Browsing by Author "Baloglu P."

Now showing 1 - 4 of 4

Bioinformatics and its utilization in green biotechnology
(2020-01-01) Altunoglu Y.C.; Ugurlu A.; Baloglu P.; Baloğlu M.C.
Bioinformatics use computer technology to manage and process those data from biological experiments. Many bioinformatics methods have been developed to compute those huge data by genomics. Collection, storage and application of bioinformatics methods of plant genetic resources can contribute to the production of plants with higher crop quality and resistant to abiotic stresses, diseases and insects. These approaches can lead to understanding of biological systems.
Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects
(2022-06-28) Baloglu M.C.; Celik Altunoglu Y.; Baloglu P.; Yildiz A.B.; Türkölmez N.; Özden Çiftçi Y.
Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.
Genome-wide identification and comparative expression analysis of LEA genes in watermelon and melon genomes
(2017-01-01) Celik Altunoglu Y.; Baloglu M.C.; Baloglu P.; Yer E.N.; Kara S.
Late embryogenesis abundant (LEA) proteins are large and diverse group of polypeptides which were first identified during seed dehydration and then in vegetative plant tissues during different stress responses. Now, gene family members of LEA proteins have been detected in various organisms. However, there is no report for this protein family in watermelon and melon until this study. A total of 73 LEA genes from watermelon (ClLEA) and 61 LEA genes from melon (CmLEA) were identified in this comprehensive study. They were classified into four and three distinct clusters in watermelon and melon, respectively. There was a correlation between gene structure and motif composition among each LEA groups. Segmental duplication played an important role for LEA gene expansion in watermelon. Maximum gene ontology of LEA genes was observed with poplar LEA genes. For evaluation of tissue specific expression patterns of ClLEA and CmLEA genes, publicly available RNA-seq data were analyzed. The expression analysis of selected LEA genes in root and leaf tissues of drought-stressed watermelon and melon were examined using qRT-PCR. Among them, ClLEA-12-17-46 genes were quickly induced after drought application. Therefore, they might be considered as early response genes for water limitation conditions in watermelon. In addition, CmLEA-42-43 genes were found to be up-regulated in both tissues of melon under drought stress. Our results can open up new frontiers about understanding of functions of these important family members under normal developmental stages and stress conditions by bioinformatics and transcriptomic approaches.
Identification and expression analysis of LEA gene family members in cucumber genome
(2016-11-01) Celik Altunoglu Y.; Baloglu P.; Yer E.N.; Pekol S.; Baloglu M.C.
LEA (late embryogenesis abundant) proteins are firstly discovered in seeds and then identified in vegetative tissues of different plant species. They are mainly regulated under abiotic stress conditions. Although genome wide studies of different gene family members have been performed in cucumber, there is no such a study for LEA genes. We have identified 79 LEA genes in the cucumber genome. Based on phylogenetic analysis, CsLEA genes could be classified into seven groups in which structural motifs are relatively conserved. Tandem duplications play an important role in cucumber genome for LEA gene expansion. Orthologous and chromosomal relationships of CsLEA genes were observed based on comparative mapping analysis with other species. The in silico micro-RNA (miRNA) target analyses indicated that 37 CsLEA genes were targeted by different miRNAs, especially mir854 and mir414 are the most abundant identified ones. Public available RNA-seq data were analyzed for expression analysis of CsLEA genes in different tissues of cucumber. According to genome-wide expression analysis, nine CsLEA genes showed higher expression profiles in all tissues. The expression profiles of ten CsLEA genes in the root and leaf tissues of drought-stressed cucumber were examined using qRT-PCR. Among them, CsLEA-54 induced after stress application in leaf and root tissues and might provide adaptation to drought stress for cucumber. CsLEA-09, CsLEA-32 and CsLEA-57 genes responded to drought after 3 h later and might be considered as early response genes to water limitation. This research could help us to improve understanding of contribution of CsLEAs to drought tolerance in cucumber.