Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - WoS: 1Citation - Scopus: 1Association Mapping of Plant Structure and Yield Traits in Faba Bean (vicia Faba L.)(John Wiley and Sons Inc., 2023) Abuzayed, M.A.; Baytar, A.A.; Yanar, E.G.; Doğanlar, Sami; Frary, AnneTens of thousands of faba bean accessions are available in germplasm collections throughout the world. Morphological characterization of these materials can enrich these collections and aid in the selection of genotypes for use in breeding programs. Results: In this study, 26 morphological characters were analyzed for 61 faba bean landraces and 53 cultivars over two seasons in Izmir, Turkey. The genotypes had high diversity for several yield traits including number of pods per plant, dry seed yield, and 100-seed weight. Association mapping was conducted for the morphological characters using 651 alleles from 100 simple sequence repeat (SSR) markers and a general linear model based on the Q matrix. A false discovery rate of 0.20 was used to test the significance of marker–trait associations resulting in 75 loci detected for 20 of the morphological characters (p ≤ 0.001). Conclusion: Overall, 44% of the quantitative trait loci (QTLs) were for seed traits, with 24%, 15%, and 17% of QTL identified for vegetative, inflorescence, and pod traits, respectively. The phenotypic data and marker–trait associations generated by this work can help breeding programs in the selection and improvement of faba bean. © 2023 Society of Chemical Industry.Article Citation - WoS: 3Citation - Scopus: 3Gras-Di Snp-Based Molecular Characterization and Fingerprinting of a Turkish Corylus Avellana Core Set Provide Insights Into the Cultivation and Breeding of Hazelnut in Turkey(Springer, 2023) Yanar, Ertuğrul Gazi; Doğanlar, Sami; Frary, AnneHazelnut (Corylus avellana L.) is an economically and socially important product for Turkey, the country that leads global production of this crop. The preservation of Turkish hazelnut genetic diversity and informed breeding of new cultivars are crucial for maintaining quality and crop yield stability. In this study, genotyping by random amplicon sequencing (GRAS-Di) was used to identify single-nucleotide polymorphisms (SNPs) in a panel of 96 individuals representing the Turkish national hazelnut collection. The resulting 7609 high-quality SNPs were physically mapped to the Tombul cultivar reference genome and used for population structure and diversity analyses. These analyses revealed that cultivars are not less diverse than wild accessions and that 44% of the panel had admixed ancestry. The results also indicated that recently released Turkish cultivars are highly similar to each other, suggesting that diversity analysis is an important tool that should be employed to prevent future genetic bottlenecks in this crop. A minimal marker algorithm was used to select a set of seven SNP markers that were capable of differentiating the panel accessions. These fingerprinting markers should be useful for the propagation of true-to-type elite cultivars that can be used to renew Turkey's aging hazelnut orchards.Article Citation - Scopus: 2Qtl Mapping of Broomrape (orobanche Cumana Wallr.) Resistance in Sunflower (helianthus Annuus L.) Using Gbs-Snps(Society of Field Crops Science, 2021) Akköse Baytar, Asena; Çelik, İbrahim; Doğanlar, Cafer; Frary, Anne; Doğanlar, SamiBroomrape is one of the most important biotic stresses causing serious yield reductions in sunflower. Control of this parasitic plant is difficult and physical and chemical strategies are usually insufficient. Therefore, introduction of genetic resistance to broomrape in sunflower is a key breeding goal. Breeding efforts on broomrape resistance have been conducted for decades, however, new broomrape races, such as race F, have emerged and rapidly evolved to be more aggressive and devastating. Although a few quantitative trait loci (QTLs) were identified for race F resistance, none of these loci are suitable for marker assisted selection because of their small phenotypic effects. In the present study, three major QTLs for broomrape race F resistance were identified on LG7, LG11 and LG12 using a high density SNP map constructed with the genotyping by sequencing approach in an intraspecific F2 population. The population consisted of 300 individuals derived from a cross between susceptible Helianthus annuus cv. RHA 436 as the recipient parent and resistant H. annuus cv. H08 M1 as the donor parent. Breeder-friendly SNP-based cleaved amplified polymorphic sequence markers were developed for the QTLs. The QTLs and CAPS markers identified in this study will be