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Background Research activities aiming to investigate the genetic diversity are very crucial because they provide information for the breeding and germplasm conservation activities. Wheat is one of the most important cereal crops globally by feeding more than a third of the human population around the world. Methods and results During present investigation, a total of 74 Turkish bread wheat accessions (54 landraces and 20 cultivars) were used as plant material and iPBS-retrotransposons marker system was used for the molecular characterization. 13 polymorphic primers used for molecular characterization resulted a total of 152 bands. Range of calculated diversity indices like polymorphism information content (0.11–0.702), effective numbers of alleles (1.026–1.526), Shannon’s information index (0.101–0.247) and gene diversity (0.098–0.443) confirmed higher genetic variations in studied germplasm. Bread wheat landraces reflected higher genetic variations compared to commercial cultivars. Analysis of molecular variance resulted that higher (98%) genetic variations are present within populations. The model-based structure algorithm separated 74 bread wheat accessions in to two populations. Diversity indices based on structure evaluated population’s revealed population B as a more diverse population. The principal coordinate analysis and neighbor-joining analysis separated 74 bread wheat accessions according to their collection points. Genetic distance for 74 Turkish bread wheat accessions explored Bingol and Asure accessions as genetically diverse that can be used as parents for breeding activities. Conclusions The extensive diversity of bread wheat in Turkish germplasm might be used as genetic resource for the exhaustive wheat breeding program. For instance, accessions Bingol and Asure were found genetically diverse and can be used as parents for future breeding activities.

Laural ( ) is a Mediterranean plant with reported antibacterial properties, yet the genetic basis of its antibacterial efficacy remains largely unexplored. This study evaluated the antibacterial activity of methanolic extracts against , , and , combined with genome-wide association studies (GWAS) and machine learning (ML) approaches to identify genetic markers and predict antibacterial efficacy in 92 plant samples. Antibacterial tests revealed significant variability in inhibition zones, with showing the highest inhibition (Canakkale2: 24.5 mm), followed by (Aydin2: 26.0 mm). Minimum inhibitory concentration (MIC) analysis demonstrated notable regional differences; extracts from Mersin3 showed the highest efficacy (MIC = 6.25 mg/mL), while Aydin1 exhibited the lowest activity (MIC = 100 mg/mL). Population structure and neighbor joining tree analysis split the germplasm into two groups. GWAS identified significant genetic markers associated with antibacterial traits, including marker 26557159 for EC-MEAN ( -Mean) ( = 1.10 × 10 , MarkerR = 0.1799, genetic variance = 9.41792) and marker 26584774 for BC-MEAN ( -Mean) ( = 8.89 × 10 , MarkerR = 0.18512, genetic variance = 12.48948). Protein-protein interaction network of loci associated with marker trait association (MTA) marker (26557159) indicated involvement in high-affinity secondary active ammonium transmembrane transporter activity, providing insights into genetic regions influencing antibacterial properties. ML models predicted antibacterial activity with high accuracy. XGBoost achieved the best performance for MIC predictions (R = 0.999, RMSE = 0.434), while random forest (R = 0.984) demonstrated robust performance for both MIC and disc diffusion assays. LightGBM performed well for MIC prediction (R = 0.988) but showed limited accuracy for disc diffusion outcomes (R = 0.695). This study is the first to combine GWAS and ML for predicting antibacterial efficacy in , identifying specific genetic markers (e.g., 26557159, 26584774) and demonstrating that XGBoost achieves near-perfect MIC prediction (R = 0.999). These findings provide a genomic and computational foundation for marker-assisted breeding of laurel with enhanced antibacterial properties and support the sustainable use of plant-derived anti-microbials.

With the development of molecular marker technology in the 1980s, the fate of plant breeding has changed. Different types of molecular markers have been developed and advancement in sequencing technologies has geared crop improvement. To explore the knowledge about molecular markers, several reviews have been published in the last three decades; however, all these reviews were meant for researchers with advanced knowledge of molecular genetics. This review is intended to be a synopsis of recent developments in molecular markers and their applications in plant breeding and is devoted to early researchers with a little or no knowledge of molecular markers. The progress made in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a more comprehensive understanding of molecular markers and provided deeper insights into the diversity available for crops and greatly complemented breeding stratagems. Genotyping-by-sequencing and association mapping based on next-generation sequencing technologies have facilitated the identification of novel genetic markers for complex and unstructured populations. Altogether, the history, the types of markers, their application in plant sciences and breeding, and some recent advancements in genomic selection and genome editing are discussed.

With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops’ audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research.

