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SNP-based markers for drought tolerance in sunflower
No full textDeveloping SNP-based markers, such as KASP, HRM and STARP, from RNASeq data is a quick and effective method to support marker-assisted breeding for drought tolerance in sunflower. RNASeq reads (150 bp PE, 12 Gb raw data per sample) from the two sunflower cultivars DF-AB-2 and AB-OR-8 were mapped to the sunflower reference genome HanXRQr2.0. The SNP calling with GATK 4.1.4.1 and SNP annotation with SnpEff resulted in a total of 3,021,255 SNPs over all samples. Perl scripts were used to compare SNPs from the two cultivars and to receive SNPs that are only present in DF-AB-2 or AB-OR-8, but not in both. With this procedure, 64,098 SNPs were identified for DF-AB-2, while in AB-OR-8 only 37,092 SNPs were observed in comparison to HanXRQr2.0. To get an overview of the SNPs, density plots for each chromosome were created for both cultivars. The list of SNPs will be further used to develop markers in a set of candidate genes involved in ABA biosynthesis and signalling pathway. SNPs that lead to missense mutations are most interesting for marker developments, because the mutations might have an influence on the protein responsible for a trait. The putative beta-carotene 3-hydroxylase (HanXRQr2_Chr15g0719741) on chromosome 15 is part of the ABA biosynthesis. The gene shows two SNPs at position 168,965,031 bp and 168,965,042 bp. These SNPs leading to missense mutations are present in all RNAseq samples (tissues and treatments) of the cultivar AB-OR-8, but not in the cultivar DF-AB-2. The next step is to design primers e.g. for KASP markers in order to associate the SNPs with drought tolerance. With the presence of the SNP in only one cultivar, KASP markers can be used and tested in an association panel of 100-200 sunflower genotypes, which has been screened for drought tolerance. KASP markers associated with drought tolerance can then be used for marker-assisted selection in sunflower breeding programs in order to breed for climate resilient cultivars
Introducing transcriptomics in IFVCNS sunflower breeding program
No full textSunflower is one of the most important oil crops globally and the leading oil crop in Serbia. In 2024, FAO ranked Serbia among the top 10 countries with the highest sunflower seed production, highlighting the significance of sunflower breeding. Over the past six decades, the Institute of Field and Vegetable Crops (IFVCNS) has developed thousands of diverse sunflower lines and hybrids, continuously refining its breeding program. The IFVCNS breeding program follows multiple strategic directions, with a primary focus on developing high-yielding, high-quality sunflower lines and hybrids. Climate change has increasingly impacted breeding programs, prompting a faster the need for a more rapid approach to gene and trait discovery. One of the most critical abiotic stressors affecting sunflower production is drought, which significantly reduces yield and quality, particularly during germination and flowering. Among omics techniques, transcriptomics has proven invaluable in identifying key pathways and genes associated with drought tolerance. To address this challenge, two IFVCNS sunflower inbred lines—one drought-tolerant and one drought-sensitive—were subjected to drought stress, and their transcriptomes were analyzed. This research aims to uncover major drought tolerance candidate genes that could be integrated into future breeding programs to enhance sunflower resilience
STSM Troubleshooting and protocol standardization of -omics tools in improvement for drought tolerance held in March 2025 UNIPD report
No full textThis dataset contains the report from STSM Troubleshooting and protocol standardization of -omics tools in improvement for drought tolerance held on 24-28 March 2025 by UNIPD for six IFVCNS researchers, two UNIPD researchers and one UROS researcher within CROPINNO project. It highlights the work done, main achievements and planned follow-up activities
Omics integrated data
No full textDrought stress treatments (three replicates) were applied to a sunflower drought-resistant line grown under controlled greenhouse conditions. Measurement of physiological parameters was used to monitor plant stress conditions. Leaf samples (from 5 plants X each time points) were collected before and after the drought stress application for RNA-Seq and the subsequent analysis of changes happening at the chromatin level (ChIp-Seq). The leaf transcriptomes were evaluated by performing a principal component analysis (PCA) for the clustering of replicates from the respective timepoints. PCA indicated that the first two PCs explain most of the variance and samples from each time point are projected together, with exception of one replicate of CT1 (Figure 1). After raw RNA-seq reads quality check (FastQC), the trimmed reads were mapped