarium in Maize Resistance, Obtained by Next-Generation Sequencing (NGS)
On the basis of studies carried out in the last few years, it is estimated that maize diseases cause yield losses of up to 30% each year. The most dangerous diseases are currently considered to be caused by fungi of the genus Fusarium, which are the main culprits of root rot, ear rots, and stalk rot. Early plant infection causes grain diminution, as well as a significant deterioration in nutritional value and fodder quality due to the presence of harmful mycotoxins. Therefore, the aim of the research was to identify new markers of the SilicoDArT and SNP type, which could be used for the mass selection of varieties resistant to fusarium. The plant material consisted of 186 inbred maize lines. The lines came from experimental plots belonging to two Polish breeding companies: Plant Breeding Smolice Ltd., (Co., Kobylin, Poland). Plant Breeding and Acclimatization Institute—National Research Institute Group (51°41′23.16″ N, 17°4′18.241″ E), and Małopolska Plant Breeding Kobierzyce, Poland Ltd., (Co., Kobierzyce, Poland) (50°58′19.411″ N, 16°55′47.323″ E). As a result of next-generation sequencing, a total of 81,602 molecular markers were obtained, of which, as a result of the associative mapping, 2962 (321 SilicoDArT and 2641 SNP) significantly related to plant resistance to fusarium were selected. Out of 2962 markers significantly related to plant resistance in the fusarium, seven markers (SilicoDArT, SNP) were selected, which were significant at the level of 0.001. They were used for physical mapping. As a result of the analysis, it was found that two out of seven selected markers (15,097—SilicoDArT and 58,771—SNP) are located inside genes, on chromosomes 2 and 3, respectively. Marker 15,097 is anchored to the gene encoding putrescine N-hydroxycinnamoyltransferase while marker 58,771 is anchored to the gene encoding the peroxidase precursor 72. Based on the literature data, both of these genes may be associated with plant resistance to fusarium. Therefore, the markers 15,097 (SilicoDArT) and 58,771 (SNP) can be used in breeding programs to select lines resistant to fusarium.
Investigation of the Influence of Polyamines on Mature Embryo Culture and DNA Methylation of Wheat (Triticum aestivum L.) Using the Machine Learning Algorithm Method
Numerous factors can impact the efficiency of callus formation and in vitro regeneration in wheat cultures through the introduction of exogenous polyamines (PAs). The present study aimed to investigate in vitro plant regeneration and DNA methylation patterns utilizing the inter-primer binding site (iPBS) retrotransposon and coupled restriction enzyme digestion–iPBS (CRED–iPBS) methods in wheat. This investigation involved the application of distinct types of PAs (Put: putrescine, Spd: spermidine, and Spm: spermine) at varying concentrations (0, 0.5, 1, and 1.5 mM). The subsequent outcomes were subjected to predictive modeling using diverse machine learning (ML) algorithms. Based on the specific polyamine type and concentration utilized, the results indicated that 1 mM Put and Spd were the most favorable PAs for supporting endosperm-associated mature embryos. Employing an epigenetic approach, Put at concentrations of 0.5 and 1.5 mM exhibited the highest levels of genomic template stability (GTS) (73.9%). Elevated Spd levels correlated with DNA hypermethylation while reduced Spm levels were linked to DNA hypomethylation. The in vitro and epigenetic characteristics were predicted using ML techniques such as the support vector machine (SVM), extreme gradient boosting (XGBoost), and random forest (RF) models. These models were employed to establish relationships between input variables (PAs, concentration, GTS rates, Msp I polymorphism, and Hpa II polymorphism) and output parameters (in vitro measurements). This comparative analysis aimed to evaluate the performance of the models and interpret the generated data. The outcomes demonstrated that the XGBoost method exhibited the highest performance scores for callus induction (CI%), regeneration efficiency (RE), and the number of plantlets (NP), with R2 scores explaining 38.3%, 73.8%, and 85.3% of the variances, respectively. Additionally, the RF algorithm explained 41.5% of the total variance and showcased superior efficacy in terms of embryogenic callus induction (ECI%). Furthermore, the SVM model, which provided the most robust statistics for responding embryogenic calluses (RECs%), yielded an R2 value of 84.1%, signifying its ability to account for a substantial portion of the total variance present in the data. In summary, this study exemplifies the application of diverse ML models to the cultivation of mature wheat embryos in the presence of various exogenous PAs and concentrations. Additionally, it explores the impact of polymorphic variations in the CRED–iPBS profile and DNA methylation on epigenetic changes, thereby contributing to a comprehensive understanding of these regulatory mechanisms.
