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Seed traits are very important agronomic traits that contribute significantly into crop yield and are considered useful indicators to monitor the inheritance of quantitative traits influenced by genotype and environmental conditions. To investıgate genomic regions useful for breeding high-yielding and highly nutritious common bean (Phaseolus vulgaris L.) cultivars, a mini core collection of Turkish common bean germplasm was screened under five environments and two locations for seed traits (seed width, seed yield/plant (SYP), and hundred seed weight). The results of analysis of variance (ANOVA) across the environments revealed significant effects of genotypes and genotype by environment interaction (G × E) for all studied traits except hundred seed weight (HSW), where G × E was found nonsignificant. During this study, mean seed width, SYP, and HSW were 7.038 mm, 21.815 g, and 42.1 g, respectively. Pearson's correlation coefficient revealed a significant and positive correlation (p = 0.01) of seed width with SYP and HSW. At the provinces level, minimum and maximum HSW was reflected by Elazığ and Bolu provinces, respectively. Studied germplasm was grouped into two populations in constellation analysis based on their HSW. A total of 7900 DArTseq markers identified through genotyping by sequencing (GBS) were used for the investigation of marker-trait association. DArT-3373385 marker present on chromosome Pv08 showed a significant association for seed width. DArT-8215545 marker showed a significant association for SYP and this marker was also present on chromosome Pv08. A total of four DArTseq markers were determined to be associated with HSW, and DArT-3372052 contributed maximum (11.32%) to phenotypic variations. We believe that the reported genomic regions will be helpful for future marker-assisted breeding regarding yield-related traits in common bean. [ABSTRACT FROM AUTHOR]

Faba bean is protein-enriched legume crop consumed in the form of pods, and cooked seeds and is a part of the traditional food of many Mediterranean countries. It shows variations in its phenotypes, especially in seed size and color. Therefore, it is very important to investigate faba bean genotypes having less cooking time. Keeping this in view, a total of 399 faba bean accessions including three commercial varieties were obtained from International Center for Agricultural Research in the Dry Areas (ICARDA) and Aegean Agricultural Research Institute National Gene Bank for the investigation of cooking traits variations. The field experiments were conducted according to the augmented block design in three provinces (Sivas, Adana, and İzmir) of Türkiye for two consecutive years (2017 and 2018). A good range of variations was observed for all studied traits and the mean cooking time was 114.16 min. İzmir10 had better cooking properties due to its shorter cooking time than other cultivars and landraces. Higher values of the swelling index revealed the higher swelling ability of Balıkesir74. Correlation analysis was performed and swelling capacity showed significant and positive correlations with swelling index and hydration capacity at a significance level of p = 0.05. As this germplasm was collected from 45 provinces, the landrace from Şanlıurfa reflected minimum cooking time and maximum swelling capacity. Principal component analysis (PCA) was performed and the 1st five PCs accounted for a total of 100.00% variations. Biplot analysis resulted in a total of 63.02% variations and the studied germplasm was divided based on cooking time, hydration capacity, and swelling capacity. İzmir10 showed minimum cooking time, it should be also used as a candidate parent to develop faba bean cultivars requiring lesser cooking time to save time and energy. We believe that the results presented herein will be very helpful for the faba bean breeding community interested in quality and cooking traits. [ABSTRACT FROM AUTHOR]

Human being has strong and historic connections with plants to fulfill food, feed, and shelter. Moreover, human uses plants as medicine for the treatment of various diseases. Plants are chemical factories for the biosynthesis of the huge number of secondary metabolites (SMs) that are directly used as a medicine or indirectly used in the development of commercial pharmaceutical drugs. Their improvement through classical breeding remains a difficult struggle for plant breeders. Hence, rapidly advancing research on the plant omics era has accelerated our understanding of the complex structure of SMs synthesis in medicinal and aromatic plants (MAPs). In addition, sequencing technologies and the completion of several genome sequences of MAPs have opened numerous opportunities for fine mapping and gene characterization. The accessibility of these technologies together with research of quantitative trait loci (QTL) and candidate genes for key characteristics such as SMs content and biologic activity and resistance to biotic and abiotic stresses pave the way for the development of new strategies for the improvement of MAPs. To explore the knowledge of SMs in MAPs, several reviews have been published over the last three decades for researchers with advanced knowledge of plant biotechnology. However, this review has offered a summary of the recent developments, limitations, and future potential in molecular breeding of MAPs species and their application to plant breeding. [ABSTRACT FROM AUTHOR]