to the reference genome (HanXRQr2.0-SUNRISE). The differential expressed analysis was performed using DESeq2 to identify differentially expressed genes (DEGs, Figure 2 Venn-diagram) between drought-stressed and control group. Gene Ontology (GO) enrichment analysis was performed on genes significantly differentially expressed (adjusted p-value 1 or <-1) to identify overrepresented biological processes, molecular functions (Figure 3), and cellular components. Trimethylation of histone H3 at lysine 4 (H3K4me3) distribution in sunflower genome was analyzed using ChIP-Seq. The summary of genome wide distribution of peaks on chromosome is shown in Figure 4. The number of the peaks mapping to the chromosome and its distribution can reflect the distribution of the chromatin mark distribution. ChIPseeker software was used to calculate the distribution of peaks in various functional areas (Figure 5). Analysis of sequencing data revealed the typical peak of reads around the Transcription Start Site (TSS), commonly associated with H3K4me3. However, other peaks relative to gene body and TSS were detected from the analysis (Figure 6). Peak overlapping gene GO enrichment bar, which directly reflect the distribution of the number of the peak overlapping genes enrichment on the biological process, cellular component and molecular function were identified (Figure 7)
Exploring the genetic diversity and population structure of Serbian and selected European bread wheat cultivars through iPBS-retrotransposon markers
No full textBread wheat is a globally vital crop, sustaining millions and contributing to food security. The present study investigated the molecular characterization of 60 bread wheat accessions, using 12 interprimer binding site (iPBS) retrotransposon markers, which yielded a total of 260 distinct bands. Out of the 260 bands, 42 were monomorphic while the remaining 218 (83.84%) were polymorphic, with polymorphism information content values ranging from 0.38 to 0.45. Genetic diversity indices, including Shannon’s information index (I = 0.01–0.53), effective number of alleles (Ne = 1.00–1.63), gene diversity (He = 0.0037–0.36), and marker index (MI = 0.31– 0.51), revealed moderate variability across the accessions. Analysis of molecular variance indicated 99% genetic variation within populations, underscoring the genetic richness of the germplasm. Principal coordinate analysis, neighbor-joining tree, and model-based STRUCTURE clustering divided the accession into two distinct groups. The average genetic distance was 0.23, with a minimum of 0.063 between Mohikana and NS Lenija and a maximum of 0.56 between LG Airbus and BC Bernarda accessions. Given their high genetic divergence, LG Airbus and BC Bernarda are suggested as potential candidate parents for future wheat breeding programs. Our study highlights the genetic variation within Serbian wheat germplasm and could be valuable for parental selection and the strategic planning of future breeding programs
Evaluation of oil and protein content variability in camelina genotypes
No full textCamelina sativa (L.) Crantz, a re-emerging oilseed crop of the Brassicaceae family, has attracted growing attention due to its valuable seed oil composition and high-quality meal. The oil is rich in essential fatty acids and potentially beneficial for human health, while the protein-rich meal has value for animal feed. This study assessed the oil and protein content variability in 20 camelina genotypes selected from diverse origins. A field trial was conducted at the experimental site of Rimski Šančevi, Serbia, and seed composition was analyzed using near-infrared reflectance spectroscopy (NIRS). Oil content ranged from 29.90% to 36.73% (mean 33.22%), while protein content ranged from 29.02% to
35.59% (mean 32.84%). Analysis of variance showed significant genotypic differences (p < 0.001), and cluster analysis grouped genotypes into three major clusters with one unclassified genotype. The results confirm the existence of substantial genetic variability, which can be exploited in breeding programs aiming to improve camelina seed composition. As a result of ongoing breeding activities at the Institute of Field and Vegetable Crops (IFVCNS), two camelina cultivars have been developed and commercially released: NS Slatka and NS Zlatka. These findings support the potential of camelina as a source of health-promoting bioactive compounds and contribute to its development as a sustainable crop for food and feed applications
SoyPredict: Data-Driven strategies of soybean breeding
No full textThe goal of SoyPredict is to increase the efficiency of breeding new soybean varieties that are
suited to the agro-climatic conditions of Serbia and Europe by using sophisticated breeding
tools, multi-omics data, and mathematical modeling for yield prediction. The project focuses
on soybean, a commodity of significant economic and environmental significance, by creating
