Ahu Altinkut Uncuoglu

Background The genus Colchicum, belonging to the family Colchicaceae, holds significant economic and medicinal value globally. However, precise identification of many species within this genus is challenging. In order to address this obstacle, we carried out a study involving 155 genotypes from various locations in Türkiye to assess the effectiveness of DNA barcoding, specifically utilizing the matK, rbcL, trnH-psbA chloroplast DNA (cp-DNA) barcode regions, by comparing their effectiveness in distinguishing Colchicum species. Methods and results Following PCR amplification and sequence analysis, multiple sequence alignment was conducted. Stop codons were detected and sequences were cleaned. Conserved region identification, and GC content analysis were carried out. Species discrimination was analysed (best match, best close-match, all species barcodes functions). The Wilcoxon Ranked Sum test was used to assess differences in genetic variation within and between species. As a result, trnH-psbA emerged as the most effective locus for species differentiation, with significantly higher intra-specific (mean: 3.915) and inter-specific distances (maximum: 1.844) compared to matK and rbcL. matK displayed moderate identification success rates, while rbcL had the lowest performance. trnH-psbA excelled in the ‘best match’ and ‘best close match’ categories; rbcL recorded the highest incorrect identification rates. Conclusion This study highlights the importance of DNA barcoding, specifically the trnH-psbA locus, in distinguishing Colchicum species. The locus shows significantly higher genetic distances than the matK and rbcL loci, underscoring its effectiveness for species identification. These insights are crucial for comprehending the genetic diversity of Colchicum species and enhancing resources for future taxonomy and conservation efforts.

Nanoparticles, thanks to their superior properties such as large surface area and high reactivity, can be an alternative to traditional fertilizers for improving nutrient uptake. Furthermore, considering that chemical and physical synthesis methods require high energy consumption and cause environmental pollution, plant-mediated green synthesis of NPs has attracted great attention since it provides eco-friendly, biocompatible, and inexpensive solutions. In this present study, plant mediated green synthesis of Iron Oxide (Fe₂O₃), Zinc Oxide (ZnO) and Titanium Dioxide (TiO₂) nanoparticles by using Laurus nobilis leaves (bay leaves) were carried out and their structural properties were characterized by UV visible spectra, Dynamic Light Scattering (DLS), Fourier Transform Infrared (FTIR), X-Ray Diffraction (XRD) and Transmission Electron Microscopy (TEM). UV spectrum and FTIR analysis exhibited characteristic peaks indicating the presence of the desired NPs, while DLS analysis and TEM images confirmed that synthesized particles are in nano-scale. The potential of nanoparticles as biofertilizer in agricultural uses were assessed by investigating their effects on sunflower growth in hydroponic system. TEM images of the NP applied plant tissues proved the uptake and translocation of NPs from root to leaf. Furthermore, Fe₂O₃, ZnO and TiO₂ NP applications on sunflower up to 5 ppm generally improved physiological growth parameters such as root length, fresh weight and leaf surface area while 20 ppm of Fe₂O₃ and ZnO NPs application cause a significant decrease. Graphical abstract

Molecular markers play a crucial role in accelerating crop production for sustainable agriculture by identifying resistant traits and enhancing genetic diversity. In this review, we examine the impact of the molecular markers on advancing our understanding of stress tolerance mechanisms in plants, addressing the pressing imperative to bolster global food production to meet the escalating demands of the growing population. Additionally, the application of molecular markers to evaluate the genetic accuracy of plants due to genetic changes caused by somaclonal variation during in vitro propagation is mentioned. Specifically, we highlight emerging technologies like MAS, MARS, MABC, GWAS, GS, DH production, speed breeding, and genome editing, which offer promising opportunities to enhance stress tolerance and genetic integrity in crop cultivars, aiding in addressing global food security challenges. The literature search focused on studies published in the last ten years. We utilized a combination of specific and broad keywords such as genetic stability, in vitro propagation, molecular markers, abiotic-biotic stress, and plant biotechnology. In conclusion, this review analyzes the use of molecular markers in assessing the stress tolerance and genetic fidelity of in vitro grown plants.