Human body needs sufficient quantity of protein on daily basis for the normal functioning. Dietary protein in sufficient quantity is becoming a key issue for huge population of the world particularly in developing countries. Present investigation aimed to explore the phenotypic variation and to investigate the genomic regions associated with seed protein contents in Turkish common bean germplasm collected from 19 provinces. Field experiments were conducted according to augmented block design at two locations (Bolu and Sivas) for two consecutive years (2017 and 2018). Analysis of variance revealed highly significant environmental effects (p < 0.05) on seed protein contents within environments, while genotype by environment interaction revealed nonsignificant effects. Overall mean protein contents were 36.36%, while Balikesir-3 and Hakkari-38 yielded minimum (31.64%) and maximum (40.70%) protein contents. Among 19 provinces, accessions from Hakkari and Erzincan provinces disclosed maximum and minimum mean protein contents respectively. Scatter plot between seed protein contents and plant height divided the accessions according to their protein contents and plant height. A total of eight stable accessions were selected and can be recommended for future breeding activities. The implemented constellation plot separated the studied germplasm into two populations on the basis of their protein contents. Genotyping by sequencing resulted 7900 DArTseq markers was used for marker-trait association and a total of 11 markers showed significant association for protein contents. During this study, DArT-3365703 marker was identified in both locations (Sivas and Bolu) during 2017 and might be used for future common bean breeding. Physical map revealed the presence narrow regions between identified markers on Pv02 and Pv05. Therefore, these regions should be considered for future breeding activities. We are confident that results of present study will be helpful for marker-assisted breeding of common bean. [ABSTRACT FROM AUTHOR]

Safflower is an underutilized and minor oilseed crop that received less attention from the scientific community compared to other oilseed crops like soybean and sunflower. Exploring the genetic basis associated with agronomic traits is crucial for markerassisted breeding of safflower. A genome-wide association study was conducted using a total of 12,232 DArTseq markers to identify the marker-trait association for important agronomic traits in an international safflower panel derived from 26 different geographical countries of the world. Statistically significant genotypic effects (p < 0.05) were observed across mean data of both locations (Pakistan and Turkey). Moderate to high heritability estimates were observed for the studied traits. Studied material showed higher performance for all traits except seeds per capitulum in Pakistan compared to Turkey. Phenotypic diversity for important agronomic traits, such as plant height (60.08 to 121.48 cm), capitula per plant (8.7 to 80.4), seeds per capitulum (15 to 42.05), and seed yield per plant (4.85 to 51.02 g), was illustrated. Seed yield per plant showed a highly significant and positive correlation with capitula per plant (0.4985***). Constellation plot analysis resulted in four groups, i.e. A, B, C, and D. Genotyping by sequencing resulted in 12,232 DArTseq markers being used for the investigation of marker-trait association through mixed linear model (Q + K) approach. DArT-38077549 showed significant association with capitula per plant, while two markers (DArT-22763576, DArT-22763253) were associated with plant height. A total of two markers (DArT-38079422, DArT-100043360) were associated with seeds per capitulum. A total of five DArTseq markers showed significant association with seed yield per plant and maximum variation was resulted by DArT-100004992. The results of this study provide a new insight to understand the genetic basis associated with agronomic traits in safflower. We envisage that significant markers identified through this investigation may be applicable in future safflower marker-assisted breeding programs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Quinoa