valuable molecular genetic tools for sunflower breeding.Article Citation - WoS: 3Citation - Scopus: 3Chromatographic Analysis for Targeted Metabolomics of Antioxidant and Flavor-Related Metabolites in Tomato(Bio-Protocol, 2021) Gürbüz Çolak, Nergiz; Tek, Neslihan; Frary, Anne; Doğanlar, SamiTargeted metabolomics is a useful approach to evaluate crop breeding studies. Antioxidant and flavor-related traits are of increasing interest and are considered quality traits in tomato breeding. The present study presents chromatographic methods to study antioxidants (carotenoids, vitamin C, vitamin E, phenolic compounds, and glutathione) and flavor -related characters (sugars and organic acids) in tomato. Two different extraction methods (for polar and apolar entities) were applied to isolate the targeted compounds. The extraction methods developed in this work were time and cost-effective since no further purification was needed. Carotenoids, vitamin C, glutathione, and phenolic acids were analyzed by HPLC-PDA using a RP C18 column at an appropriate wavelength for each compound. Vitamin E and sugars were analyzed by HPLC with RP C18 and NH2 columns and detected by FLD and RI detectors, respectively. In addition, organic acids were analyzed with GC-FID using a Rtx 5DA column after derivatization with MSTFA. As a result, sensitive analytical methods to quantify important plant metabolites were developed and are described herein. These methods are not only applicable in tomato but are also useful to characterize other species for flavor-related and antioxidant compounds. Thus, these protocols can be used to guide selection in crop breeding.Article Citation - WoS: 9Citation - Scopus: 11Development of Simple Sequence Repeat Markers in Hazelnut (corylus Avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars(Springer, 2018) Özturk, Süleyman Can; Göktay, Mehmet; Doğanlar, Sami; Allmer, Jens; Frary, AnneEuropean hazelnut (Corylus avellana) is a diploid tree species and is widely used in confections. Hazelnuts are, to a large part, produced in Turkey with the cultivar "Tombul" widely grown in the Black Sea region. In this work, the "Tombul" genome was partially sequenced by next-generation sequencing technology yielding 29.2% (111.85 Mb) of the similar to 385 Mb (1C). This sequence information was used to develop genetic markers in order to enable differentiation of material before the long maturation process and to facilitate future breeding strategies. A total of 90,142 simple sequence repeats (SSRs) were identified in the contigs giving a frequency of 1 SSR per 1240 nt in the assembly. Mononucleotides were the most abundant SSR marker type (60.9%) followed by di- and trinucleotides. Primer pairs were designed for 75,139 (83.3%) of the SSRs. Fifty SSR primers were applied to 47 hazelnut accessions from nine countries to test their effectiveness and polymorphism. The markers amplified an average of 3.2 fragments. The highest polymorphism information content value was for cavSSR11062 (0.97) and the lowest (0.04) was for cavSSR13386. Two markers were monomorphic: cavSSR12855 and cavSSR13267. Single-copy SSR primers were also assessed for their ability to discriminate 19 Turkish cultivars, and it was found that seven primer pairs (Cav4217, Cav14875, Cav14418, Cav2704, Cav12862, Cav3909, Cav1361) were sufficient for this task. Thus, this study developed new SSR markers for use in hazelnut breeding and genetic studies and also provide a method to distinguish and identify true-type Turkish cultivars.Article Citation - WoS: 10Citation - Scopus: 13Analysis of European Hazelnut (corylus Avellana) Reveals Loci for Cultivar Improvement and the Effects of Domestication and Selection on Nut and Kernel Traits(Springer Verlag, 2019) Frary, Amy; Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Kayalak Balık, Selda; Kızılcı, Gökhan; Doğanlar, Sami; Frary, AnneTurkey is a rich source of European hazelnut (Corylus avellana) germplasm with nearly 400 accessions in the national collection. This genetic material encompasses cultivars, landraces and wild genotypes which were characterized for 12 nut and 13 kernel traits over 2years in the 1990s. Analysis of these attributes revealed both the positive and negative impacts that human selection and breeding have had on hazelnut. Thus, while selection has resulted in larger nuts and kernels, cultivars have fewer nuts per cluster and kernels with larger internal cavities. Breeding has also resulted in a propensity for cultivars to have higher proportions of double kernels and empty nuts, two traits which reduce quality and yield. In addition, it is clear that while selection