Potential of Paulownia Leaves Silage in Lamb Diet to Improve Ruminal Fermentation and Fatty Acid Profile − An in vitro Study
Abstract Environmental impact, quality, and quantity of food products of ruminant origin (especially beef and mutton) are considered major challenges in meeting the nutritional requirements of the growing human population worldwide. Therefore, we conducted this in vitro study to explore the potential of Paulownia leaves silage to reduce the environmental impact of feedlot lamb production and improve ruminal fatty acids (FAs) profile by influencing ruminal biohydrogenation. In the present study, Paulownia leaves silage (PLS) and alfalfa silage (AAS) were mixed in a proportion of 1:0 (Control, PLS 0%), 0.75:0.25 (PLS 25%), 0.5:0.5 (PLS 50%), 0.25:0.75 (PLS 75%) and 0:1 (PLS 100%) on dry matter basis in the lamb diet. The experimental findings demonstrated that 100% replacement of AAS with PLS in the lamb diet significantly improved the ruminal fermentation by increasing the in vitro DM degradability (P<0.01), total volatile fatty acid (P<0.01), and propionate production (P<0.01) while reducing the acetate: propionate (A/P) ratio (P<0.01) and CH4 concentration (mM; L and Q P<0.05) and CH4 production, mM/g DM (L and Q P<0.05). Meanwhile, 100% PLS inclusion in the diet increased the total monounsaturated fatty acids (P<0.05), total unsaturated fatty acids (P<0.01) and total n-3 fatty acids (P<0.05) particularly alpha-linolenic acid (ALA; C18:3 n-3; P<0.05) in the rumen fluid after incubation. Moreover, the total saturated fatty acids concentration was reduced (P<0.01). These findings suggested that PLS could be a climate-friendly and sustainable alternative to AAS in the lamb feedlot diet for quality meat production.
Monitoring and Signaling of the Most Important Aphid Species in the Territory of Greater Poland and Silesia Provinces
Aphids are significant pests affecting crop yields both through direct feeding and as vectors of viruses. The monitoring focused on 10 of the most important aphid species. This study investigates the dynamics of aphid populations in two Polish regions, Winna Góra (Greater Poland Province) and Sośnicowice (Silesia Province), over a five-year period (2019–2023) using Johnson suction traps. Data collection covered species composition, migration timing, and seasonal variations in aphid abundance. Dominance patterns were assessed using a species-specific index, and inter-regional comparisons were analyzed through correlation and principal component analysis. Results indicate notable population peaks during autumn, suggesting this period is optimal for implementing control measures. The Johnson traps proved valuable for timely pest monitoring, offering predictive potential for future aphid migration, particularly in relation to virus-transmitting species critical to plants.
Comparison of Six Measures of Genetic Similarity of Interspecific Brassicaceae Hybrids F2 Generation and Their Parental Forms Estimated on the Basis of ISSR Markers
Genetic similarity determines the extent to which two genotypes share common genetic material. It can be measured in various ways, such as by comparing DNA sequences, proteins, or other genetic markers. The significance of genetic similarity is multifaceted and encompasses various fields, including evolutionary biology, medicine, forensic science, animal and plant breeding, and anthropology. Genetic similarity is an important concept with wide application across different scientific disciplines. The research material included 21 rapeseed genotypes (ten interspecific Brassicaceae hybrids of F2 generation and 11 of their parental forms) and 146 alleles obtained using 21 ISSR molecular markers. In the presented study, six measures for calculating genetic similarity were compared: Euclidean, Jaccard, Kulczyński, Sokal and Michener, Nei, and Rogers. Genetic similarity values were estimated between all pairs of examined genotypes using the six measures proposed above. For each genetic similarity measure, the average, minimum, maximum values, and coefficient of variation were calculated. Correlation coefficients between the genetic similarity values obtained from each measure were determined. The obtained genetic similarity coefficients were used for the hierarchical clustering of objects using the unweighted pair group method with an arithmetic mean. A multiple regression model was written for each method, where the independent variables were the remaining methods. For each model, the coefficient of multiple determination was calculated. Genetic similarity values ranged from 0.486 to 0.993 (for the Euclidean method), from 0.157 to 0.986 (for the Jaccard method), from 0.275 to 0.993 (for the Kulczyński method), from 0.272 to 0.993 (for the Nei method), from 0.801 to 1.000 (for the Rogers method) and from 0.486 to 0.993 (for the Sokal and Michener method). The results indicate that the research material was divided into two identical groups using any of the proposed methods despite differences in the values of genetic similarity coefficients. Two of the presented measures of genetic similarity (the Sokal and Michener method and the Euclidean method) were the same.