is an important staple food crop for millions of impoverished rural inhabitants of the Andean region. Quinoa is considered a good source of protein, vitamins, minerals, and antioxidants. This study aimed to investigate the genetic diversity and population structure of world quinoa germplasm originating from 8 countries through the iPBS-retrotransposon marker system. Molecular characterization was performed using the 11 most polymorphic primers. A total of 235 bands were recorded, of which 66.8% were polymorphic. Mean polymorphism information content (PIC) was 0.410. Various diversity indices including mean effective number of alleles (1.269), mean Shannon's information index (0.160) and gene diversity (0.247) revealed the existence of sufficient amount of genetic diversity in studied germplasm. Bolivia-17 and Mexico-1 were found to be genetically distinct accessions and can be suggested as candidate parents for future breeding activities. Various diversity indices were also calculated among germplasm collection counries and the results clearly showed the existence of higher genetic diversity in Bolivian and Peruvian accessions. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) grouped quinoa germplasm according to their collection country. Analysis of molecular variance (AMOVA) revealed that most of the variations (69%) in world quinoa germplasm are due to differences within populations. Findings of this study can be used for deeper understanding of the genetic relationship and in the determination of appropriate breeding and conservation strategies for quinoa. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Antioxidants play an important role in animal and plant life owing to their involvement in complex metabolic and signaling mechanisms, hence uncovering the genetic basis associated with antioxidant activity is very important for the development of improved varieties. Here, a total of 182 common bean (Phaseolus vulgaris) landraces and six commercial cultivars collected from 19 provinces of Turkey were evaluated for seed antioxidant activity under four environments and two locations. Antioxidant activity was measured using ABTS radical scavenging capacity and mean antioxidant activity in common bean landraces was 20.03 µmol TE/g. Analysis of variance reflected that genotype by environment interaction was statistically non-significant and heritability analysis showed higher heritability of antioxidant activity. Variations in seed color were observed, and a higher antioxidant activity was present in seeds having colored seed as compared to those having white seeds. A negative correlation was found between white-colored seeds and antioxidant activity. A total of 7900 DArTseq markers were used to explore the population structure that grouped the studied germplasm into two sub-populations on the basis of their geographical origins and trolox equivalent antioxidant capacity contents. Mean linkage disequilibrium (LD) was 54%, and mean LD decay was 1.15 Mb. Mixed linear model i.e., the Q + K model demonstrated that four DArTseq markers had significant association (p < 0.01) for antioxidant activity. Three of these markers were present on chromosome Pv07, while the fourth marker was located on chromosome Pv03. Among the identified markers, DArT-3369938 marker showed maximum (14.61%) variation. A total of four putative candidate genes were predicted from sequences reflecting homology to identified DArTseq markers. This is a pioneering study involving the identification of association for antioxidant activity in common bean seeds. We envisage that this study will be very helpful for global common bean breeding community in order to develop cultivars with higher antioxidant activity. [ABSTRACT FROM AUTHOR]

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon's information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean = 8.6 bands/primer), of which ~92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPGMA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper germplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Spring durum wheat occupies over 0.5 M ha in Kazakhstan and represents an important domestic and export commodity. This study aimed to characterize 151 durum wheat cultivars and advanced lines originating from eight breeding programs of the Kazakhstan–Siberia Spring Wheat Improvement Network (KASIB) between 2003 and 2018. The phenotypic characterization was performed in two contracting evaluation sites more than 1000 km apart (Almaty in the Southeast and Shortandy in the North) for two years and a total of 11 agronomic traits were recorded. Field trials at both locations followed regional agronomy practices, including sowing, harvesting, and genotype evaluation using a randomized complete block design (RCBD). The growing season was longer in