Molecular characterisation of the oldest domesticated Turkish einkorn wheat landraces with simple sequence repeat (SSR) markers

Einkorn (Triticum monococcum L. ssp. monococcum) is an ancient diploid wheat species with many useful traits and used as a wheat gene discovery model. In this research, a total of 41 diploid and tetraploid wheat accessions were tested using simple sequence repeat (SSR) markers. A total of 33 genotypes of T. monococcum along with four genotypes each of tetraploid wheat (T. dicoccon and T. durum) were used as plant material. The analysis utilized 10 polymorphic markers, including a total number of 41 alleles with an average frequency of 4.1 alleles per locus during exploration of the level of genetic variations. Various diversity analyses, which are the effective number of alleles (Ne), gene diversity (h), Polymorphic Information Content (PIC), and Shannon's information index (I), were performed for 10 'A' genome wheat SSR markers. The results showed a narrow variation in einkorn genotypes, supported by Analysis of Molecular Variance (AMOVA), with 66% maximum variation in all genotypes. The structure analysis divided the whole germplasm into two populations. A dendrogram was constructed to determine the genetic similarities using the unpaired group method with arithmetic averages (UPGMA), which separated tetraploid wheat from other genotypes/accessions. Principal Coordinate Analysis (PCoA) co-supported the clustering of UPGMA and structure by differentiating the diploid and tetraploid wheat. These findings will help understand the genetic relationships among these wheat accessions and their use in breeding programs in the future works

Genetic diversity, population structure and marker- trait association for 100-seed weight in international safflower panel using silicodart marker information

Safflower is an important oilseed crop mainly grown in the arid and semi-arid regions of the world. The aim of this study was to explore phenotypic and genetic diversity, population structure, and marker-trait association for 100-seed weight in 94 safflower accessions originating from 26 countries using silicoDArT markers. Analysis of variance revealed statistically significant genotypic effects (p < 0.01), while Turkey samples resulted in higher 100-seed weight compared to Pakistan samples. A Constellation plot divided the studied germplasm into two populations on the basis of their 100-seed weight. Various mean genetic diversity parameters including observed number of alleles (1.99), effective number of alleles (1.54), Shannon’s information index (0.48), expected heterozygosity (0.32), and unbiased expected heterozygosity (0.32) for the entire population exhibited sufficient genetic diversity using 12232 silicoDArT markers. Analysis of molecular variance (AMOVA) revealed that most of the variations (91%) in world safflower panel are due to differences within country groups. A model-based structure grouped the 94 safflower accessions into populations A, B, C and an admixture population upon membership coefficient

Oil content and fatty acid composition of safflower (Carthamus Tinctorius l.) germplasm

Safflower (Carthamus tinctorius L.) is a promising oilseed crop with potential applications in the food, pharmaceutical, and industrial sectors. Understanding the oil content and fatty acid composition of safflower germplasm is crucial for breeding programs aimed at enhancing its agronomic and nutritional traits. This study assessed the oil content and fatty acid composition in 87 safflower accessions. Significant variations were observed, with the oil content ranging from 36.88% to 18.44%. Genotype Egypt 1 exhibited the highest oil content. Among fatty acids, China 1 had the highest myristic acid (0.170%) content, while Remzibey had the lowest (0.100%). Palmitic acid ranged from 6.13% to 8.20%, with Egypt 3 and Bangladesh 3 at the extremes. For palmitoleic acid, Jordan 5 had the highest content (0.53%) and Bangladesh 2/Portugal 2 the lowest (0.03%). Linoleic acid varied from 37.7% (China 7) to 77.73% (Iran 1). A correlation analysis indicated strong positive correlations between protein and oil content, as well as between palmitic and myristic acids, and between palmitic and linoleic acids. Conversely, protein exhibited highly negative correlations with myristic, palmitic, and palmitoleic acids. The protein percentage showed a high heritability but a low genetic advance, while palmitic acid, oil percentage, stearic acid, linoleic acid, palmitoleic acid, and oleic acid showed a high heritability and a moderate genetic advance as a percentage of the mean. These findings can aid in developing cultivars with enhanced fatty acids, oil quality, and nutritional value, facilitating sustainable production for a wide range of industrial applications

Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics

Common bean is an important legume crop having high quality protein, micronutrients, vitamins and antioxidants, which makes it a “grain of hope” for poor communities. Hence, a good number of breeding activities have been performed on the improvement of various key traits for years. However, recent advancements in molecular markers, sequencing technologies and the completion of the common bean genome sequence have opened numerous opportunities for fine mapping and gene characterization. The availability of these tools together with investigations of quantitative trait loci (QTL) and candidate genes for key traits such as morpho-agronomic, iron and zinc contents, cooking and quality traits, antioxidant activity, biotic and abiotic stresses pave the way to the development of new strategies for common bean genetic improvement. As a food source, it can contribute to the reduction of food scarcity worldwide in the coming years. Therefore, it is very important to take synergic efforts to integrate common bean genetic and genomic resources in breeding activities to ensure food security and contribute significantly to improved livelihoods in developing countries. Moreover, Kompetitive allele specific PCR (KASP) and CRISPR-Cas9 should be used to develop climate resilience common bean varieties. Here, we provide an overview of the evolution of common bean research by highlighting the past and recent advances in genomics, transgenics, transcriptomics and proteomics and also critically discuss the future prospects for further genetic improvement and better expansion of this crop

Application Potentials of Plant Growth Promoting Rhizobacteria and Fungi as an Alternative to Conventional Weed Control Methods

Weeds are the plants usually grown on unwanted places and are notorious for causing interruptions in agricultural settings. Remarkable yield losses have been reported in fields infested with weeds worldwide. So far, these weeds cause about 34% of losses to yields of major agricultural crops and pose threats to economic condition of the farmers. Conventionally, weed control was achieved by the use of chemical herbicides and traditional agronomic practices. But these methods are no more sustainable as the magnitude of threats imposed by these conventionally outdated methods such as chemical herbicides is greater than the benefits achieved and their continuous use has disturbed biodiversity and weed ecology along with herbicide resistance in some weeds. Herbicide residues are held responsible for human health hazards as well. Therefore the future of weed control is to rely on alternative approaches which may be biological agents such as bacteria and fungi. This chapter highlights the potentials of using bacterial and fungal biocontrol agents against weeds in farmer fields. Moreover, detailed review on merits and demerits of conventional weed control methods is discussed in this chapter

Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel

Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Nigde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r(2) value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.Scientific and Technological Research Council of Turkey (TUBITAK) [115O406]This study was financially supported by The Scientific and Technological Research Council of Turkey (TUBITAK) under the Project #115O406. The paper is a part of Phd thesis of corresponding author. I would also like to thank Dr. Marion Roeder for providing me the opportunity to work under her supervision in Institute of Plant Genetics and Crop Plant Research (IPK). I would also like to thank Dr. Quddoos ul Haq Muqaddasi and Dr. Dalia Alomari for their support throughout my stay in GERMANY

Elucidating the genetic diversity and population structure of international cotton germplasm using inter-primer binding site (iPBS) retrotransposon marker system

Cotton (Gossypium hirsutum L.) is an important crop throughout the world and is one of the most important industrial raw materials. It is very important to characterize the available cotton germplasm aiming to identify novel genetic and genomic resources that can be used for future cotton breeding. Keeping this in view, a total of 179 cotton genotypes were characterized with the inter-primer binding site (iPBS) retrotransposon marker system. Seven iPBSretrotransposon primers yielded a total of 134 scoreable bands and among these, 128 bands were polymorphic. The mean polymorphic bands per primer were 18.28, with values ranging between 16 and 21. The mean polymorphism rate of 7 iPBS retrotransposon primers was calculated as 96.28%. The polymorphism information content value varied between 0.31 and 0.46 with an average of 0.395. Genetic similarity was calculated using the POPGENE software and values ranged between 0.320 and 0.955. Population structure and neighbor-joining analysis divided the evaluated germplasm into two populations. The analysis of molecular variance revealed that maximum variations (96%) are due to differences within the populations. The information presented here has comprehensively demonstrated the potential of iPBSretrotransposon markers in detecting genetic diversity and phylogenetic association analyses of cotton. This knowledge will be helpful for future cotton breeding.Scientific Research Project Coordination Unit of Nigde Omer Halisdemir University; [TGT 2020/22-LUETEP]This research (Project Number: TGT 2020/22-LUETEP) was funded by the Scientific Research Project Coordination Unit of Nigde Omer Halisdemir University

Exploring the population structure and genetic diversity in apple germplasm using iPBS-retrotransposon markers