Drought and salinity are among the most important abiotic stress factors that limit the productivity in economically important plants. Although genes from wild relatives or unadapted germplasm have often been used for stress tolerance breeding, only few studies have examined wild relatives to understand the genetic and molecular basis of stress tolerance. In this study, we monitored the changes in gene expression profiles of leaf and root tissues of two wild barleys (Hordeum spontaneum L.) accessions from Israel after treatment with salt (NaCl) and drought (PEG) stress. We identified a total of 641 differentially expressed genes across 24 conditions (2 accessions, 2 stress conditions, 2 tissues and 3 time points). Our gene expression analyses revealed large numbers of differentially expressed genes in different accessions by different stress treatments. In addition, the number of genes altered in the leaves of stress-exposed plants of both genotypes was higher than those altered in the roots. Interestingly, there was a relatively little overlap between the leaf and the root stress-responsive gene expression patterns, suggesting that different stress-associated processes might be operating in these tissues during stress adaptation. Overall, our results revealed a number of candidate genes and plant processes associated with stress tolerance in wild barley. Wild barley would be a useful source of new genetic variation for drought and salt stress tolerance. Our results could provide new insights into the mechanisms of drought and salt stress tolerance in wild barley and should be useful for genetic improvement of salt-drought tolerance in cultivated barley.

The creation of homozygous plants is essential for both genetic studies and the production of hybrid seeds, particularly in plants that were pollinated by an alien species. Dihaploid (DH) technology is an important application in obtaining homozygous lines used to plant speed breeding programs. The generation of haploid embryos by pollen irradiation and pollination of female flowers with irradiated pollen has been successfully applied. The influence of irradiated pollen on the induction of haploids in sunflower (Helianthus annuus L.) has been evaluated on 16 different sunflower lines from Turkey’s National Sunflower Breeding Program. In this study, pollen grains were irradiated with varying dosages of Gamma rays (500-1000 Gy) to generate parthenogenetic haploid embryos in oilseed sunflowers. At a period of 12–20 days following the process of pollination, embryos were plated into modified MS culture media under a 16/8 h photoperiod and a temperature of 25◦C. Parthenogenetic 18457 embryos at different developmental stages were rescued in vitro and 650 were germinated. The ploidy analysis of regenerants was made with chromosome count and flow cytometry. Except for 500 Gy, all dosages were effective for inducing embryos and haploid plants. Obtained results indicate that parthenogenetic haploid embryos can be produced in K3AD SN:8, IMI 069, and IMI 044 sunflower genotypes by selecting the appropriate Gamma ray dose and embryonic developmental stage. This study was focused to recover sunflower doubled haploids to accelerate the production of non-segregating lines for breeding.

Sunflower (Helianthus annuus L.) is the most widespread plant used for production of oil among all oilseeds cultivated in Turkey in terms of agricultural area and production. Sunflower with high oleic acid content is always desirable because of benefits on health and industrial use. The enzyme FAD2-1 catalyzes the conversion of oleic acid to linoleic acid in sunflower. The fatty acid composition can be enhanced by gene editing of FAD2-1 gene by CRISPR/Cas9 technique which has been applied recently as a new breeding technique to improve productivity and enhance sustainability in agriculture. Hence, CRISPR/Cas9 genome editing systems were utilized to knockout the FAD2-1 gene in order to increase production of oleic acid content. For this purpose, two low oleic sunflower genotypes were transformed with two sgRNA that target FAD2-1 gene. sgRNA expression cassettes were assembled into the binary vector by Golden Gate assembly in a single reaction which is followed by A. tumefaciens-mediated transformation and in vitro germination. Putatively transformed shoots were selected with A. tumefaciens-mediated the optimized kanamycin concentration (100 mg/L) in the medium. The challenges of transformation of sunflower were summarized and possible solutions were proposed. This study indicated that sunflower still can be modified by CRISPR/Cas9 genome editing system to develop high oleic sunflower.