Almaty, resulting in a higher number of grains per spike. Though grains are smaller in size with an overall higher yield, 243 g/m2 versus 170 g/m2, there was no correlation between germplasm performance at the two sites. Molecular characterization was performed with 10 iPBS-retrotransposons primers that resulted in a total of 345 bands and showed a mean polymorphism of 91.9%. Mean values of gene diversity (0.251), Shannon's information index (0.388), and expected heterozygosity (0.233) revealed a relatively high level of genetic diversity in the KASIB set. AMOVA revealed higher genetic variations due to differences within the populations. Marker-based cluster analysis, including STRUCTURE and neighbor-joining algorithms, divided the material into two populations with clear differences in geographic origin. Superiors and diverse germplasm identified in the study are recommended for marker assisted selection and breeding. [ABSTRACT FROM AUTHOR]

Knowledge of genetic diversity could be beneficial by contributing important information in the selection of breeding material. The objective of this study was to explore the genetic diversity and relationship in the Turkish tobacco germplasm with the iPBS-retrotransposons marker that emerged as a universal method. A total of 90 landraces and 6 commercial cultivars collected from different geographical regions of Turkey were used in this study. Eleven most polymorphic iPBS-retrotransposons primers yielded a total of 119 scorable bands and 98 of these bands were found to be polymorphic (82.35%), with an average of 8.91 polymorphic fragments for each primer. The mean polymorphism information contents were found to be 0.33, ranging from 0.10 to 0.80. The unweighted pair group method with arithmetic mean revealed that the genotypes belonging to the same geographical regions were often present in the same group and very close to each other. Based on the Bayesian clustering model, the genetic structure of Turkish tobacco germplasm was divided into 2 main groups. This is first study to explore the genetic diversity of Turkish tobacco by the iPBS-retrotransposons and we believe that in future the results of this study will serve as a foundation for the development of new and improved tobacco varieties in Turkey and the rest of world. [ABSTRACT FROM AUTHOR]

Optimization of in vitro regeneration protocol using multiple input variables is highly significant, and can be achieved by validating the data using machine learning algorithms. Shoot tip and nodal segment explants of Alternanthera reineckii mini were inoculated on Murashige and Skoog (MS) medium enriched with different concentrations of benzylaminopurine (BAP), and cultured under five different monochromic light-emitting diodes (LEDs). The attained results were validated through the application of four different supervised machine learning models (RF, XGBoost, KNN, and GP). The prediction of the data were validated by using regression coefficient (R2), mean squared error (MSE), and mean absolute percentage error (MAPE) performance metrics. Results revealed R2 values of 0.61 and 0.59 for shoot counts and shoot length, respectively. The results of MSE were registered between 3.48–5.42 for shoot count and 0.40–0.74 for shoot length, whereas, 28.9–35.1% and 13.2–18.4% MAPE values were recorded for both shoot count and shoot length. Among the utilized models, the RF model validated and predicted the results more accurately, followed by the XGBoost model for both output variables. The results confirm that ML models can be used for data validation, and opens a new era of employing ML modeling in plant tissue culture of other economically important plants. Schematic structure presenting input features and outputs together with ML models, used validation and performance metrics [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a non-essential heavy metal having toxic effects on all living organisms. Durum wheat (Triticum durum Desf.) is widely used in human diets but has the potential to accumulate Cd. It also has a high level of genetic diversity, which may be exploited to develop cultivars with low Cd content. We aimed to perform marker-assisted selection and validate previously identified Cd markers in durum wheat germplasm for use in the investigation of accessions that accumulate low grain Cd content. We assessed 130 durum wheat accessions phenotypically and using three different molecular markers. Grain Cd contents of the studied germplasm varied 4.91-fold (26.2–128.7 μg/kg) with an average of 58.2 μg/kg. Landraces showed lower average values of grain Cd content than cultivars. Three molecular markers (usw47, Cad-5B and KASP marker Cad-5B) were used to differentiate high and low Cd accumulating lines. Results showed high correlation and successfully classified the accessions to the expected