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Öğe Characterization of cellulose synthase A (CESA) gene family in eudicots(Springer/Plenum Publishers, 2019) Nawaz, Muhammad Amjad; Lin, Xiao; Chan, Ting-Fung; Imtiaz, Muhammad; Rehman, Hafiz Mamoon; Baloch, Faheem ShehzadCellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms. Duplications have played an important role in expansion of CESA gene family members in eudicots. Co-expression networks showed that primary and secondary cell wall modules are duplicated in eudicots. We also identified 230 simple sequence repeat markers in 103 eudicot CESAs. The 13 identified conserved motifs in eudicots will provide a basis for gene identification and functional characterization in other plants. Furthermore, we characterized (in silico) eudicot CESAs against senescence and found that expression levels of CESAs decreased during leaf senescence.Öğe Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information(Public Library Science, 2018) Nadeem, Muhammad Azhar; Habyarimana, Ephrem; Çiftçi, Vahdettin; Nawaz, Muhammad Amjad; Karaköy, TolgaTurkey 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.Öğe Development of a competent and trouble free dna isolation protocol for downstream genetic analyses in glycine species(2016) Nawaz, Muhammad Amjad; Baloch, Faheem Shehzad; Rehman, Hafiz Mamoon; Le, Bao; Akther, FahimaExtraction of deoxyribose nucleic acid (DNA) from plants is preliminary step in molecular biology. Fast and cost effective genomic DNA isolation from Glycine species for downstream application is a major bottleneck. Here we report a high throughput and trouble free method for genomic DNA extraction from leaf and seeds of Glycine species with high quality and quantity. Protocol reports the optimization by employing different concentrations of CTAB and PVP in extraction buffer. Efficiency of optimized protocol was compared with frequently used DNA extraction methods. Wide adoptability and utility of this protocol was confirmed by DNA extraction from leaves as well as seeds of G. max, G. soja, G. tomentella and G. latifolia. Extracted DNA was successfully subjected to PCR amplification of five microsatellite markers and four putative glycosyltransferase genes. DNA extraction protocol is reproducible, trouble free, rapid and can be adopted for plant molecular biology applications.Öğe Development of a Competent and Trouble Free DNA Isolation Protocol for Downstream Genetic Analyses in Glycine Species(2016) Nawaz, Muhammad Amjad; Baloch, Faheem Shehzad; Rehman, Hafiz Mamoon; Le, Bao; Akther, Fahima; Yang, Seung Hwan; Chung, GyuhwaExtraction of deoxyribose nucleic acid (DNA) from plants is preliminary step in molecular biology. Fast and cost effective genomic DNA isolation from Glycine species for downstream application is a major bottleneck. Here we report a high throughput and trouble free method for genomic DNA extraction from leaf and seeds of Glycine species with high quality and quantity. Protocol reports the optimization by employing different concentrations of CTAB and PVP in extraction buffer. Efficiency of optimized protocol was compared with frequently used DNA extraction methods. Wide adoptability and utility of this protocol was confirmed by DNA extraction from leaves as well as seeds of G. max, G. soja, G. tomentella and G. latifolia. Extracted DNA was successfully subjected to PCR amplification of five microsatellite markers and four putative glycosyltransferase genes. DNA extraction protocol is reproducible, trouble free, rapid and can be adopted for plant molecular biology applications.Öğe DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing(Taylor & Francis Ltd, 2018) Nadeem, Muhammad Azhar; Nawaz, Muhammad Amjad; Shahid, Muhammad Qasim; Doğan, Yıldız; Cömertpay, Gönül; Yıldız, Mehtap; Hatipoğlu, RüştüWith 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.Öğe Genetic diversity and population structure of Korean wild soybean (Glycine soja Sieb. and Zucc.) inferred from microsatellite markers(Pergamon-Elsevier Science Ltd, 2017) Nawaz, Muhammad Amjad; Yang, Seung Hwan; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad; Lee, Jeong DongKorea is considered one of the centers of genetic diversity for cultivated as well as wild soybeans. Natural habitats of wild soybeans are distributed across the Korean mainland and the islands surrounding the Korean peninsula. In this study, the genetic diversity of 100 mainland Korean wild soybean accessions was evaluated by using 42 simple sequence repeat markers covering 17 soybean chromosomes. All analyzed loci were polymorphic and a total of 114 alleles were found. The observed average genetic diversity was low (0.4). The results showed that the 100 selected accessions did not exactly follow the geographical distribution. These results were further confirmed by the phylogeny inferred from five morphological characteristics (i.e., leaf shape, leaf area, plant shape, seed area, and 100-seed weight). Together, the genetic and morphological evaluations suggested conclusively that the selected population did not follow the geographical distribution pattern. The present study could provide useful information for the ex situ conservation and exploitation of wild soybean accessions in soybean improvement stratagems, and will aid in further understanding about the phylogeography of the species in the Korean center of diversity. (C) 2017 Elsevier Ltd. All rights reserved.