Meta-Analysis of Influence of Diversity of Parental Forms on Heterosis and Specific Combining Ability of Their Hybrids
An important stage in any breeding activity is selection of suitable individuals for further breeding. Thus, the main goal of breeders becomes such a selection of parental forms that leads to the consolidation and maximization of the value of traits of significant utility and economic importance. Heterosis and specific combining ability are very important parameters in plant and animal breeding. The ability to predict their value and relevance could significantly shorten the breeding process. One way to predict the effects of heterosis and specific combining ability is to select parental forms for crosses. This selection can be made on the basis of variation in parental forms. An analysis was made of publicly available data that contain information about the effects of heterosis, the effects of specific combining ability, and phenotypic and genetic diversity of parental forms. Preliminary studies show that the best approach for obtaining favorable hybrids would be selection of parental forms that are very genetically diverse while being phenotypically equal.
Effect of Different Plant Growth-Promoting Rhizobacteria on Biological Soil Properties, Growth, Yield and Quality of Oregano (Origanum onites L.)
Intensive agriculture uses continuous chemical fertilizers to increase crop yields, but excessive use of fertilizers leads to environmental pollution, permanent changes in physicochemical conditions in soil ecology, deterioration of soil biological health, leaching of nutrients, surface and groundwater pollution and eutrophication. Plant growth-promoting rhizobacteria (PGPR) are becoming increasingly important for ensuring crop safety, increasing nutrient uptake and output, lowering fertilizer costs, preventing environmental contamination and promoting sustainable agriculture and agricultural resources. Therefore, the purpose of this study was to identify and evaluate the effects of fifteen bacteria strains that were isolated from various acidic rhizospheric soils as biofertilizers on soil biological properties. Growth, yield and quality traits were analyzed, and various PGPR were identified using 16S ribosomal RNA of Turkish oregano. Fifteen bacterial inoculations with 1-aminocyclopropane-1-carboxylate (ACC) deaminase, N2-fixing, P-solubilizing and/or IAA-producing genes were used in the experiment, which was carried out in a randomized block design with five replicates (each with three pots) and a control without inoculation. Increased biological activity in soil inoculated with bacteria with multiple traits was confirmed by high C and N content in microbial biomass, urease, dehydrogenase and acid and alkaline phosphatase activities. Essential oil content, oil yield, thymol and carvacrol contents increased by 0.5–40.1%, 5.9–71.9%, 0.07–16.7% and 0.3–9.2%, respectively, as a result of bacterial inoculation. Oil content ranged from 2.02% to 2.83%; carvacrol (66.1–72.2%) was the main constituent, followed by thymol (14.5–16.9%) and linalool (1.38–3.68%). Two large PGPR groups were formed based on genetic distance analysis. Responses were variable and depended on the inoculant strain and the parameters being evaluated. The results indicate PGPR has clear potential for improving the yield of cultivated aromatic and essential oil plants, such as oregano.
