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Öğe Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers(Springer, 2022) Yeken, Mehmet Zahit; Emiralioğlu, Orkun; Çiftçi, Vahdettin; Bayraktar, Harun; Palacıoğlu, Gülsüm; Özer, GökselBackground Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems. Materials and methods In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification. Results The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin. Conclusions A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.Öğe Bolu koşullarında farklı kişniş (Coriandrum sativum L.) çeşit ve popülasyonlarının verim ve kalite özelliklerinin belirlenmesi(2020) Emiralioğlu, Orkun; Yaldiz, GülsümBu çalışmada Bolu ekolojik koşullarında Türkiye’ninfarklı bölgelerinden tedarik edilen yirmi sekiz farklıkişnişin (Coriandrum sativum L.) verim ve uçucu yağbileşenleri belirlenmiştir. Çalışmada, çimlenmesüresi (8-14 gün), çiçeklenme süresi (27-30 gün),olgunlaşma süresi (39-67 gün), bitki boyu (40.2-69cm), dal sayısı (3.6-9.6 adet), bin tane ağırlığı (5.14-16.8 g), tohum verimi (12.2-73.4 kg/da), hasatindeksi (%6.3-60), biyolojik verimi (41.59-343.75kg/da), ham yağ oranı (%1.63-24.26), uçucu yağoranı (%0.3-1.3), ile uçucu yağ bileşenleri linalool(%32-87.43), camfor (%0.13-7.6) ?-terpinene(%0.04-13.8), p-cymene (%0.1-15.77), ?-pinene(%0.09-5.38) arasında değişmiştir. Bolu ekolojikkoşullarında tek yıllık yürütülen çalışmada bütünkişniş çeşit ve popülasyonlarının bölge şartlarındayetişebileceği, fakat araştırılan özellikler bakımındançeşit ve popülasyonlar arasında önemli farklılıklarolduğu tespit edilmiştir. Bu çalışma sonuçlarına görebölge şartlarında tohum verimi ve uçucu yağ oranıbakımından Erzurum K.T popülasyonu ile K.T Pop-2popülasyonu önerilebilir.Öğe Bolu koşullarında farklı kişniş (coriandrum sativum l.) çeşit ve popülasyonlarının verim ve kalite özelliklerinin belirlenmesi(Bolu Abant İzzet Baysal Üniversitesi, 2017) Emiralioğlu, Orkun; Yaldız, GülsümBu çalışmada Bolu ekolojik koşullarında Türkiye'nin farklı bölgelerinden tedarik edilen kişnişin (Coriandrum sativum) verim ve uçucu yağ içeriğinin belirlenmesi araştırılmıştır. Yirmi sekiz farklı kişniş tohumunun kullanıldığı çalışma 2015 yılında Abant İzzet Baysal Üniversitesi Araştırma ve Uygulama alanında Tesadüf Blokları Deneme Desenine göre üç tekerrürlü olarak yürütülmüştür. Çalışmada çimlenme süresi, çiçeklenme süresi, olgunlaşma süresi, bitki boyu, dal sayısı, bin tane ağırlığı, biyolojik verim, tohum verimi, hasat indeksi, uçucu yağ oranı, ham yağ oranı ve uçucu yağ bileşenleri incelenmiştir. Çalışmada çimlenme süresi (8-14 gün), çiçeklenme süresi (27-30 gün), olgunlaşma süresi (39-67 gün), bitki boyu (40,2-69 cm), dal sayısı (3,6-9,6 adet), bin tane ağırlığı (5,14-16,8 g), tohum verimi (12,2-73,4 kg/da), hasat indeksi (%6,3-60), biyolojik verim (41,59-343,75 kg/da), ham yağ oranı (%1,63-24,26), uçucu yağ oranı (%0,3-1,3), ile uçucu yağ bileşenleri linalool (%32-87,43), camfor (%0,13-7,6), ?-terpinene (%0,04-13,8), p-cymene (%0,1-15,77), ?-Pinene (%0,09-5,38) de belirlenmiştir. Bolu ekolojik koşullarında yürütülen çalışmada bütün kişniş çeşit ve popülasyonlarının bölge şartlarında yetişebileceği, fakat araştırılan özellikler bakımından çeşit ve popülasyonlar arasında önemli farklılıklar olduğu tespit edilmiştir. Daha sağlıklı ve kesin sonuçlar elde edebilmek için denemenin birkaç yıl daha tekrarlanması gerekmekle birlikte; bu çalışma sonuçlarına göre bölge şartlarında tohum verimi ve uçucu yağ oranı bakımından Erzurum K.T popülasyonu ile K.T Pop-2 popülasyonu önerilebilir.Öğe EXPLORING I, bc-12 AND bc-3 GENE LOCUS IN PROMISING COMMON BEAN LINES(2023) Emiralioğlu, Orkun; Yeken, Mehmet Zahit; Çelik, Ali; Çiftçi, VahdettinCommon beans (Phaseolus vulgaris L.), known as the \"poor man's meat\", is an internationally important legume crop that appeals to farmers as well as consumers. Many biotic stressors such as bean common mosaic virus (BCMV), bean common mosaic necrosis virus (BCMNV) cause significant yield and quality losses in common bean. The most efficient and cost-effective way to lessen of these factors is to develop resistant cultivars. Local genotypes have been cultivated in many areas for years and have varied distinguishing characteristics as a result of spontaneous mutations. Identifying bean germplasm harboring gene sources is critical for developing resistant cultivars against BCMV and