long-term breeding plans utilizing cutting-edge technologies. The main consequences of
climate change in Serbia are reflected in the reduction of the yield of the main crops. Taking
into account the negative effects of climate change on agricultural production in general, the
availability of new and improved soybean varieties is an important component in overcoming
the negative effects. SoyPredict ambition is the development of an efficient, long-term
breeding strategy by combining different prediction models based on big data of different
aspects of soybean biology. The term ‗breeding strategy‘ implies a plan to optimize the
production of soybean varieties using the full suite of technologies and to release the
improved varieties faster. Specific strategies will determine how to integrate traditional and
multi-omics approaches for improving the efficiency of a breeding process. The primary idea
behind SoyPredict is the ability and accuracy of GP, HTPP, and PP models to predict soybean
yield (both within and between environments, at various stages of genotype evaluations), as
well as the implementation of model compilation and the development of cost-effective
strategies for the application of one or more models. SoyPredict‘s goal is to establish the
foundation for economically viable soybean breeding so that improved varieties can be
continuously released to meet the demands of industry, producers, and consumers. Improved
breeding due to access to high-tech breeding tools and methods, will reside on mechanisms
for long-term crop improvement and overcoming the negative impacts of climate change
Medicinal Properties of Buckwheat Grain, Rutin and Honey and Use in Medicine
No full textTherapeutic Potential of Medicinal Plants: The Science Behind Natural Remedies, investigates the bioactive compounds and functionality of medicinal plants and herbs which are recommended to help certain health conditions and overall well-being while highlighting cultivation that can be done sustainably to promote biodiversity conservation
Economic status of maize production
No full textMaize has a high caloric value, which is why it is used to the greatest extent in the diet of humans and domestic animals. The areas on which corn is grown, in the world, amounted to about 200 million hectares. The largest corn producers in the world are the USA, China and Brazil, the EU and Argentina. According to FAO data, corn production by continent in the period 2019-2023 was the largest in America, followed by Asia and Europe. In Serbia, there is the most arable land under grain (1698993ha), of which over 60% is under corn. Maize is most abundant in Vojvodina, Pomoravlje and Mačva. The areas under corn in Serbia vary in the period from 2019 to 2023. Yields show a growth trend in 2023 (7.2 t/ha-1)
Essential oil fractions of hemp profiles at different hydro-distillation periods
No full textThe hypothesis of this study was that hemp (Cannabis sativa L.) essential oil (EO) constituents from high-cannabinoid hemp are eluted at different times during the hydro-distillation process, allowing the generation of fractions with distinct chemical profile, with or without cannabinoids. The objective was to reveal changes in the compositional profile of EO fractions captured at ten sequential distillation timeframes (DT) and a control. Regression analysis was conducted to model the relationship between DT and 20 EO compounds, classified in four groups (monoterpenes, sesquiterpenes, cannabinoids, and others (acid esters, ketone, alcohol)) using ten DT values (5, 10, 20, 40, 80, 120, 160, 200, 240, and 280 min). The results showed that most of the EO compounds were eluted early in the distillation process, until 10 min, then the EO compounds gradually decreased until 120 min and decreased to negligible amounts after 160 min DT. Monoterpenes eluted early in the distillation process, accounting for 69.79% of the total EO collected during the 0–5 min distillation interval. After that, the monoterpenes gradually decreased to 13.77% in the 240–280 min DT, while their concentration in the 0–180 min non-stop distillation was 33.55%. Conversely, the sesquiterpenes were eluted late in the distillation process. The concentration of sesquiterpenes in the 0–5 min DT EO was 25.73%, then gradually increased to reach a plateau at 160–280 min DT (75.3–76.8%), while their concentration in the 0–180 min DT was 54.4%. The results demonstrated that hemp EO with higher concentration of monoterpenes and free of cannabinoids can be obtained by separating the initial fractions, while hemp EO with higher concentration of sesquiterpenes and cannabinoids such as cannabidiol (CBD), cannabichromene (CBC), δ8-tetrahydrocannabinol (commonly known as δ8-THC), and δ9-tetrahydrocannabinol (commonly known as δ9-THC or dronabinol) can be obtained by capturing the fraction eluted after 160 min DT