high or low Cd level; 87 accessions showed the low Cd alleles, and 43 accessions the high Cd alleles, except for five accessions with the usw47 marker that showed heterozygous status. A significant correlation coefficient (r = 0.944*) was observed among the three molecular markers. Based on molecular markers, 96.2% of the accessions were classified accurately. The KASP assay was highly effective in successfully separating low from high Cd content accessions and could be used as a molecular tool in durum wheat breeding programs, with less cost and time, targeting reduced grain Cd levels. The results of this study will allow durum wheat breeders to accelerate their progress to select suitable genotypes with the desired alleles. Durum wheat (Triticum durum Desf.) has great genetic diversity and is widely used in human diets but has the potential to accumulate Cd, which has significant adverse effects on human health. We assessed 130 durum wheat accessions phenotypically and using three different molecular markers. Results showed that utilisation of appropriate molecular markers will reduce the time and cost for grain Cd evaluation, and will allow durum breeders to accelerate progress to select genotypes with desired alleles. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a non-essential heavy metal having toxic effects on all living organisms. Durum wheat (Triticum durum Desf.) is widely used in human diets but has the potential to accumulate Cd. It also has a high level of genetic diversity, which may be exploited to develop cultivars with low Cd content. We aimed to perform marker-assisted selection and validate previously identified Cd markers in durum wheat germplasm for use in the investigation of accessions that accumulate low grain Cd content. We assessed 130 durum wheat accessions phenotypically and using three different molecular markers. Grain Cd contents of the studied germplasm varied 4.91-fold (26.2–128.7 μg/kg) with an average of 58.2 μg/kg. Landraces showed lower average values of grain Cd content than cultivars. Three molecular markers (usw47, Cad-5B and KASP marker Cad-5B) were used to differentiate high and low Cd accumulating lines. Results showed high correlation and successfully classified the accessions to the expected high or low Cd level; 87 accessions showed the low Cd alleles, and 43 accessions the high Cd alleles, except for five accessions with the usw47 marker that showed heterozygous status. A significant correlation coefficient (r = 0.944*) was observed among the three molecular markers. Based on molecular markers, 96.2% of the accessions were classified accurately. The KASP assay was highly effective in successfully separating low from high Cd content accessions and could be used as a molecular tool in durum wheat breeding programs, with less cost and time, targeting reduced grain Cd levels. The results of this study will allow durum wheat breeders to accelerate their progress to select suitable genotypes with the desired alleles. [ABSTRACT FROM AUTHOR]

Durum wheat (Triticum turgidum L.) is the 10th most cultivated crop and is a vital food source for human consumption. Genetic diversity in durum wheat is still an unexplored subject, and gene banks are filled with accessions waiting to be screened. Here, four different groups of durum wheat, Turkish and foreign cultivars, and in situ and ex situ landraces were evaluated for population structure and genetic diversity. A collection of 129 durum wheat accessions were genotyped, with a total of 6,357 markers (SilicoDArT, SNP [single‐nucleotide polymorphism], and simple sequence repeats [SSRs]). The highest mean allele number per marker (1.562) was obtained with SNP markers in ex situ landraces; the lowest mean allele number per marker (0.788) was obtained with SSR markers in the foreign cultivars. The minimum percentage of polymorphic loci was 38.70% observed with SSR markers in foreign cultivars; the maximum was 76.20% in SilicoDArT markers in ex situ landraces. According to Neighbor‐Joining analyses, the studied collection was divided into groups of cultivars and landraces, with some level of admixtures. Structure and principal coordinate analysis obtained distinct clusters for ex situ landraces and foreign cultivars, supported by Neighbor‐Joining analysis. A significant level of intergroup and intragroup variation was observed, and Turkish ex situ landraces were found as the most diverse and distinct group in the collection. Turkish landraces may be a promising source of novel allelic diversity that can be used in durum wheat breeding worldwide. Core Ideas: Turkish durum wheat landraces may provide novel allelic diversity.Turkish durum wheat cultivars released in the late 20th century has close pedigree relations with foreign cultivars.Turkish modern wheat germplasm/gene pool have experienced a bottleneck for several reasons.Turkish cultivars divide into two distinct groups: foreign related and landrace related. [ABSTRACT FROM AUTHOR]