Evaluation of Drought Tolerance in Oat × Maize Addition Lines Through Biochemical and Yield Traits
Oat × maize addition lines (OMAs) are plants of oat (Avena sativa L.) obtained by wide crossing with maize (Zea mays L.) that retained one or more maize chromosomes in the oat genome, which can result in morphological and physiological changes. The aim of the study was to determine the relationship between phenolics, pigments, sugars, and yield components in 14 OMAs and oat cv. Bingo under soil drought. The plants were sown in pots in a vegetation tunnel. The pots were watered to the level of 70% field water capacity (FWC) and then drought treated to 20% FWC for 2 weeks. Analysis of variance (ANOVA) showed that genotype and treatment significantly influenced the measured parameters. Out of 14 OMAs, lines 9 and 78b showed the highest grain weight and number, with the least amount of biomass loss under drought. These OMAs were the only two to equal or surpass the oat cv. Bingo under drought and control conditions. On average, soil drought caused decrease in biomass and the number and mass of grains (30%, 44%, 46%, respectively). Soil drought increased the amount of sugars by 15% and phenolics by 9% but decreased pigment contents by 8%. According to Pearson’s correlation coefficients, fifteen pairs of traits were positively and statistically significantly correlated in control and drought conditions. Significant relationships were found between the yield components and biochemical parameters on the fourteenth day of drought. A positive correlation occurred between the number and weight of kernels and the content of soluble sugars, chlorophyll a, b, and the sum of a and b. A negative correlation was found between all analyzed yield components and the content of phenolics. The results suggest the possibility of using such biochemical parameters as a quick physiological indicator of plant tolerance to soil drought. Variation in studied OMA lines reveals substantial differences in drought response, offering promising opportunities for targeted selection and breeding strategies.
The AMMI model application to analyze the genotype–environmental interaction of spring wheat grain yield for the breeding program purposes
AbstractChanging climatic conditions and the emphasis on the cultivation of genetically stable and resilient varieties as well as efficiently managing water and mineral resources require the commencement of appropriate research already at the stage of plant breeding. For this purpose, breeders must have the necessary tools not only in the form of an experimental network, but also statistical tools that enable the correct interpretation of the obtained results. In the presented research, the additive main effects and multiplicative interaction (AMMI) model, supplemented with cluster analysis, was used to assess the stability and yielding level of 26 spring wheat genotypes, in six locations. The main reason for the yield variability in studied genotypes was environmental factor (89%). In spite of differential conditions in the experimental network locations, the studied environments, which had a similar effect on the genotypes, in the growing season of 2021, were grouped. The AMMI stability value (ASV), yield stability index (YSI) and genotype selection index (GSI) coefficients were used to evaluate the studied genotypes. Based on the analyses, the following genotypes were selected for further breeding work: STH 21-03, STH 21-09 and KOH 18279, as stable and widely adapted.
How the Pollen Grains of the Varieties of Cannabis sativa L. Respond to Biostimulant of Plant Growth and Development and Habitat Conditions?
Przydatność pszenżyta ozimego w różnych warunkach gospodarowania w świetle wymogów integrowanej ochrony oraz Europejskiego Zielonego Ładu
The introduction of the European Green Deal by the European Commission poses new challenges in breeding work on varieties that will demonstrate natural resistance or tolerance to diseases and abiotic factors. Based on the results of research conducted by the Central Research Centre for Cultivar Testing, obtained within the framework of Post-registration Variety Testing and Ecological Variety Testing, an assessment was made of the impact of limiting the use of plant protection products and mineral fertilization on the resistance of the Belcanto variety to selected pathogens, yield and selected morphological features. The suitability of the variety for cultivation in a system limiting the use of pesticides and mineral fertilization was also assessed. Giving up fungicide protection and nitrogen fertilization led to a decrease in yield and 1000-grain weight and reduced the height of the plants. The Belcanto variety showed the greatest resistance to powdery mildew and a higher 1000-grain weight in 3 out of 5 growing seasons in the organic cultivation system.
Revealing Genetic Diversity and Population Structure in Türkiye’s Wheat Germplasm Using iPBS-Retrotransposon Markers
Investigating the genetic diversity and population structure of wheat germplasm is crucial for understanding the underlying variability essential for breeding programs and germplasm preservation. This research aims to contribute novel insights with respect to the genetic makeup and relationships among these wheat genotypes, shedding light on the diversity present within the Turkish wheat germplasm. In this study, iPBS-retrotransposon markers were employed to analyze 58 wheat genotypes, encompassing 54 landraces and 4 cultivars sourced from Türkiye. These markers serve as genetic indicators that can be used to evaluate genetic variation, build genealogical trees, and comprehend evolutionary connections. The PCR products were visualized on agarose gel, and bands were scored as present/absent. The ten iPBS primers collectively yielded an average of 16.3 alleles, generating a total of 163 polymorphic bands. The number of alleles produced by individual markers ranged from 4 (iPBS-2386) to 29 (iPBS-2219). The genetic parameters were calculated using the popgen and powermarker programs. The genetic relationships and population structures were assessed using the ntsys and structure programs. Polymorphism information content (PIC) per marker varied from 0.13 (iPBS-2390) to 0.29 (iPBS-2386), with an average value of 0.22. Shannon’s information index (I) was calculated as 1.48, while the number of effective alleles (Ne) and Nei’s genetic diversity (H) were determined to be 0.26 and 0.31, respectively. Genotype numbers 3 (Triticum dicoccum) and 10 (Triticum monococcum) exhibited the maximum genetic distance of 0.1292, signifying the highest genetic disparity. Population structure analysis revealed the segregation of genotypes into three distinct subpopulations. Notably, a substantial portion of genotypes clustered within populations correlated with the wheat species. This population structure result was consistent with the categorization of genotypes based on wheat species. The comprehensive assessment revealed noteworthy insights with respect to allele distribution, polymorphism content, and population differentiation, offering valuable implications for wheat breeding strategies and germplasm conservation efforts. In addition, the iPBS markers and wheat genotypes employed in this study hold significant potential for applications in wheat breeding research and germplasm preservation.