Safflower (Carthamus tinctorius L.) is a multipurpose crop of dry land yielding very high quality of edible oil. Present study was aimed to investigate the genetic diversity and population structure of 131 safflower accessions originating from 28 different countries using 13 iPBS-retrotransposon markers. A total of 295 iPBS bands were observed among which 275 (93.22%) were found polymorphic. Mean Polymorphism information content (0.48) and diversity parameters including mean effective number of alleles (1.33), mean Shannon's information index (0.33), overall gene diversity (0.19), Fstatistic (0.21), and inbreeding coefficient (1.00) reflected the presence of sufficient amount of genetic diversity in the studied plant materials. Analysis of molecular variance (AMOVA) showed that more than 40% of genetic variation was derived from populations. Model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 131 safflower accessions into four main populations A, B, C, D and an unclassified population, with no meaningful geographical origin. Most diverse accessions originated from Asian countries including Afghanistan, Pakistan, China, Turkey, and India. Four accessions, Turkey3, Afghanistan4, Afghanistan2, and Pakistan24 were found most genetically distant and might be recommended as a candidate parents for breeding purposes. The findings of this study are most probably supported by the seven similarity centers hypothesis of safflower. This is a first study to explore the genetic diversity and population structure in safflower accessions using the iPBS-retrotransposon markers. The information provided in this work will therefore be helpful for scientists interested in safflower breeding.

Until now, little attention has been paid to the geographic distribution and evaluation of genetic diversity of durum wheat from the Central Fertile Crescent (modern-day Turkey and Syria). Turkey and Syria are considered as primary centers of wheat diversity, and thousands of locally adapted wheat landraces are still present in the farmers' small fields. We planned this study to evaluate the genetic diversity of durum wheat landraces from the Central Fertile Crescent by genotyping based on DArTseq and SNP analysis. A total of 39,568 DArTseq and 20,661 SNP markers were used to characterize the genetic characteristic of 91 durum wheat land races. Clustering based on Neighbor joining analysis, principal coordinate as well as Bayesian model implemented in structure, clearly showed that the grouping pattern is not associated with the geographical distribution of the durum wheat due to the mixing of the Turkish and Syrian landraces. Significant correlation between DArTseq and SNP markers was observed in the Mantel test. However, we detected a non-significant relationship between geographical coordinates and DArTseq (r = -0.085) and SNP (r = -0.039) loci. These results showed that unconscious farmer selection and lack of the commercial varieties might have resulted in the exchange of genetic material and this was apparent in the genetic structure of durum wheat in Turkey and Syria. The genomic characterization presented here is an essential step towards a future exploitation of the available durum wheat genetic resources in genomic and breeding programs. The results of this study have also depicted a clear insight about the genetic diversity of wheat accessions from the Central Fertile Crescent.

Turkey presents a great diversity of common bean landraces in farmers' fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2-3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.

The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus . A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.

Due to increased industrialization, arsenic (As) in the soil has become a serious issue for wheat production since past few decades. We investigated the role of Azospirillum brasilense and trans-zeatin riboside (tZR) in the mitigation of arsenic toxicity in wheat for 2 years (2018–2019 and 2019–2020) in pot experiments. Wheat plants grown in soil artificially spiked with arsenic (50, 70, and 100 μM) was left alone or amended with A. brasilense , tZR, or their combination as mitigation strategies. A treatment without arsenic or amendments was maintained as control. Arsenic-induced physiological damages were noticed in the wheat plants. Detrimental effects on the plant physiological functions, such as disruption of cell membrane stability, reduced water uptake, and stomatal functions, were noticed with increase in As toxicity. Application of biological amendments reversed the effects of As toxicity by increasing wheat plant growth rate, leaf area, and photosynthesis and also yield. Therefore, application of tZR and wheat seed inoculation with A. brasilense could be a sustainable and environmentally friendly strategy to mitigate arsenic-induced crop physiological damages.

Micronutrient malnutrition is a global health concern, highlighting the importance of essential micronutrients like zinc in human diet, and enhancing zinc concentration in staple crops like common beans is a promising strategy. In this study, we performed genome-wide association studies to identify genetic loci associated with Zn accumulation in a diverse panel of 177 Turkish common bean landraces and six commercial varieties. Field trials were conducted across two locations over two years to assess Zn concentration variation. The results revealed significant genetic variability, with Zn concentrations ranging from 11.6 to 105.3 mg/kg. Two significant marker-trait associations (MTAs) were identified on chromosomes Pv06 and Pv08, with loci linked to Zn translocation and brassinosteroid-mediated cell-wall remodeling. Candidate genes, Vacuolar Iron Transporter 1 (VIT1) and Wall-Associated Kinase-Like 4 (WAKL4) , were implicated in Zn homeostasis and distribution. In silico transcriptomics analysis further validated the role of these genes under Zn-deficient conditions in Arabidopsis. Protein-protein interaction (PPI) network analysis identified key regulatory pathways, including ZIP transporters, heavy metal ATPases, and cell-wall modification enzymes. These findings provide valuable genetic insights for biofortification strategies, facilitating the development of Zn-enriched common bean cultivars to enhance nutritional security. The study underscores the potential of GWAS in identifying stable genetic markers for Zn biofortification, paving the way for future breeding efforts aimed at improving dietary Zn intake through staple crops.