Öğe Genetic diversity assessment in Nicotiana tabacum L. with iPBS-retrotransposons(2018) Yaldız, Gülsüm; Çamlıca, Mahmut; Nadeem, Muhammad Azhar; Nawaz, Muhammad Amjad; Baloch, Faheem ShehzadKnowledge 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 iPBSretrotransposons 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.Öğe Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean(Elsevier GmbH, 2017) Nawaz, Muhammad Amjad; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad; Ijaz, Babar; Ali, Muhammad Amjad; Khan, Iqrar Ahmad; Lee, Jeong DongThe plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages. © 2017 Elsevier GmbHÖğe Genome-wide identification, classification, expression profiling and DNA methylation (5mC) analysis of stress-responsive ZFP transcription factors in rice (Oryza saliva L.)(Elsevier, 2019) Ahmad, Fiaz; Farman, Kiran; Waseem, Muhammad; Rana, Rashid Mehmood; Nawaz, Muhammad Amjad; Baloch, Faheem ShehzadCytosine DNA methylation (5mC) is an epigenetic mark that regulates gene expression in plant responses to environmental stresses. Zinc-finger protein (ZFP) is the largest family of DNA-binding transcription factors that also plays an essential role in eukaryote. In plant we have already identified and characterized different useful ZFP-genes. While, the main objective of this research was to observe and identify more targeted stress responsive genes of ZFPs epigenetically throughout genome in rice for the first time. A comprehensive correlation analysis was performed through methylated DNA immunoprecipitation (MeDIP)-chip hybridization in rice under salt and osmotic stresses. High salinity and drought are two major abiotic hazards that are destroying the crop world-wide. As a result, Through-out genome 14 unique stress responsive transcription factors of ZFP-genes with varying level of methylation and expression under two conditions (control vs. stress) were isolated. All the identified genes were confirmed from different databases for their specific structure, cis-regulatory elements, phylogenetic analysis, and synteny analysis. Moreover, the tissue-specific expression patterns, and expression under abiotic and phytohormones stresses were also investigated. Phylogenetically all the genes were divided into 6 distinct subgroups with Arabidopsis and orthologous proteins were find-out through synteny analysis. Available RNA-seq data in response to various phytohormones provided hormone inducible gene expression profile. Through Reverse Transcriptase qPCR (RT-qPCR) analysis tissue-specific expression in shoot and root over various time points against salt and osmotic stresses exhibited the diverse expression patterns of identified genes. Overall, the present study providing a foundation for in-depth characterization of identified genes and to further understand the epigenetic role of DNA methylation for genes expression and environmental stresses regulation in higher plant.Öğe Isoflavone profile diversity in Korean wild soybeans (Glycine soja Sieb. & Zucc.)(2018) Tsukamoto, Chigen; Nawaz, Muhammad Amjad; Kurosaka, Ayaka; Le, Bao; Lee, Jeong Dong; Baloch, Faheem ShehzadIsoflavones prevent the incidence of cancer, reduce cardiovascular problems, and decrease menopausal symptoms. In soybean (Glycine soja Sieb. & Zucc.) seeds, the content is greatly affected by growing conditions. The variations in soy-isoflavone content were investigated by growing 346 Korean wild soybean accessions from natural habitats under the same agroclimatic conditions. Highperformance liquid chromatography was used to measure the profiles of six soy-isoflavones, i.e. glycosides (daidzin, glycitin, genistin) and malonyl glycosides (malonyl-daidzin, malonyl-glycitin, and malonyl-genistin). The soy-isoflavone content of the wild soybeans ranged from 0.5 to 5.51 mg/g with an average of 2.78 mg/g. The highest mean total soy-isoflavone was genistin (1.393 mg/g), followed by daidzin (0.939 mg/g) and glycitin (0.250 mg/g). Korean wild soybean seeds examined in this study were rich in malonyl-genistin. An increasing trend for total soy-isoflavone content was observed from the north to the southeast in the geographical distribution sites, which signifies the effect of genotype and collection site. The information generated in this report will greatly aid soybean breeding stratagems aimed at improving soy-isoflavone concentration in soybean seeds.Öğe Laurel (Laurus nobilis L.): A less-known medicinal plant to the world with diffusion, genomics, phenomics, and metabolomics for genetic improvement(Springer Singapore, 2018) Nadeem, Muhammad Azhar; Aasim, Muhammad; Kırıcı, Saliha; Karık, Ünal; Nawaz, Muhammad Amjad; Yılmaz, Abdurrahim; Baloch, Faheem ShehzadMedicinal plants have gained the world’s attention due to their application in various ways. Laurel (Laurus nobilis. L) is a very important medicinal plant of the Mediterranean region. Traditionally this plant has been successfully used in medicine, and its essential oil has great importance. Genomics, breeding, and metabolomics of different crops have remained the main focus of researchers, which made this plant to less known to the world. Most of the researchers only worked about the essential oil and its antibacterial and antioxidant activities. However, still almost no work has been done about the breeding aspects of this important plant. The present review offers an overview about the origin, diffusion, genomics, phenomics, breeding, and metabolomics of laurel. This information would be very helpful for the researchers who are interested in the breeding of this plant. © Springer Nature Singapore Pte Ltd. 2018.