has successfully increased hazelnut fat content it has not impacted overall flavor, a much more complex trait. The nut and kernel phenotypic data were combined with genotypic data from 406 simple sequence repeat marker alleles for association mapping of the quantitative trait loci (QTL) for the traits. A total of 78 loci were detected in the population with the highest proportions for nut (24%) and kernel (26%) appearance parameters followed by quality (19%), shell thickness (16%) and yield-related (15%) traits. It is hoped that some of the identified QTL will be useful for future breeding of hazelnut for improved nut and kernel yield and quality.Article Citation - WoS: 20Citation - Scopus: 24Newly Developed Ssr Markers Reveal Genetic Diversity and Geographical Clustering in Spinach (spinacia Oleracea)(Springer Verlag, 2017) Göl, Şurhan; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnneSpinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.Article Citation - WoS: 33Citation - Scopus: 44Relationship Between Geographical Origin, Seed Size and Genetic Diversity in Faba Bean (vicia Faba L.) as Revealed by Ssr Markers(Springer Verlag, 2017) Göl, Şurhan; Doğanlar, Sami; Frary, AnneFaba bean (Vicia faba L.) is an important legume species because of its high protein and starch content. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the nitrogen fixing bacteria in its roots. In this work, 255 faba bean germplasm accessions were characterized using 32 SSR primers which yielded 302 polymorphic fragments. According to the results, faba bean individuals were divided into two main groups based on the neighbor-joining algorithm (r = 0.91) with some clustering based on geographical origin as well as seed size. Population structure was also determined and agreed with the dendrogram analysis in splitting the accessions into two subpopulations. Analysis of molecular variance (AMOVA) revealed high levels of within population genetic variation. Genetic similarity and geographical proximity were related with separation of European accessions from African and Asian ones. Interestingly, there was no significant difference between landrace (38%) and cultivar (40%) diversity indicating that genetic variability has not yet been lost due to breeding. A total of 44 genetically well-characterized faba bean individuals were selected for a core collection to be further examined for yield and nutritional traits.Article Citation - WoS: 30Citation - Scopus: 34Gddom: an Online Tool for Calculation of Dominant Marker Gene Diversity(Springer Verlag, 2017) Abuzayed, Mazen; El-Dabba, Nourhan; Frary, Anne; Doğanlar, SamiGene diversity (GD), also called polymorphism information content, is a commonly used measure of molecular marker polymorphism. Calculation of GD for dominant markers such as AFLP, RAPD, and multilocus SSRs is valuable for researchers. To meet this need, we developed a free online computer program, GDdom, which provides easy, quick, and accurate calculation of dominant marker GD with a commonly used formula. Results are presented in tabular form for quick interpretation. © 2016, Springer Science+Business Media New York.Article Citation - WoS: 6Citation - Scopus: 5Development of Genomic Simple Sequence Repeat Markers in Faba Bean by Next-Generation Sequencing(Springer Verlag, 2017) Abuzayed, Mazen A.; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnneFaba bean (Vicia faba L.) is an important food legume crop with a huge genome. Development of genetic markers for faba bean is important to study diversity and for molecular breeding. In this study, we used Next Generation Sequencing (NGS) technology for the development of genomic simple sequence repeat (SSR) markers. A total of 14,027,500 sequence reads were obtained comprising 4,208 Mb. From these reads, 56,063 contigs were assembled (16,367 Mb) and 2138 SSRs were identified. Mono and dinucleotides were the most abundant, accounting for 57.5 % and 20.9 % of all SSR repeats, respectively. A total of 430 primer pairs were designed from contigs larger than 350 nucleotides and 50 primers pairs were tested for validation of SSR locus amplification. Nearly all (96 %) of the markers were found to produce clear amplicons and to be reproducible. Thirty-nine SSR markers were then applied to 46 faba bean accessions from worldwide origins, resulting in 161 alleles with 87.5 % polymorphism, and an average of 4.1 alleles per marker. Gene diversity (GD) of the markers ranged from 0 to 0.48 with an average of 0.27. Testing of the markers showed that they were useful in determining genetic relationships and population structure in faba bean accessions.