BCMNV. For this purpose, a total of 43 promising common bean lines selected from local genotypes cultivated across various regions of Türkiye were subjected to screening using diverse molecular markers (ROC11, SBD-5 and SW-13) to investigate gene sources associated with BCMV and BCMNV. The findings revealed that 21 lines had both I and bc-12 gene locus. In addition, the bc-12+bc-3 gene loci were discovered to be present in the 8 common bean lines. The combination of I+bc-3 resistance genes, which guarantees immune reaction to BCMV and BCMNV, was found in only one line; YLV-32. These gene sources can be evaluated in marker-assisted breeding to develop modern cultivars resistant to BCMV and BCMNV by breeders.Öğe A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris(Frontiers Media SA, 2023) Çelik, Ali; Emiralioğlu, Orkun; Yeken, Mehmet Zahit; Çiftçi, Vahdettin; Özer, Göksel; Kim, Yoonha; Baloch, Faheem ShehzadAccurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.Öğe The use of colorimetric loop-mediated isothermal amplification assay for naked-eye detection of bean common mosaic virus(Academic Press Ltd- Elsevier Science Ltd, 2023) Çelik, Ali; Morca, Ali Ferhan; Emiralioğlu, Orkun; Yeken, Mehmet Zahit; Özer, Göksel; Çiftçi, VahdettinBean common mosaic virus (BCMV), one of the most prevalent viral diseases of common beans, has been intensively studied since its initial identification. In this paper, a one-step colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method was performed by designing oligonucleotide primers to amplify the gene encoding the coat protein of BCMV. Positive LAMP reactions were observed with the naked eye using WarmStart 2 x Master Mix from NEB, changing from pink to yellowish if the test is positive. The sensitivity of this method was similar to that of conventional PCR. The method was tested on common bean and another virus, bean common mosaic necrosis virus (BCMNV), and it was shown to specifically detect BCMV and not produce false positive from other RNAs. The RT-LAMP test was quite reliable for the diagnosis of BCMV from infected samples, and the precise, sensitive. The cost analysis showed that the development of a less expensive and efficient RT-LAMP assay for BCMV detection is an important step in expanding testing capacity and improving access to accurate testing in resource-limited settings. The test can be utilized in laboratory and in the field for the diagnosis and monitoring of BCMV, and is the first reported use of RT-LAMP for BCMV detection.Öğe Wild Relatives and Their Contributions to Wheat Breeding(Springer International Publishing, 2022) Tekin, Mehmet; Emiralioğlu, Orkun; Yeken, Mehmet Zahit; Nadeem, Muhammad Azhar; Çiftçi, Vahdettin; Baloch, Faheem ShehzadThe world is witnessing simultaneous problems of climate change and rapidly increasing population. Research activities have confirmed that the climate change scenario will become more and more adverse and will put extra pressure on the agriculture to produce enough food to feed this and upcoming generations. Wheat is one of the staple crops, serving as a source of nutrition for millions of people all over the world. However, human activities resulted in the genetic erosion in wheat cultivars. Keeping this in view, wheat breeders need new genetic resources having novel alleles that can be used to develop cultivars having higher production, better quality, and resistance to biotic and abiotic stresses. Wild relatives of wheat are promising genetic resources having novel genetic variations that have been used in ensuring food and nutritional security, economic development, as well as environmental sustainability. Technological advances in biotechnology and genomics have broadened our scientific understandings regarding phylogenetic relationships among wheat species and consequently have opened new avenues to reconsider the potential of wheat wild relatives and to provide a context for how we can employ them in future wheat breeding programs. This chapter is focused on revealing the contribution of wild relatives in wheat breeding. We made our best effort by compiling existing information regarding the wild relatives and their contributions to wheat breeding. We are confident that provided information will be helpful to the wheat breeders to utilize wheat wild relatives for future wheat breeding. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022.