Öğe Mobile genomic element diversity in world collection of safflower (Carthamus tinctorius L.) panel using iPBS-retrotransposon markers(Public Library Science, 2019) Ali, Fawad; Yılmaz, Abdurrahim; Nadeem, Muhammad Azhar; Habyarimana, Ephrem; Subaşı, İlhan; Nawaz, Muhammad Amjad; Chaudhary, Hassan JavedSafflower (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.Öğe Molecular characterization of genetic diversity and similarity centers of safflower accessions with ISSR markers(Soc Botanica Sao Paulo, 2020) Ali, Fawad; Nadeem, Muhammad Azhar; Habyarimana, Ephrem; Yılmaz, Abdurrahim; Nawaz, Muhammad Amjad; Khalil, Iftikhar Hussain; Ercişli, Sezai; Baloch, Faheem ShehzadCrop genetic resources are vital inputs in crop genetic improvement. In this study, genetic diversity, population structure, and similarity centers for 131 safflower accessions obtained from 28 countries were investigated using 12 ISSR markers. A sum of 201 ISSR bands were obtained among which 188 (93.844%) were found polymorphic. Mean polymorphism information content (0.448) and diversity parameters including mean effective number of alleles (1.655), mean Shannon's information index (0.557), mean expected heterozygosity (0.354), and mean overall gene diversity (0.377) showed a good level of genetic diversity in the studied safflower materials. Model-based structure, unweighted pair-group method with arithmetic means, and principal coordinate analysis clustered all accessions into three main populations; A, B, and C and an unclassified population. Accessions originated from Asian countries like Pakistan and Israel were found most diverse. Three accessions, Pakistan-11, Israel-1, and Pakistan-26, were found most genetically distant and might be used as parental sources for genetic combinations in safflower breeding activities. Analysis of molecular variance revealed highly significant differentiation among the identified populations and population x country combinations. The results presented in this work most probably supported the hypothesis of seven similarity centers of safflower but need to be validated with further confirmed investigations. The information provided herein is expected to be helpful for the scientific community interested in safflower breeding.Öğe Phenotypic characterization of 183 Turkish common bean accessions for agronomic, trading, and consumer-preferred plant characteristics for breeding purposes(Mdpi, 2020) Nadeem, Muhammad Azhar; Karaköy, Tolga; Yeken, Mehmet Zahit; Habyarimana, Ephrem; Hatipoğlu, Rüştü; Çiftçi, Vahdettin; Nawaz, Muhammad Amjad; Sönmez, Ferit; Baloch, Faheem ShahzadPlant 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 x 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.Öğe Phylogenetic and taxonomic relationship of Turkish wild and cultivated emmer (triticum turgidum ssp. dicoccoides) revealed by ipbs-retrotransposons markers(Friends Science Publ, 2019) Arystanbekkyzy, Meerim; Nadeem, Muhammad Azhar; Aktaş, Hüsnü; Yeken, Mehmet Zahit; Zencirci, Nusret; Nawaz, Muhammad Amjad; Ali, Fawad; Baloch, Faheem ShahzadWild emmer (Triticum turgidum ssp. dicoccoides) is the progenitor of cultivated wheat. Turkey is the main center of wheat and plays a vital role in the spread of various crops among the continents. Karacadag region is considered as the domestication center of wheat and still, hundreds of landraces are prevalent. A total of 29 wild emmer landraces, 4 cultivated emmer wheat (T. turgidum ssp. dicoccum) and five durum wheat (T. turgidum ssp. durum) cultivars were investigated for the genetic diversity and phylogenetic relationship using the iPBS-retrotransposons markers. Mean polymorphism and polymorphic information contents (PIC) were 87.85% and 0.660, respectively. Mean effective numbers of alleles (1.961), Shannon's Information Index (0.682) and gene diversity (0.489) reflected the occurrence of a great level of variations. T17 and Chermik-1 genotypes were found much distinct and breeding valuable genotypes for wheat breeding. The unweighted pair-group method with arithmetic means (UPGMA) divided all genotypes by their genetic makeup and geographical locations. Among 3 species, UPGMA based clustering clearly separated the durum wheat from wild emmer and cultivated emmer wheat. Results are clearly supported by the principal coordinate analysis (PCoA) and model-based structure algorithm. Information provided herein comprehensively reflected the power of iPBS-retrotransposons for the diversity and phylogenetic relationship investigation and reflected that this marker system can be effectively applied to investigate phylogenetic and taxonomic relationship in any crop due to its universal nature. (C) 2019 Friends Science PublishersÖğe Systems identification and characterization of cell wall reassembly and degradation related genes in Glycine max (L.) Merill, a bioenergy legume(Nature Publishing Group, 2017) Nawaz, Muhammad Amjad; Rehman, Hafiz Mamoon; Imtiaz, Muhammad; Baloch, Faheem Shehzad; Lee, Jeong DongSoybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.