Background Pistacia is a genus of dioecious plant species whose trees can take 4–5 years to reach the economically valuable fruit-bearing stage. The fruits have great importance as raw material in the food, healthcare, and baking industries. For that reason, the identification of individual plants in the early juvenile period for the pollination and positioning of trees is crucial for growers. The objective of this study is to develop markers for each Pistacia species that can help in screening the sex of plant seedlings before they reach the reproductive stage, without waiting for morphological characteristics to appear. Methods and results Within this context, by using the power of the kompetitive allele-specific PCR (KASP) assay technology as a marker screening system, we successfully discriminated seven out of eight Pistacia species: P. atlantica, P. integerrima, P. khinjuk, P. mutica, P. terebinthus, P. vera, and P. lentiscus. We used a high-throughput DNA sequence read archive (SRA) to assemble a reference genome that was employed in our studies as a de novo bioinformatics method. Four genomic regions from SRA and three single-nucleotide polymorphism (SNP) positions from Kafkas et al. BMC Genomics 16:98, 2015) were selected and sequenced with collected plant material from predominantly the Antepfıstıgı Research Institute Collection Garden, and eight species were aligned intraspecifically for SNP mining. In total, 12 SNP markers were converted to KASP markers, and 5 of them (SNP-PIS-133396, SNP-PIS-167992, P-ATL-91951–565, P-INT-91951–256, P-KHI-91951–115) showed clear allelic discrimination between male and female plants. SNP-PIS-167992 and P-ATL-91951–565 were identified as the best marker assays because they showed allelic frequency differences for all individuals and for both homozygous and heterozygous characters. These markers could be the most comprehensive ones for the whole genus because they showed discriminative power for several species. Conclusions This study is the first one to use the KASP assay for sex discrimination in Pistacia species, and it can be regarded as a precursor study for sex discrimination by KASP for plants in general.

I. Background: Pistacia is kind of unisexual plant species that can take 4–5 years to initiate bearing stage of trees in terms of economic value. The fruits of species have an extreme importance in food, health and baking industry as a raw material. So, identify the individual in early juvenile period for pollination and position of trees is very crucial for growers. The objective of this study is developing markers for each Pistacia species which helps the screening the sex of plant seedling quickly before they reach reproduction stage without waiting morphological data. II. Methods and Results: Within the context, by using the power of KASP (Kompetitive Allele Specific PCR) assay technology as a marker screening system, we successfully discriminate 7 Pistacia species out of 8 which are P. atlantica, P. integerrima, P. khinjuk, P. mutica, P. terebinthus, P. vera and P. lentiscus. We have used a high-throughput DNA sequence read archive (SRA) to assemble a reference genome to use in our studies as de novo bioinformatics method. 4 genomic regions were sequenced with collected plant material from Antepfıstıgı Research Institute Collection Garden predominantly and 8 species were aligned intraspecifically for Single Nucleotide Polymorphism (SNP) mining. 12 SNP markers are converted to KASP markers and 5 of them (SNP-PIS-133396, SNP-PIS-167992, P-ATL-91951-565, P-INT-91951-256, P-KHI-91951-115) showed obvious allelic discrimination between male and female species. SNP-PIS-167992 and P-ATL-91951-565 were identified as best marker assays due to the allelic frequency differences in graphs which are apparent for all individuals and homozygosis/heterozygosis observed clearly. These markers could be most comprehensive for whole genus because the discriminability power of several species in once. III. Conclusions: As a conclusion, this study is reported first Pistacia gender discrimination by KASP, besides the precursor study for sex discrimination by KASP in plants.

Orobanche cumana Wallr. is a holoparasitic plant for only sunflower, hence it is called as sunflower broomrape. Yield loss created by O. cumana which is generally 50 % can reach to 100 %. In this study, it was planned to perform molecular characterization of O. cumana germplasm as nine locations of Thrace region obtained from Trakya Agricultural Research Institute by using Single Nucleotide Polymorphism (SNP) markers, widely used in plant breeding programs, in Competitive Allele Specific PCR (KASP) assay which is a fluorescent tagged allele specific PCR method based, economic, reliable and easily repeatable genotyping technology. Databases and literature were scanned to spot variations on O. cumana genome which is not known clearly. So far, four SSR (Simple Sequence Repeat) marker ( Ocum-197, Ocum-006, Ocum-023 and Ocum-151 ) regions showing polymorphic pattern were used for searching possible SNPs. Primer pairs were designed for amplification of the regions possibly having SNPs and PCR amplifications with these primer pairs were performed and 1 candidate deletion was detected on the amplicon which was amplified by Ocum-197 SSR marker. Following, the deletion was converted to KASP primers and KASP assay was performed. The deletion marker, Del-197 , has grouped the samples from nine locations in the resulting allelic discrimination plot and infestation was performed according to this grouping, As a conclusion, Del-197 is considered as a selective marker for the ability to rapidly assay allelic variation at DNA markers for O. cumana populations that have effects on infestation results were evaluated as races, F, G, H and I in Thrace region.