Simple Summary: Invertase genes are among the important genes responsible for carbon metabolism in plants, significantly contributing to plant development and stress responses. In this study, for the first time, we performed genome-wide analysis for Invertase gene family in potato, identified and conducted expression profiling in different tissues by RNA seq analysis and validated it by Q-PCR. We also performed invertase family genes expression profiling under drought, salt and heat stress to elucidate their involvement in stress responses. Findings of this study will be helpful for future functional and genetic studies not only in potato but also in other plants. The potato is one of the most important and valuable crops in terms of consumption worldwide. However, abiotic stressors are the critical delimiters for the growth and productivity of potato. Invertase genes play key roles in carbon metabolism, plant development, and responses to stress stimuli. Therefore, a comprehensive genome-wide identification, characterization and expression analysis of invertase genes was performed in the potato. The current study identified 19 invertase genes, randomly distributed throughout the potato genome. To further elucidate their evolutionary, functional and structural relationship within family and with other plant species, we performed sequence and phylogenetic analysis, which segregated invertase genes into two main groups based on their sequence homology. A total of 11 genes are included in acidic invertases and 8 genes are in neutral or alkaline invertases, elucidating their functional divergence. Tissue specific expression analyses (RNA sequencing and qRT-PCR) of different plant tissues showed differential expression pattern. Invertase genes have higher expression in flower, leaf, root and shoot tissues, while under abiotic stress conditions, the expression of the invertase gene is significantly upregulated. Results of this study revealed that vacuolar and cell wall destined invertases are mainly the functional member genes of the invertase family. This study provides comprehensive data and knowledge about StINV genes in Solanum tuberosum for future genetic and epigenetic studies. [ABSTRACT FROM AUTHOR]

Limited availability of nutrients to crops is a major agricultural concern. Deteriorated soil health and poor fertility status decrease the bioavailability of essential nutrients to the plants. Consequently, organic soil amendment biochar is gaining attention due to its potential benefits. Rhizobacterial inoculation, are also documented as an effective technology for mobilization of immobile nutrients in soil. However, limited literature is available on combined use of rhizobacteria and biochar. Therefore, this study was carried out to examine the changes in the nutrient content of einkorn wheat and the change in some soil properties during the application of plant growth-promoting rhizobacteria (PGPR) with biochar. Four doses of biochar (0, 2.5, 5, and 10%) were applied with and without PGPR in the study. Biochar increased the growth criteria such as plant fresh weight (PFW), plant dry weight (PDW), root fresh weight (RFW), root dry weight (RDW), number of tillers, germination rate (GR) and potassium (K), calcium (Ca), sodium (Na), iron (Fe), copper (Cu), zinc (Zn), manganese (Mn), and nickel (Ni) elements. While PGPR application increased soil pH, dry and fresh weight of root, R/S, K, Ca, Mg, Fe, and Ni contents, and it caused a decrease in PH, PFW, tillers, GR, P, Cu, and Zn values. Combined biochar applications and PGPR had a significant effect on the pH, RFW, R/S, P, Na, and Cu. In conclusion, the combination of biochar and PGPR applications has shown a positive effect in terms of soil properties, plant growth, and element contents of einkorn wheat. [ABSTRACT FROM AUTHOR]

Transcription factors are regulatory proteins known to modulate gene expression. These are the critical component of signaling pathways and help in mitigating various developmental and stress responses. Among them, bZIP, BBR, and BZR transcription factor families are well known to play a crucial role in regulating growth, development, and defense responses. However, limited data is available on these transcription factors in Triticum aestivum. In this study, bZIP, BBR, and BZR sequences from Brachypodium distachyon, Oryza sativa, Oryza barthii, Oryza brachyantha, T. aestivum, Triticum urartu, Sorghum bicolor, Zea mays were retrieved, and dendrograms were constructed to analyze the evolutionary relatedness among them. The sequences clustered into one group indicated a degree of evolutionary correlation highlighting the common lineage of cereal grains. This analysis also exhibited that these genes were highly conserved among studied monocots emphasizing their common ancestry. Furthermore, these transcription factor genes were evaluated for envisaging conserved motifs, gene structure, and subcellular localization in T. aestivum. This comprehensive computational analysis has provided an insight into transcription factor evolution that can also be useful in developing approaches for future functional characterization of these genes in T. aestivum. Furthermore, the data generated can be beneficial in future for genetic manipulation of economically important plants. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Developing high yielding safflower cultivars with good adaptation to diverse environmental conditions can improve production in terms of seed yield and reduce the deficiency in edible oil. The genetic variability that exists among and within populations for desirable agronomic traits can be used to develop elite cultivars. A total of 94 safflower accessions from 26 different countries were used in this study to evaluate morphoagronomic performance, determine the pattern of similarity centers, and identify the best performing accessions by conducting 2 field experiments in Pakistan and Turkey using augmented design. Genetic diversity for important yield and yield traits was described including capitulum diameter (17.30 to 28.30 mm), branches per plant (5.10 to 17.30), capitula per plant (8.70 to 80.40), and seed yield per plant (4.86 to 51.02 g). These analyses showed a good level of variation in the current study. Using principal component analysis, it was observed that days to flower initiation, days to 50% flowering, days to flower completion, seed yield per plant, capitula per plant, branches per plant, seeds per capitulum, and capitulum diameter were the major contributors to the observed genetic variability in the evaluated safflower panel. Seed yield per plant reflected a significant and positive correlation with capitula per plant, branches per plant, and capitulum diameter, and these traits can be suggested as a selection criterion in safflower breeding programs. The hierarchical clustering was in agreement with the patterns of 7 similarity centers based on seed yield per plant, capitula per plant, capitulum diameter, and branches per plant. During this study, a few promising safflower accessions were selected for future breeding programs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In vitro germination of hemp is challenging due to low germination and high contamination rates. Successful establishment of in vitro sterilization is the prerequisite of plant tissue culture studies. Recent advancements in the field of artificial neural network (ANN) and machine learning (ML) algorithms open new horizons for sustainable and precision agriculture. ANN and ML algorithms are powerful tools to evaluate the results and make more precise and high accuracy predictions in the field of plant tissue culture, especially for industrial purposes. Keeping in view, the study was designed to investigate the possible response of variable concentrations of hydrogen peroxide (H 2 O 2) on germination and morphological traits of in vitro -grown hemp seedlings by using ML algorithms. Five different ML algorithms used in this study to evaluate the prediction of the output variables were: Support Vector Classifier (SVC), Gaussian Process (GP), Extreme Gradient Boosting (XGBoost), Random Forest (RF) models, and Multilayer Perceptron (MLP) neural network utilizing accuracy, F1 score, precision, and recall values. Among the tested models, the RF model exhibited better prediction of output variables with a high F1 score in the range of 0.98–1.00. The F1 scores of the other models ranged between 0.69 and 0.86. Response surface methodology (RSM) used to compute the optimum concentration of H 2 O 2 revealed the statistically significant effect of H 2 O 2 on in vitro germination and seedling growth. The optimum value of H 2 O 2 for the maximum germination and seedling was optimized to about ~2.2% by using RSM. The present work is a case study about the application of different ML and ANN models in plant tissue culture and reveals the possibility of application in many other economic crops. An overview of ML and ANN algorithms for in vitro germination and growth indices of industrial hemp. [Display omitted] • Hydrogen per oxide concentration and exposure time enhanced hemp seed germination. • Five machine learning models were used for evaluating the results precisely. • Random forest algorithm depicted the highest performance to assess the results. • Response surface methodology predicted the optimum inputs and respective outputs. • In vitro germination may facilitate to isolate explants for in vitro regeneration. [ABSTRACT FROM AUTHOR]