Apple (Malus domestica [Suckow] Borkh) holds global economic and cultural value, particularly in temperate regions. This study investigates the genetic variations among 52 apple accessions from three research centre’s in Kazakhstan, employing the iPBS-retrotransposons marker system. Of the 35 markers initially screened, 12 highly polymorphic markers were selected for PCR amplification, producing 280 bands, 279 of which were polymorphic, yielding a polymorphism rate of 99.64%. Genetic diversity indices revealed notable variability with the effective number of alleles (ne = 1.655), Shannon’s information index (I = 0.373), gene diversity (h = 0.549), and an average genetic distance of 1.2. Analysis of molecular variance (AMOVA) demonstrated that 97% of the genetic variation occurred within the population. STRUCTURE analysis divided the germplasm into two distinct populations and one unclassified population based on collection centers. Both the neighbor-joining tree and principal coordinate analysis (PCoA) supported these results, confirming the genetic separation into two groups. This study highlighted the significant genetic diversity among apple accessions, demonstrating the effectiveness of the iPBS-retrotransposons marker system. Additionally, the highest genetic distance (1.2) observed between the Tyulpan and Red Chief samples, positions these accessions as suitable and promising candidates for future breeding initiatives

Genome-wide association studies (GWAS) revealed a genetic basis associated with floral traits in potato germplasm

Potato is an important noncereal staple crop serving as a source of food for a large number of the world's population. Genomewide association study (GWAS) analysis has become a useful tool to uncover the genetic basis of important plant traits by revealing significant association with the trait of interest. The present study aimed to explore the phenotypic diversity and to identify the genetic basis associated with important floral traits. A total of 237 tetraploid potato genotypes were used as plant material, and field experiments were conducted according to augmented block design for two consecutive years (2016, 2017). Analysis of variance for the studied floral traits reflected highly significant genotypic effects. Mean data for both years revealed the significant variation for pistil length (5.53 to 9.92 mm), stamen length (6.04 to 9.26 mm), and pistil length above stamen (1.31 to 4.47 mm). Pearson's correlation analysis reflected a highly significant and positive correlation of pistil length with stamen length (r = 0.42) and pistil length above stamen (r = 0.28). Principal component analysis was performed, and the first two PCs were considered accounting for a total of 81.2% variation. Constellation plot divided the studied potato panel into two main populations on the basis of stamen and pistil length. A total of 12,720SNP markers were used for the marker-trait association, and a total of 15 markers were found significantly associated with studied traits across both years. Identifying the same markers across both years helped in the validation of the obtained marker-trait associations. The identified significant markers reflected some of the putative candidate genes that might be beneficial in potato breeding programs. To the best of our knowledge, this is the first study identifying the genetic basis of important floral traits and might be helpful to the scientific community interested in potato marker-assisted breeding in these traits

Phenotypic Characterization of 183 Turkish Common Bean Accessions for Agronomic, Trading, and Consumer-Preferred Plant Characteristics for Breeding Purposes

Plant landraces represent a repository of a gene pool, local adaptation of their domestic species, and thereby are considered a great source of genetic variations. Such genetic variation can be helpful to mitigate the current and future food challenges. A total of 183 common bean accessions including three commercial varieties collected from 19 Turkish provinces were grown to record their morpho-agronomic variations and to evaluate the best performing accessions under multi-environmental conditions. Plant height, days to maturity, pods weight, seed length, and 100-seed weight were used to evaluate the best performing accessions under different environmental conditions. A wide range of variations for traits like days to maturity (99–161), plant height (21–168.7 cm), seed length (7.41–16.4 mm), seeds per plant (17.8–254.4), and 100-seeds weight (24.97–73.8 g) were observed and can be useful for breeding purposes. The analytic results derived from the first three eigenvectors suggested that plant height, plant weight, 100-seed weight, and days to flowering were biologically significant bean traits. Seed yield per plant was positively and significantly correlated with plant weight and pods weight. Genotype × environment biplot discriminated the studied common bean accessions based on their plant height and growth habit. Plant height, days to maturity, seed width, and first pod height were found highly heritable traits and were least affected by environmental forces. Among 19 provinces, accessions of Bilecik showed maximum pods per plant, seed yield per plant and 100-seed weight, while Erzincan and Sivas provinces reflected the prevalence of bushy and early maturing accessions. Information provided herein comprehensively explored the occurrence of genotypic variations which can be used for the development of candidate varieties responding to breeder, farmer, and consumer preferences