Genotype by year interaction and additive and epistasis gene effects for Fusarium stalk rot resistance in doubled haploid lines of maize (Zea mays L.)
Pollen Morphological Inter- and Intraspecific Variability in Selected Species of Rubus L. (Rosaceae)
Pollen morphology is one of the important vehicles in resolving some taxonomic problems on the family, genera or species level and has become part of the many disciplines and collaborative approaches in plant systematics and evolution. Palynological studies on the large and taxonomically highly complex genus Rubus L. have been limited, particularly concerning pollen variability. The aim of current study was to investigate the scope of inter- and intraspecific variability of the studied species based on pollen morphology, as well as verify taxonomic usefulness of pollen traits in distinguishing the studied taxa. The sixteen native Poland and Europe Rubus species were studied. Over a dozen quantitative and qualitative features of 2100 pollen (70 samples of 30 pollen each) were analyzed. Exine ornamentation and pollen size proved to be most useful pollen traits in the assessment of variability in the studied Rubus species. Pollen traits did not confirm the currently adopted taxonomical division of the genus Rubus into subgenera, sections and series. The greatest interspecific variability was found for traits P, E, Le and d, while variability was lowest in the case of Exp, Exe, P/E, Le/P, d/E, Exp/P and Exe/E. Intraspecific variability was determined by the following features ordered from those least to most variable: P, E, d, Le, d/E, Exp/P, Exp, P/E and Le/P.
Wykorzystanie technologii NGS, mapowania asocjacyjnego i fizycznego w celu identyfikacji genów kandydujących związanych z plonem kukurydzy
Selection of High-Yielding and Stable Genotypes of Barley for the Cold Climate in Iran
The interaction between genotypes and environments plays an important role in selecting superior genotypes for target locations. The main objectives of the present study were to analyze the effect of the genotype-by-environment interaction (GEI) and identify superior, newly developed, and promising barley genotypes for cold regions in Iran. For these purposes, a set of genotypes obtained from breeding programs for cold climates in Iran, along with two reference genotypes, were investigated at eight research stations (Tabriz, Ardabil, Arak, Miandoab, Mashhad, Jolge Rokh, Karaj, and Hamadan) during two consecutive growing seasons (2019–2020 and 2020–2021). The results of the freezing test (LT50) showed that most of the tested genotypes had significant cold tolerance at the seedling stage. Based on the additive main effect and multiplicative interaction (AMMI) analysis, environment (E) and GEI effects explained 49.44% and 16.55% of the total variation in grain yield, respectively. Using AMMI1 and AMMI2 models, G2 and G20 were found to be superior genotypes in terms of grain yield and stability. Moreover, AMMI-based stability parameters considered the G20 genotype to be the ideal genotype. A two-plot analysis of the genotype-by-environment interaction (GGE) biplot showed that the 16 experimental environments were grouped into 2 mega-environments. Of the test environments, ARK1 and KAJ2 had the highest discriminating power and representativeness ability, and these were identified as ideal environments for testing advanced genotypes for yield and stability performance during early barley breeding practices in cold areas in Iran. In conclusion, both AMMI and GGE biplot models identified several superior genotypes, among which G20, with a high average yield relative to the overall average yield and the lowest IPC1 score, was found to have high yield stability and is recommended for inclusion in breeding programs for cold climates in Iran.
